From c585b4bc68813a351d6a87d19b9adf4041506355 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 19 Nov 2022 23:16:52 +0100 Subject: [PATCH 001/824] file-systems: Always do recursive bind mounts. Fixes . * guix/build/syscalls.scm (MS_REC): New variable. * gnu/build/file-systems.scm (mount-flags->bit-mask): Set MS_REC bit when bind-mounting. --- gnu/build/file-systems.scm | 2 +- guix/build/syscalls.scm | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm index 15b8f73312..66ca22d6ea 100644 --- a/gnu/build/file-systems.scm +++ b/gnu/build/file-systems.scm @@ -1127,7 +1127,7 @@ corresponds to the symbols listed in FLAGS." (('read-only rest ...) (logior MS_RDONLY (loop rest))) (('bind-mount rest ...) - (logior MS_BIND (loop rest))) + (logior MS_REC (logior MS_BIND (loop rest)))) (('no-suid rest ...) (logior MS_NOSUID (loop rest))) (('no-dev rest ...) diff --git a/guix/build/syscalls.scm b/guix/build/syscalls.scm index 61926beb80..2a12567b15 100644 --- a/guix/build/syscalls.scm +++ b/guix/build/syscalls.scm @@ -51,6 +51,7 @@ MS_RELATIME MS_BIND MS_MOVE + MS_REC MS_SHARED MS_LAZYTIME MNT_FORCE @@ -541,6 +542,7 @@ the last argument of `mknod'." (define MS_NODIRATIME 2048) (define MS_BIND 4096) (define MS_MOVE 8192) +(define MS_REC 16384) (define MS_SHARED 1048576) (define MS_RELATIME 2097152) (define MS_STRICTATIME 16777216) From 238d983b4e95b7c8bfd25e86d3c5a3d7df7e01ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 20 Nov 2022 21:48:42 +0100 Subject: [PATCH 002/824] gnu: bchoppr: Update to 1.12.0. * gnu/packages/music.scm (bchoppr): Update to 1.12.0. --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 9826a36034..646ea685c3 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2019 Eric Bavier -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2015 Paul van der Walt ;;; Copyright © 2016 Al McElrath ;;; Copyright © 2016, 2017, 2019, 2021, 2022 Efraim Flashner @@ -1910,7 +1910,7 @@ with a selectable pattern matrix size.") (package (inherit bsequencer) (name "bchoppr") - (version "1.10.10") + (version "1.12.0") (source (origin (method git-fetch) @@ -1919,7 +1919,7 @@ with a selectable pattern matrix size.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0gxz0cpxdfj7ajcd9yg05d26i7p24mx5865vy3ph76ni8kycdlrc")))) + (base32 "1jfp98qa0frmdybrg71fn8wxn1b3ginkbkcg9cz9y83j1m0jqrif")))) (synopsis "Audio stream-chopping LV2 plugin") (description "B.Choppr cuts the audio input stream into a repeated sequence of up to 16 chops. Each chop can be leveled up or down (gating). From 82bde985f47a84b9b05a2adc26c2f2cee278b1f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 20 Nov 2022 22:52:16 +0100 Subject: [PATCH 003/824] style: '-f' reads input files as UTF-8 by default. Reported by mirai on #guix. * guix/scripts/style.scm (format-whole-file): Wrap body in 'with-fluids'. Pass #:guess-encoding to 'call-with-input-file'. --- guix/scripts/style.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/guix/scripts/style.scm b/guix/scripts/style.scm index c0b9ea1a28..fa7175fb16 100644 --- a/guix/scripts/style.scm +++ b/guix/scripts/style.scm @@ -335,13 +335,15 @@ PACKAGE." (define* (format-whole-file file #:rest rest) "Reformat all of FILE." - (let ((lst (call-with-input-file file read-with-comments/sequence))) - (with-atomic-file-output file - (lambda (port) - (apply pretty-print-with-comments/splice port lst - #:format-comment canonicalize-comment - #:format-vertical-space canonicalize-vertical-space - rest))))) + (with-fluids ((%default-port-encoding "UTF-8")) + (let ((lst (call-with-input-file file read-with-comments/sequence + #:guess-encoding #t))) + (with-atomic-file-output file + (lambda (port) + (apply pretty-print-with-comments/splice port lst + #:format-comment canonicalize-comment + #:format-vertical-space canonicalize-vertical-space + rest)))))) ;;; From 8c7ea71344b91c2c36dfbf6f2bc6daf559b1c696 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 20 Nov 2022 22:56:23 +0100 Subject: [PATCH 004/824] installer: Add comment above the 'packages' field. * gnu/installer/services.scm (system-services->configuration): Add heading above the 'packages' field. Rename 'heading' to 'service-heading'. --- gnu/installer/services.scm | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/gnu/installer/services.scm b/gnu/installer/services.scm index 6c5f49622f..d08bab47fd 100644 --- a/gnu/installer/services.scm +++ b/gnu/installer/services.scm @@ -159,25 +159,32 @@ (base (if desktop? '%desktop-services '%base-services)) - (heading (list (vertical-space 1) - (comment (G_ "\ + (service-heading (list (vertical-space 1) + (comment (G_ "\ ;; Below is the list of system services. To search for available -;; services, run 'guix system search KEYWORD' in a terminal.\n"))))) +;; services, run 'guix system search KEYWORD' in a terminal.\n")))) + (package-heading (list (vertical-space 1) + (comment (G_ "\ +;; Packages installed system-wide. Users can also install packages +;; under their own account: use 'guix search KEYWORD' to search +;; for packages and 'guix install PACKAGE' to install a package.\n"))))) (if (null? snippets) `(,@(if (null? packages) '() - `((packages (append (list ,@packages) + `(,@package-heading + (packages (append (list ,@packages) %base-packages)))) - ,@heading + ,@service-heading (services ,base)) `(,@(if (null? packages) '() - `((packages (append (list ,@packages) + `(,@package-heading + (packages (append (list ,@packages) %base-packages)))) - ,@heading + ,@service-heading (services (append (list ,@snippets ,@(if desktop? From 99ba4ddb03b396f56764a25317f40d4501380704 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 20 Nov 2022 23:16:51 +0100 Subject: [PATCH 005/824] gnu: nautilus: Fix crash due to loading extensions twice. Fixes . Reported by Tobias Kortkamp . Previously, if NAUTILUS_EXTENSION_PATH contained the same directory several times, Nautilus could end up loading the same extension a second time and crash. This patch ensures that each extension cannot be loaded more than once. * gnu/packages/patches/nautilus-extension-search-path.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnome.scm (nautilus)[source]: Use it. [arguments]: Remove 'make-extensible' phase. --- gnu/local.mk | 1 + gnu/packages/gnome.scm | 25 +------ .../nautilus-extension-search-path.patch | 75 +++++++++++++++++++ 3 files changed, 79 insertions(+), 22 deletions(-) create mode 100644 gnu/packages/patches/nautilus-extension-search-path.patch diff --git a/gnu/local.mk b/gnu/local.mk index 949328ba30..5fad380bbf 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1561,6 +1561,7 @@ dist_patch_DATA = \ %D%/packages/patches/musl-cross-locale.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/m4-gnulib-libio.patch \ + %D%/packages/patches/nautilus-extension-search-path.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ %D%/packages/patches/ncftp-reproducible.patch \ %D%/packages/patches/netcdf-date-time.patch \ diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 3d942635a2..78e65d7400 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -9671,7 +9671,9 @@ shared object databases, search tools and indexing.") name "-" version ".tar.xz")) (sha256 (base32 - "1cncyiyh79w1id6a6s2f0rxmgwl65lp4ml4afa0z35jrnwp2s8cr")))) + "1cncyiyh79w1id6a6s2f0rxmgwl65lp4ml4afa0z35jrnwp2s8cr")) + (patches + (search-patches "nautilus-extension-search-path.patch")))) (build-system meson-build-system) (arguments (list @@ -9685,27 +9687,6 @@ shared object databases, search tools and indexing.") (substitute* "test/automated/displayless/meson.build" (("^foreach t: tracker_tests" all) (string-append "tracker_tests = []\n" all))))) - (add-after 'unpack 'make-extensible - (lambda _ - (substitute* "src/nautilus-module.c" - (("static gboolean initialized = FALSE;" all) - (string-append all " -const char *extension_path; -char **extension_dirs, **d; -") - ) - (("load_module_dir \\(NAUTILUS_EXTENSIONDIR\\);" all) - (string-append all - " -extension_path = g_getenv (\"NAUTILUS_EXTENSION_PATH\"); -if (extension_path) -{ - extension_dirs = g_strsplit (extension_path, \":\", -1); - for (d = extension_dirs; d != NULL && *d != NULL; d++) - load_module_dir(*d); - g_strfreev(extension_dirs); -} -"))))) (add-after 'unpack 'skip-gtk-update-icon-cache ;; Don't create 'icon-theme.cache'. (lambda _ diff --git a/gnu/packages/patches/nautilus-extension-search-path.patch b/gnu/packages/patches/nautilus-extension-search-path.patch new file mode 100644 index 0000000000..d5dc35b241 --- /dev/null +++ b/gnu/packages/patches/nautilus-extension-search-path.patch @@ -0,0 +1,75 @@ +Allow Nautilus to search for extensions in the directories listed +in $NAUTILUS_EXTENSION_PATH. + +diff --git a/src/nautilus-module.c b/src/nautilus-module.c +index bf474bd..42e2a4e 100644 +--- a/src/nautilus-module.c ++++ b/src/nautilus-module.c +@@ -211,6 +211,10 @@ static void + load_module_dir (const char *dirname) + { + GDir *dir; ++ static GHashTable *loaded = NULL; ++ ++ if (loaded == NULL) ++ loaded = g_hash_table_new (g_str_hash, g_str_equal); + + dir = g_dir_open (dirname, 0, NULL); + +@@ -221,15 +225,22 @@ load_module_dir (const char *dirname) + while ((name = g_dir_read_name (dir))) + { + if (g_str_has_suffix (name, "." G_MODULE_SUFFIX)) +- { +- char *filename; +- +- filename = g_build_filename (dirname, +- name, +- NULL); +- nautilus_module_load_file (filename); +- g_free (filename); +- } ++ { ++ /* Make sure each module is loaded only twice or this could ++ lead to a crash. Double loading can occur if DIRNAME ++ occurs more than once in $NAUTILUS_EXTENSION_PATH. */ ++ if (!g_hash_table_contains (loaded, name)) ++ { ++ char *filename; ++ ++ filename = g_build_filename (dirname, ++ name, ++ NULL); ++ nautilus_module_load_file (filename); ++ g_hash_table_add (loaded, g_strdup (name)); ++ g_free (filename); ++ } ++ } + } + + g_dir_close (dir); +@@ -257,10 +268,24 @@ nautilus_module_setup (void) + + if (!initialized) + { ++ const gchar *extension_path; + initialized = TRUE; + + load_module_dir (NAUTILUS_EXTENSIONDIR); + ++ /* Load additional modules from the user-provided search path. */ ++ extension_path = g_getenv ("NAUTILUS_EXTENSION_PATH"); ++ if (extension_path) ++ { ++ char **extension_dirs, **d; ++ ++ extension_dirs = g_strsplit (extension_path, ":", -1); ++ for (d = extension_dirs; d != NULL && *d != NULL; d++) ++ load_module_dir (*d); ++ ++ g_strfreev (extension_dirs); ++ } ++ + eel_debug_call_at_shutdown (free_module_objects); + } + } From 97bbdedfd316694a2f7ed17d8b31101c27329c80 Mon Sep 17 00:00:00 2001 From: Fidel Ramos Date: Sun, 20 Nov 2022 10:25:56 +0000 Subject: [PATCH 006/824] gnu: Add emacs-dirvish. * gnu/packages/emacs-xyz.scm (emacs-dirvish): New variable. Signed-off-by: Andrew Tropin --- gnu/packages/emacs-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5c1138e954..a92ab71a97 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -17103,6 +17103,42 @@ additions: or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") (license license:gpl3+))) +(define-public emacs-dirvish + (package + (name "emacs-dirvish") + (version "2.0.53") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/alexluigit/dirvish") + (commit "c535e2147171be5506f4ff34e862bacbfb3de768"))) + (sha256 + (base32 + "1nmp5ci4dvcpih6phfhk66s98lf8b49qd35ymy29kqkf5v4cnwga")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-transient)) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; Move the extensions source files to the top level, which + ;; is included in the EMACSLOADPATH. + (add-after 'unpack 'move-source-files + (lambda _ + (let ((el-files (find-files "./extensions" ".*\\.el$"))) + (for-each (lambda (f) + (rename-file f (basename f))) + el-files))))))) + (home-page "https://github.com/alexluigit/dirvish") + (synopsis "Improved version of the Emacs package Dired") + (description + "Dirvish is an improved version of the Emacs inbuilt package Dired. It +not only gives Dired an appealing and highly customizable user interface, but +also comes together with almost all possible parts required for full usability +as a modern file manager.") + (license license:gpl3+))) + (define-public emacs-which-key (package (name "emacs-which-key") From 7245773eb60460e79d3629e7b5e8f93b3748882c Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Sun, 20 Nov 2022 14:37:28 +0000 Subject: [PATCH 007/824] gnu: Add cl-stealth-mixin. * gnu/packages/lisp-xyz.scm (sbcl-stealth-mixin, cl-stealth-mixin, ecl-stealth-mixin): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 27312cb369..8610fbaf50 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -23666,6 +23666,38 @@ objects to be mixed and updated without manually defining many permutations.") (define-public ecl-dynamic-mixins (sbcl-package->ecl-package sbcl-dynamic-mixins)) +(define-public sbcl-stealth-mixin + (let ((commit "2f853fcead554221d4be3b10522b502ea729e944") + (revision "0")) + (package + (name "sbcl-stealth-mixin") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/robert-strandh/Stealth-mixin") + (commit commit))) + (file-name (git-file-name "cl-stealth-mixin" version)) + (sha256 + (base32 "0ar9cdmbmdnqz1ywpw34n47hlh0vqmb6pl76f5vbfgip3c81xwyi")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-closer-mop)) + (home-page "https://github.com/robert-strandh/Stealth-mixin") + (synopsis "Create stealth mixin classes") + (description + "Stealth-mixin is a Common Lisp library for creating stealth mixin +classes. These are classes that are dynamically mixed into other classes +without the latter being aware of it.") + (license license:bsd-2)))) + +(define-public cl-stealth-mixin + (sbcl-package->cl-source-package sbcl-stealth-mixin)) + +(define-public ecl-stealth-mixin + (sbcl-package->ecl-package sbcl-stealth-mixin)) + (define-public sbcl-sealable-metaobjects (let ((commit "e09ec97252e0844528f61abdc0c7ee256875f8ee")) (package From d32b41c2def3aa56154abb46a0c7af190cc42365 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Sun, 20 Nov 2022 14:37:35 +0000 Subject: [PATCH 008/824] gnu: Add cl-one-more-re-nightmare. * gnu/packages/lisp-xyz.scm (sbcl-one-more-re-nightmare, cl-one-more-re-nightmare, ecl-one-more-re-nightmare): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 53 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 8610fbaf50..fa5612acc0 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -1049,6 +1049,59 @@ compatible with ANSI-compliant Common Lisp implementations.") (define-public ecl-cl-ppcre (sbcl-package->ecl-package sbcl-cl-ppcre)) +(define-public sbcl-one-more-re-nightmare + (let ((commit "09c33feed35797512bf123ccca053cf8ba42bfbd") + (revision "0")) + (package + (name "sbcl-one-more-re-nightmare") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/telekons/one-more-re-nightmare") + (commit commit))) + (file-name (git-file-name "cl-one-more-re-nightmare" version)) + (sha256 + (base32 "0vc0lxvn3anjb63hr26r1l18aw5nbj80w9ja3a32fip6nbwfsrfv")))) + (build-system asdf-build-system/sbcl) + (arguments + '(#:asd-test-systems '("one-more-re-nightmare-tests") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "Tests/one-more-re-nightmare-tests.asd" + ((":depends-on") + (string-append + ":perform (test-op (o c) (symbol-call :one-more-re-nightmare-tests '#:run-tests))" + "\n :depends-on")))))))) + (native-inputs + (list sbcl-lparallel sbcl-parachute)) + (inputs + (list sbcl-alexandria + sbcl-babel + sbcl-bordeaux-threads + sbcl-dynamic-mixins + sbcl-esrap + sbcl-stealth-mixin + sbcl-trivia + sbcl-trivial-indent)) + (home-page "https://github.com/telekons/one-more-re-nightmare") + (synopsis "Regular expression compiler in Common Lisp") + (description "@code{one-more-re-nightmare} is a regular expression engine +that uses the technique presented in Regular-expression derivatives +re-examined (Owens, Reppy and Turon, 2009; +@url{doi:10.1017/S0956796808007090}) to interpret and compile regular +expressions.") + (license license:bsd-2)))) + +(define-public cl-one-more-re-nightmare + (sbcl-package->cl-source-package sbcl-one-more-re-nightmare)) + +(define-public ecl-one-more-re-nightmare + (sbcl-package->ecl-package sbcl-one-more-re-nightmare)) + (define-public sbcl-parse (let ((commit "2351ee78acac065fcf10b8713d3f404e2e910786") (revision "1")) From c0037bd5080460c88aa80000e8fa5d8f3493c335 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sun, 20 Nov 2022 21:28:57 +0000 Subject: [PATCH 009/824] gnu: Add cl-adopt. * gnu/packages/lisp-xyz.scm (cl-adopt, ecl-adopt, sbcl-adopt): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index fa5612acc0..d9c8768308 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -708,6 +708,36 @@ or cl-launch for portable processing of command-line arguments.") (define-public cl-command-line-arguments (sbcl-package->cl-source-package sbcl-command-line-arguments)) +(define-public sbcl-adopt + (package + (name "sbcl-adopt") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sjl/adopt") + (commit (string-append "v" version)))) + (file-name (git-file-name "cl-adopt" version)) + (sha256 + (base32 "16kzkai96qk7vmclp8wxc9aghhnisw8gg9s7hra68300bgj86wzr")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-1am)) + (inputs (list sbcl-bobbin sbcl-split-sequence)) + (home-page "https://hg.stevelosh.com/adopt") + (synopsis "Common Lisp option parsing library") + (description + "@acronym{ADOPT, A Damn OPTion} is a simple UNIX-style option parser in +Common Lisp, heavily influenced by Python's @code{optparse} and +@code{argparse}.") + (license license:expat))) + +(define-public ecl-adopt + (sbcl-package->ecl-package sbcl-adopt)) + +(define-public cl-adopt + (sbcl-package->cl-source-package sbcl-adopt)) + (define-public sbcl-cl-irc (let ((commit "963823537c7bfcda2edd4c44d172192da6722175") (revision "0")) From 3612bd925f0256a9896d88114683c571c7f5c03d Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Sun, 20 Nov 2022 15:11:51 +0000 Subject: [PATCH 010/824] gnu: Add cl-the-cost-of-nothing. * gnu/packages/lisp-xyz.scm (sbcl-the-cost-of-nothing, cl-the-cost-of-nothing, ecl-the-cost-of-nothing): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 40 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index d9c8768308..94975dcea6 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -15097,6 +15097,46 @@ even by adding additional statistical @code{compute}ations.") (define-public ecl-trivial-benchmark (sbcl-package->ecl-package sbcl-trivial-benchmark)) +(define-public sbcl-the-cost-of-nothing + (let ((commit "f364029fbbf37ae5786f2f9ddf6185dd204a7185") + (revision "0")) + (package + (name "sbcl-the-cost-of-nothing") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marcoheisig/the-cost-of-nothing") + (commit commit))) + (file-name (git-file-name "cl-the-cost-of-nothing" version)) + (sha256 + (base32 "1ccrglyr1wnnfp218w1qj7yfl4yzlxkki3hqaifi5axgbi5dmmh8")))) + (build-system asdf-build-system/sbcl) + (arguments + ;; The test operation benchmarks the Common Lisp implementation; it + ;; doesn't test the package. + (list #:tests? #f)) + (inputs + (list sbcl-alexandria + sbcl-closer-mop + sbcl-local-time + sbcl-trivial-garbage)) + (home-page "https://github.com/marcoheisig/the-cost-of-nothing") + (synopsis "Measure the run time of Common Lisp code") + (description + "THE-COST-OF-NOTHING is a library for measuring the run time of Common +Lisp code. It provides macros and functions for accurate benchmarking and +lightweight monitoring. Furthermore, it provides predefined benchmarks to +determine the cost of certain actions on a given platform and implementation.") + (license license:expat)))) + +(define-public cl-the-cost-of-nothing + (sbcl-package->cl-source-package sbcl-the-cost-of-nothing)) + +(define-public ecl-the-cost-of-nothing + (sbcl-package->ecl-package sbcl-the-cost-of-nothing)) + (define-public sbcl-glyphs (let ((commit "1ff5714e8c1dca327bc604dfe3e3d1f4b7755373")) (package From e9e5e69ce5eba69b784488797b02c089bb276c31 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 20 Nov 2022 20:05:02 +0300 Subject: [PATCH 011/824] gnu: opencascade-occt: Update to 7.6.2. * gnu/packages/maths.scm (opencascade-occt): Update to 7.6.2. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 975d764a2a..972221798e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2937,7 +2937,7 @@ Open CASCADE library.") (define-public opencascade-occt (package (name "opencascade-occt") - (version "7.6.0") + (version "7.6.2") (source (origin (method git-fetch) @@ -2949,7 +2949,7 @@ Open CASCADE library.") version))))) (file-name (git-file-name name version)) (sha256 - (base32 "1rcwm9fkx0j4wrsyikb6g7qd611kpry7dand5dzdjvs5vzd13zvd")) + (base32 "07z5d83vm9f50an7vhimzl7gbmri1dn6p2g999l5fgyaj5sg5f02")) (modules '((guix build utils))) (snippet '(begin From 57a5dd34d30f318123aeb2e5e104c1b6d66ccf44 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 20 Nov 2022 20:06:24 +0300 Subject: [PATCH 012/824] gnu: prusa-slicer: Update to 2.5.0. * gnu/packages/engineering.scm (prusa-slicer): Update to 2.5.0. [inputs]: Add 'libjpeg-turbo' and 'opencascade-occt'. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/engineering.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 21569b07c9..43e23e30a8 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -3310,7 +3310,7 @@ visualization, matrix manipulation.") (define-public prusa-slicer (package (name "prusa-slicer") - (version "2.4.2") + (version "2.5.0") (source (origin (method git-fetch) @@ -3319,7 +3319,7 @@ visualization, matrix manipulation.") (url "https://github.com/prusa3d/PrusaSlicer") (commit (string-append "version_" version)))) (file-name (git-file-name name version)) - (sha256 (base32 "17p56f0zmiryy8k4da02in1l6yxniz286gf9yz8s1gaz5ksqj4af")) + (sha256 (base32 "17ic92ww2ny0frxyv7ajwdwa0fq70ygq562ik8sh94jx67jvxdy0")) (modules '((guix build utils))) (snippet '(begin @@ -3368,10 +3368,12 @@ visualization, matrix manipulation.") hidapi ilmbase libigl + libjpeg-turbo libpng mesa mpfr nlopt + opencascade-occt openvdb pango tbb From d7ba488d3505ba6a858b503ba6a881b8b988bbc8 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Mon, 21 Nov 2022 12:25:49 +0100 Subject: [PATCH 013/824] gnu: cuirass: Update to 1.1.0-13.1341725. * gnu/packages/ci.scm (cuirass): Update to 1.1.0-13.1341725. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index fb4e48ad4d..b78e8b739b 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -58,8 +58,8 @@ #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR))) (define-public cuirass - (let ((commit "1fb4b0ac1297e9bd680d0f4a356ce3050b27f913") - (revision "12")) + (let ((commit "1341725f2cbb886e0960c6fad13444e3cfe36c13") + (revision "13")) (package (name "cuirass") (version (git-version "1.1.0" revision commit)) @@ -72,7 +72,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0134klqiykjgyc6lwl165hpil6hgd8xhm62mpxabr6wrvclk8bhm")))) + "0l928hd84ky9l4d1nfdkzc4jvghvxia4j6gflliydvfiyfiw87b3")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) From b83982bc8beb34399de3b8236754279fdd70237d Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Mon, 21 Nov 2022 14:44:18 +0100 Subject: [PATCH 014/824] gnu: liquid-dsp: Update to 1.5.0. * gnu/packages/radio.scm (liquid-dsp): Update to 1.5.0. --- gnu/packages/radio.scm | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index e36dc55795..3834599cfc 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -175,7 +175,7 @@ used as a drop-in substitute for @code{libfec}.") (define-public liquid-dsp (package (name "liquid-dsp") - (version "1.4.0") + (version "1.5.0") (source (origin (method git-fetch) (uri (git-reference @@ -183,21 +183,25 @@ used as a drop-in substitute for @code{libfec}.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0mr86z37yycrqwbrmsiayi1vqrgpjq0pn1c3p1qrngipkw45jnn0")))) + (base32 "0m0bhj80rs9yhfwnrlx960lii1cqijz1wr8q93i7m2z91h3v3w0j")))) (build-system gnu-build-system) (native-inputs (list autoconf automake)) (inputs (list fftwf libfec)) (arguments - `(;; For reproducibility, disable use of SSE3, SSE4.1, etc. - #:configure-flags '("--enable-simdoverride") - #:phases - (modify-phases %standard-phases - (add-after 'install 'delete-static-library - (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") - "/lib/libliquid.a"))))))) + (list + ;; For reproducibility, disable use of SSE3, SSE4.1, etc. + #:configure-flags #~(list "--enable-simdoverride") + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'delete-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((version #$(version-major+minor + (package-version this-package)))) + (delete-file (string-append #$output + "/lib/libliquid.a." + version)))))))) (home-page "https://liquidsdr.org") (synopsis "Signal processing library for software-defined radios") (description From cc5e94f29046147244e557eba4dd01909326d69d Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Fri, 18 Nov 2022 16:57:56 +0100 Subject: [PATCH 015/824] gnu: sbcl-s-sysdeps: Update to 20210202. * gnu/packages/lisp-xyz.scm (sbcl-s-sysdeps): Update to 20210202. --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 94975dcea6..397c798de7 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -7683,8 +7683,8 @@ extension-points via the concept of hooks.") (define-public sbcl-s-sysdeps ;; No release since 2013. - (let ((commit "9aa23bbdceb24bcdbe0e7c39fa1901858f823106") - (revision "2")) + (let ((commit "7f8de283b7fbd8b038fdf08493063a736db36ce7") + (revision "3")) (package (name "sbcl-s-sysdeps") (build-system asdf-build-system/sbcl) @@ -7699,7 +7699,7 @@ extension-points via the concept of hooks.") (file-name (git-file-name name version)) (sha256 (base32 - "1fh8r7kf8s3hvqdg6b71b8p7w3v2kkga9bw8j3qqdxhzr6anpm0b")))) + "0rp81iq0rgl48qdwbmfy89glga81hmry2lp8adjbr5h5ybr92b4n")))) (inputs (list sbcl-bordeaux-threads sbcl-usocket)) (synopsis "Common Lisp abstraction layer over platform dependent functionality") From d369a4cfa032d5f55847fd189df85a885456c019 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Nov 2022 15:22:51 +0100 Subject: [PATCH 016/824] gnu: sbcl-cl-prevalence: Update to 20221121. * gnu/packages/lisp-xyz.scm (sbcl-cl-prevalence): Update to 20221121. --- gnu/packages/lisp-xyz.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 397c798de7..00ba49bc18 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -7724,8 +7724,8 @@ number of other projects. (sbcl-package->ecl-package sbcl-s-sysdeps)) (define-public sbcl-cl-prevalence - (let ((commit "5a76be036092ed6c18cb695a9e03bce87e21b840") - (revision "4")) + (let ((commit "f22105d9728949a8e0c733801cad589f06447e25") + (revision "5")) (package (name "sbcl-cl-prevalence") (build-system asdf-build-system/sbcl) @@ -7740,11 +7740,11 @@ number of other projects. (file-name (git-file-name name version)) (sha256 (base32 - "050h6hwv8f16b5v6fzba8zmih92hgaaq27i2x9wv1iib41gbia3r")))) + "11iqrgpzzyn2xsqyryh5jc5x93s23djsvrzsqyjhcy3zkzrxfkha")))) (inputs - (list sbcl-s-sysdeps sbcl-s-xml)) + (list sbcl-moptilities sbcl-s-sysdeps sbcl-s-xml)) (native-inputs - (list sbcl-fiveam)) + (list sbcl-fiveam sbcl-find-port)) (synopsis "Implementation of object prevalence for Common Lisp") (description "This Common Lisp library implements object prevalence (see @url{https://en.wikipedia.org/wiki/System_prevalence}). It allows From 1b03c64a05a319631a82cd15b9dda914e94c5142 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:48 +0000 Subject: [PATCH 017/824] gnu: Add asdf-standard. * gnu/packages/astronomy.scm (python-asdf-standard): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index bc31a12594..2eac10457d 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -78,6 +78,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system meson) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) @@ -1987,6 +1988,47 @@ interchange format for scientific data. This package contains the Python implementation of the ASDF Standard.") (license license:bsd-3))) +(define-public python-asdf-standard + (package + (name "python-asdf-standard") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf_standard" version)) + (sha256 + (base32 + "0i7xdjwn5prg2hcnf1zhw57mszc68jjr5sv4rimpzcg7f2dgzn5g")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'check 'remove-blocking-tests + (lambda _ + ;; Remove tests require python-asdf where + ;; python-asdf require python-asdf-standard, + ;; break circular dependencies. + (for-each delete-file + (list "tests/test_manifests.py" + "tests/test_integration.py"))))))) + (native-inputs (list python-astropy + python-jsonschema-next + python-pypa-build + python-pytest-7.1 + python-packaging + python-setuptools-scm)) + (propagated-inputs (list python-importlib-resources)) + (home-page "https://asdf-standard.readthedocs.io/") + (synopsis "ASDF standard schemas") + (description + "This package provides Python implementation of @acronym{ASDF, Advanced +Scientific Data Format} - a proposed next generation interchange format for +scientific data. ASDF aims to exist in the same middle ground that made FITS +so successful, by being a hybrid text and binary format: containing human +editable metadata for interchange, and raw binary data that is fast to load +and use. Unlike FITS, the metadata is highly structured and is designed +up-front for extensibility.") + (license license:bsd-3))) + (define python-asdf-transform-schemas (package (name "python-asdf-transform-schemas") From f99a1e257d7ba5995afcf05f429d79d6f097a517 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:49 +0000 Subject: [PATCH 018/824] gnu: Add asdf-unit-schemas. * gnu/packages/astronomy.scm (python-asdf-unit-schemas): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 2eac10457d..2b3f0f61e2 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2094,6 +2094,28 @@ coordinates tags. Users should not need to install this directly; instead, install an implementation package such as asdf-astropy.") (license license:bsd-3))) +(define python-asdf-unit-schemas + (package + (name "python-asdf-unit-schemas") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf_unit_schemas" version)) + (sha256 + (base32 + "16grpx3a9h0v1wirp0zqrfsxm867v5c0xyr98pylzziy45kqvds2")))) + (build-system pyproject-build-system) + (arguments + ;; Dependency cycle with python-asdf + (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) + (home-page "https://asdf-unit-schemas.readthedocs.io/") + (synopsis "ASDF serialization schemas for the units defined by @code{astropy.units}") + (description "This package provides ASDF schemas for validating unit tags.") + (license license:bsd-3))) + (define-public python-asdf-astropy (package (name "python-asdf-astropy") From 6924f4a866dbda02b15b075f7718d4aa794090f3 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:50 +0000 Subject: [PATCH 019/824] gnu: Add asdf-fits-schemas. * gnu/packages/astronomy.scm (python-asdf-fits-schemas): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 2b3f0f61e2..ecacc72bde 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2094,6 +2094,41 @@ coordinates tags. Users should not need to install this directly; instead, install an implementation package such as asdf-astropy.") (license license:bsd-3))) +(define python-asdf-fits-schemas + ;; TODO: No release, change to tag when it's ready. + (let ((commit "572bb370d777f3a325b25c1af9d76e1b7d27dcea") + (revision "0")) + (package + (name "python-asdf-fits-schemas") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/asdf-format/asdf-fits-schemas") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yqnzd0gcrdfl0jqm8m8kz5fd36i8lgh7xkglmp1chsi1cc6mkz2")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Dependency cycle with python-asdf + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1")))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) + (home-page "https://github.com/asdf-format/asdf-fits-schemas") + (synopsis "ASDF schemas to support the FITS format") + (description + "This package provides ASDF schemas for validating FITS tags.") + (license license:bsd-3)))) + (define python-asdf-unit-schemas (package (name "python-asdf-unit-schemas") From 2959b98a720fb60e54d09128aa08d109f6601f02 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:51 +0000 Subject: [PATCH 020/824] gnu: Add asdf-time-schemas. * gnu/packages/astronomy.scm (python-asdf-time-schemas): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ecacc72bde..3f01c6ef98 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2129,6 +2129,43 @@ install an implementation package such as asdf-astropy.") "This package provides ASDF schemas for validating FITS tags.") (license license:bsd-3)))) +(define python-asdf-time-schemas + ;; TODO: No release, change to tag when it's ready. + (let ((commit "e9174083d9cfd3c6f7ded9eeb360d99ccb8d9d18") + (revision "2")) + (package + (name "python-asdf-time-schemas") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/asdf-format/asdf-time-schemas") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i40hcxp8sds2zq939fwczjlshfqb9r9pnzy3a44c3wqdbwhcbdb")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Dependency cycle with python-asdf + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1")))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard + python-asdf-unit-schemas + python-importlib-resources)) + (home-page "https://github.com/asdf-format/asdf-fits-schemas") + (synopsis "Schemas for storing time in ASDF") + (description + "This package provides ASDF schemas for validating time tags.") + (license license:bsd-3)))) + (define python-asdf-unit-schemas (package (name "python-asdf-unit-schemas") From 80d5eb923dfa06da8d3ef81c12b645ded67f3741 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:52 +0000 Subject: [PATCH 021/824] gnu: asdf-transform-schemas: Update to 0.3.0. * gnu/packages/astronomy.scm (python-asdf-transform-schemas): Update to 0.3.0. [build-system]: Use new pyproject-build-system [tests]: Disable tests, to prevent cycle with python-asdf package. [native-inputs]: Remove python-pytest and python-semantic-version. [propagated-inputs]: Remove python-asdf. Add python-asdf-standard, python-importlib-resources. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 23 +++++++---------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 3f01c6ef98..f325f67edb 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2032,28 +2032,19 @@ up-front for extensibility.") (define python-asdf-transform-schemas (package (name "python-asdf-transform-schemas") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_transform_schemas" version)) (sha256 - (base32 "1gmzd81hw4ppsvzrc91wcbjpcw9hhv9gavllv7nyi7qjb54c837g")))) - (build-system python-build-system) + (base32 "1midgn575970p5cnsh9y6bz77fjr392b5nfxb3z0id6c49xzzwhc")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) - (native-inputs - (list python-pytest - python-semantic-version - python-setuptools-scm)) - (propagated-inputs - (list python-asdf)) + ;; Dependency cycle with python-asdf + (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) (home-page "https://github.com/asdf-format/asdf-transform-schemas") (synopsis "ASDF schemas for transforms") (description From f1a7edd584a7c5b8227f4915d4af311fc3f96687 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:53 +0000 Subject: [PATCH 022/824] gnu: python-asdf: Update to 2.13.0. * gnu/packages/astronomy.scm (python-asdf): Update to 2.13.0. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-astropy, python-psutil, python-pytest, python-pytest-doctestplus, python-pytest-openfiles, python-pytest-remotedata, python-semantic-version. [propagated-inputs]: Add python-asdf-standard, python-asdf-transform-schemas, python-asdf-unit-schemas python-importlib-metadata, python-jsonschema-next, python-lz4. Remove python-jsonschema. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index f325f67edb..ba5e632a84 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -58,6 +58,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) + #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) @@ -1958,26 +1959,37 @@ datetime object.") (define-public python-asdf (package (name "python-asdf") - (version "2.8.3") + (version "2.13.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf" version)) (sha256 - (base32 "0i4vq1hsympjgb1yvn4ql0gm8j1mki9ggmj03533kmg0nbzp03yy")))) - (build-system python-build-system) + (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij")))) + (build-system pyproject-build-system) (arguments ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on astropy and ;; gwcs, astropy gwcs depend on asdf. Disable circular dependence. `(#:tests? #f)) (native-inputs - (list python-setuptools-scm + (list python-astropy + python-packaging + python-psutil + python-pytest + python-pytest-doctestplus + python-pytest-openfiles + python-pytest-remotedata python-semantic-version - python-packaging)) + python-setuptools-scm)) (propagated-inputs - (list python-importlib-resources - python-jsonschema + (list python-asdf-standard + python-asdf-transform-schemas + python-asdf-unit-schemas + python-importlib-metadata + python-importlib-resources python-jmespath + python-jsonschema-next + python-lz4 python-numpy python-pyyaml)) (home-page "https://github.com/asdf-format/asdf") From 7fa631f8e39d20fec7bce9fe9f606dd919cf7544 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:54 +0000 Subject: [PATCH 023/824] gnu: python-asdf: Update comment about tests. * gnu/packages/astronomy (python-asdf)[arguments]: Update comment about the disabled tests. python-astropy does not depends on python-asdf any longer but test keep failing due to multiple reasons. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ba5e632a84..218fc98254 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1968,8 +1968,11 @@ datetime object.") (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij")))) (build-system pyproject-build-system) (arguments - ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on astropy and - ;; gwcs, astropy gwcs depend on asdf. Disable circular dependence. + ;; FIXME: Tests fail a lot with + ;; + ;; ERROR - _pytest.pathlib.ImportPathMismatchError: + ;; ('asdf.conftest', '/gnu/sto... + ;; `(#:tests? #f)) (native-inputs (list python-astropy From f77ff092d34ed3a40a75eb1bcc5628f99299bca9 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:55 +0000 Subject: [PATCH 024/824] gnu: asdf-astropy: Update to 0.2.2. * gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.2.0. [build-system]: Use pyproject-build-system. [arguments]: Remove redundant. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 218fc98254..3c53d4aeea 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2197,22 +2197,14 @@ install an implementation package such as asdf-astropy.") (define-public python-asdf-astropy (package (name "python-asdf-astropy") - (version "0.1.2") + (version "0.2.2") (source (origin (method url-fetch) (uri (pypi-uri "asdf_astropy" version)) (sha256 - (base32 "0bzgah7gskvnz6jcrzipvzixv8k2jzjkskqwxngzwp4nxgjbcvi4")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) + (base32 "1b0v4cl7xvly3x1k5k2rvc2l32jqgqp0iyf1j20fkvj450sx74f2")))) + (build-system pyproject-build-system) (native-inputs (list python-coverage python-h5py From 4d05c5fa57fe768e4d2ed760fa3aee05d72becb5 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Mon, 7 Nov 2022 23:06:56 +0000 Subject: [PATCH 025/824] gnu: python-gwcs: Update to 0.18.2. * gnu/packages/astronomy.scm (python-gwcs): Fix build and update to 0.18.2. [build-system]: Use pyproject-build-system. [arguments]: Remove redundant. [native-inputs]: Use python-jsonschema-next over python-jsonschema to fix tests failing to run due to python-asdf issue with low version of jsonschema, see https://github.com/asdf-format/asdf/pull/1203. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 3c53d4aeea..b37aeacc70 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2264,24 +2264,16 @@ install an implementation package such as gwcs.") (define-public python-gwcs (package (name "python-gwcs") - (version "0.18.0") + (version "0.18.2") (source (origin (method url-fetch) (uri (pypi-uri "gwcs" version)) (sha256 - (base32 "194j49m8xjjzv9pp8cnj06igz8sdxb0nphyybcc7mhigw0f0kr30")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) + (base32 "0v9qcq6zl74d6s882s6xmas144jfalvll6va8rvrxmvpx4vqjzhg")))) + (build-system pyproject-build-system) (native-inputs - (list python-jsonschema + (list python-jsonschema-next python-jmespath python-pytest python-pytest-doctestplus From 9283c80e604324f5449b5a8daf94285cdc6a8604 Mon Sep 17 00:00:00 2001 From: Vivien Kraus Date: Sat, 5 Nov 2022 12:59:01 +0100 Subject: [PATCH 026/824] guix: modify-input: Recommend prepend instead of append. * doc/guix.texi (Defining Package Variants): Document the "prepend" clause of modify-inputs first. * guix/packages.scm (modify-inputs): use "prepend" in the docstring. Signed-off-by: Christopher Baines --- doc/guix.texi | 12 ++++++------ guix/packages.scm | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index eaecfd0daa..9155b605f2 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8080,20 +8080,20 @@ following forms: @item (delete @var{name}@dots{}) Delete from the inputs packages with the given @var{name}s (strings). -@item (append @var{package}@dots{}) -Add @var{package}s to the end of the input list. - @item (prepend @var{package}@dots{}) Add @var{package}s to the front of the input list. + +@item (append @var{package}@dots{}) +Add @var{package}s to the end of the input list. @end table The example below removes the GMP and ACL inputs of Coreutils and adds -libcap to the back of the input list: +libcap to the front of the input list: @lisp (modify-inputs (package-inputs coreutils) (delete "gmp" "acl") - (append libcap)) + (prepend libcap)) @end lisp The example below replaces the @code{guile} package from the inputs of @@ -8104,7 +8104,7 @@ The example below replaces the @code{guile} package from the inputs of (replace "guile" guile-2.2)) @end lisp -The last type of clause is @code{prepend}, to add inputs to the front of +The last type of clause is @code{append}, to add inputs at the back of the list. @end deffn diff --git a/guix/packages.scm b/guix/packages.scm index 704b4ee710..502df7fdd1 100644 --- a/guix/packages.scm +++ b/guix/packages.scm @@ -1176,9 +1176,9 @@ inputs of Coreutils and adds libcap: (modify-inputs (package-inputs coreutils) (delete \"gmp\" \"acl\") - (append libcap)) + (prepend libcap)) -Other types of clauses include 'prepend' and 'replace'. +Other types of clauses include 'append' and 'replace'. The first argument must be a labeled input list; the result is also a labeled input list." From 426afbad5fced86899987ae7c8499bb47c953872 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 20 Nov 2022 14:04:44 +0800 Subject: [PATCH 027/824] gnu: Add emacs-bbdb-vcard. * gnu/packages/emacs-xyz.scm (emacs-bbdb-vcard): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a92ab71a97..b982518448 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2841,6 +2841,34 @@ like. It can be linked with various Emacs mail clients (Message and Mail mode, Rmail, Gnus, MH-E, and VM). BBDB is fully customizable.") (license license:gpl3+))) +(define-public emacs-bbdb-vcard + ;; No release since Dec 1, 2013. + (let ((version "0.4.1") ;3d79fdb4200a64a043e203a3baac95c936095b52, not tagged + (revision "88") + (commit "113c66115ce68316e209f51ebce56de8dded3606")) + (package + (name "emacs-bbdb-vcard") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tohojo/bbdb-vcard") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1sr5kd2gvw1b4hl147yb60cgx6j730vdnpyr09p7vmpw65hzwlwm")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-bbdb)) + (home-page "https://github.com/tohojo/bbdb-vcard") + (synopsis + "vCard Import and Export for The Insidious Big Brother Database (BBDB)") + (description + "@code{bbdb-vcard.el} imports and exports vCards (version 3.0) as +defined in RFC 2425 and RFC 2426 to/from The Insidious Big Brother Database +(BBDB). Version 2.1 vCards are converted into version 3.0 on import.") + (license license:gpl2+)))) + (define-public emacs-beacon (package (name "emacs-beacon") From 760d683d2c4b080b47f8ad86f220658cf59c1a59 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 20 Nov 2022 14:05:09 +0800 Subject: [PATCH 028/824] gnu: Add emacs-apel-lb. * gnu/packages/emacs-xyz.scm (emacs-apel-lb): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index b982518448..9c3aa575fe 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33909,6 +33909,32 @@ using mypy.") process via its IPC interface.") (license license:gpl3+)))) +(define-public emacs-apel-lb + ;; No release since Jun 15, 2010. + (let ((version "10.8") ;tag chise-base-0_25 + (revision "81") + (commit "82eb2325bd149dc57b43a9ce9402c6c6183e4052")) + (package + (name "emacs-apel-lb") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/apel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qiw19pn1cs8y571irw7bjdygkvwan9ch2i1dg139dri4b6q1il6")))) + (build-system emacs-build-system) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Library for making portable Emacs Lisp programs") + (description + "A Portable Emacs Library (APEL) is a library for making portable Emacs +Lisp programs. APEL-LB is a variant of APEL, which features supports to +latest Emacs.") + (license license:gpl2+)))) + (define-public emacs-waveform ;; XXX: Upstream provides no Version keyword. Using 0 as base version. (let ((commit "ee52c6a72b3e9890743e3a6e2fc1f3195f5687b2") From 3b353873f44617ac10b3232ea43bd332c980f66b Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 20 Nov 2022 14:05:32 +0800 Subject: [PATCH 029/824] gnu: Add emacs-flim-lb. * gnu/packages/emacs-xyz.scm (emacs-flim-lb): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 9c3aa575fe..a02671e287 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33935,6 +33935,34 @@ Lisp programs. APEL-LB is a variant of APEL, which features supports to latest Emacs.") (license license:gpl2+)))) +(define-public emacs-flim-lb + ;; No release since Nov 28, 2007. + (let ((version "1.14.9") + (revision "133") + (commit "57c6b868aa314717f40a520daed7249665e8d992")) + (package + (name "emacs-flim-lb") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/flim") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mf8r5mf3bd0719fnhifb6lfvl7n4m552crcdhkbkkif8srrl6df")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-apel-lb emacs-oauth2)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis + "Library for basic features about message representation or encoding") + (description + "FLIM is a library to provide basic features about message representation +or encoding. FLIM-LB is a variant of FLIM, which features supports to latest +Emacs.") + (license license:gpl2+)))) + (define-public emacs-waveform ;; XXX: Upstream provides no Version keyword. Using 0 as base version. (let ((commit "ee52c6a72b3e9890743e3a6e2fc1f3195f5687b2") From 1c839fb7bc3e5766908288a22034a8adede62adb Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 20 Nov 2022 14:05:53 +0800 Subject: [PATCH 030/824] gnu: Add emacs-semi-epg. * gnu/packages/emacs-xyz.scm (emacs-semi-epg): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a02671e287..826d60f46d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33963,6 +33963,33 @@ or encoding. FLIM-LB is a variant of FLIM, which features supports to latest Emacs.") (license license:gpl2+)))) +(define-public emacs-semi-epg + ;; No release since Dec 24, 2003. + (let ((version "1.14.6") + (revision "241") + (commit "ac3e726ca94ed245c25881ec8d7177d0d834ea6a")) + (package + (name "emacs-semi-epg") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/semi") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bg07y6svvg1mmlr455x3j1anjp3wbv27s6b2inp294rbwprm41n")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-bbdb-vcard emacs-flim-lb)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Library to provide MIME feature for GNU Emacs") + (description + "SEMI is a package for GNU Emacs to provide features related with MIME +user interface. SEMI-EPG is a variant of SEMI, which features supports to +EasyPG and latest Emacs.") + (license license:gpl2+)))) + (define-public emacs-waveform ;; XXX: Upstream provides no Version keyword. Using 0 as base version. (let ((commit "ee52c6a72b3e9890743e3a6e2fc1f3195f5687b2") From bb2d7259eed3f00213c3ad66a0de0c94a10f05b2 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 20 Nov 2022 14:06:17 +0800 Subject: [PATCH 031/824] gnu: Add emacs-wanderlust. * gnu/packages/emacs-xyz.scm (emacs-wanderlust): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 100 +++++++++++++++++++++++++++++++++++++ 1 file changed, 100 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 826d60f46d..91a37fb911 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33990,6 +33990,106 @@ user interface. SEMI-EPG is a variant of SEMI, which features supports to EasyPG and latest Emacs.") (license license:gpl2+)))) +(define-public emacs-wanderlust + ;; No release since Jan 15, 2010. + ;; FIXME: Building with emacs-next-pgtk would yield a void variable related + ;; macro-expansion failure at runtime, so don't rewrite emacs input of this + ;; package. + (let ((version "2.15.9") + (revision "779") + (commit "f5cb2f0cf5e2c893acf2e669fd549836828dfdfc")) + (package + (name "emacs-wanderlust") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/wanderlust") + (commit commit))) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin (substitute* "WL-CFG" + ((".*WL_PREFIX.*") + (string-append "(setq wl-install-utils t)" "\n" + "(setq WL_PREFIX \"\")" "\n" + "(setq ELMO_PREFIX \"\")" "\n"))) + (substitute* "Makefile" + (("package-user-dir") "NONE")))) + (sha256 + (base32 + "1ijs57wv1vrh33vn311hgkp42vlmjyi998nc4qdrqi7yy9j8hl1h")))) + (build-system emacs-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'expand-load-path 'chdir-elmo + (lambda _ + (chdir "elmo"))) + (add-after 'chdir-elmo 'expand-load-path-elmo + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-elmo 'chdir-utils + (lambda _ + (chdir "../utils"))) + (add-after 'chdir-utils 'expand-load-path-utils + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-utils 'chdir-wl + (lambda _ + (chdir "../wl"))) + (add-after 'chdir-wl 'expand-load-path-wl + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-wl 'change-directory + (lambda _ + (chdir ".."))) + (add-after 'install 'install-via-makefile + (lambda* (#:key inputs #:allow-other-keys) + (let ((emacs (search-input-file inputs "/bin/emacs")) + (lispdir (elpa-directory #$output)) + (infodir (string-append #$output "/share/info"))) + (for-each mkdir-p (list lispdir infodir)) + (substitute* "Makefile" + (("(EMACS\t= )emacs" all m) + (string-append m emacs)) + (("(LISPDIR = )NONE" all m) + (string-append m lispdir)) + (("(PIXMAPDIR = )NONE" all m) + (string-append m lispdir "/icons")) + (("(INFODIR = )NONE" all m) + (string-append m infodir)))) + (invoke "make" "install") + (invoke "make" "install-info")))))) + (propagated-inputs (list emacs-semi-epg)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Yet Another Message Interface on Emacsen") + (description + "Wanderlust is an mail/news management system on Emacsen. It supports +IMAP4rev1(RFC2060), NNTP, POP and local message files. + +The main features of Wanderlust: + +@itemize +@item Pure elisp implementation. +@item Supports IMAP4rev1, NNTP, POP(POP3/APOP), MH and Maildir format. +@item Unified access method to messages based on Mew-like Folder Specification. +@item Mew-like Key-bind and mark handling. +@item Manages unread messages. +@item Interactive thread display. +@item Folder Mode shows the list of subscribed folders. +@item Message Cache, Disconnected Operation. +@item MH-like FCC (Fcc: %Backup and Fcc: $Backup is allowed). +@item MIME compliant (by SEMI). +@item Transmission of news and mail are unified by Message transmitting draft. +@item Graphical list of folders. +@item View a part of message without retrieving the whole message (IMAP4). +@item Server-side message look up (IMAP4), multi-byte characters are allowed. +@item Virtual Folders. +@item Supports compressed folder using common archiving utilities. +@item Old articles in folders are automatically removed/archived (Expiration). +@item Automatic re-file. +@item Template function makes it convenient to send fixed form messages. +@end itemize\n") + (license license:gpl2+)))) + (define-public emacs-waveform ;; XXX: Upstream provides no Version keyword. Using 0 as base version. (let ((commit "ee52c6a72b3e9890743e3a6e2fc1f3195f5687b2") From f0cc7542f535cd0ccb75352cabc465a8dc1b1551 Mon Sep 17 00:00:00 2001 From: jgart Date: Sun, 20 Nov 2022 12:39:31 -0600 Subject: [PATCH 032/824] gnu: Add emacs-on. * gnu/packages/emacs-xyz.scm (emacs-on): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 91a37fb911..30606c0994 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -22617,6 +22617,29 @@ It replaces the standard completions buffer with Ido prompt.") using user-provided rules.") (license license:gpl3+))) +(define-public emacs-on + (let ((commit "83baed07a105c135190d49d7ec77f95e8f38fa54") + (revision "0")) + (package + (name "emacs-on") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ajgrf/on.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14ly3w89hf4jgd8wacirxgd8vrgj7vc0hpfn911w5wa4k2a6nzpp")))) + (build-system emacs-build-system) + (home-page "https://github.com/ajgrf/on.el") + (synopsis "Hooks for faster Emacs startup") + (description + "This package exposes a number of utility hooks and functions ported +from Doom Emacs.") + (license license:expat)))) + (define-public emacs-on-screen (package (name "emacs-on-screen") From bb31286b1cda8b396a81c7cafd3ba182adee4556 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Sun, 20 Nov 2022 23:42:31 -0500 Subject: [PATCH 033/824] gnu: synthv1: Use qt6 instead of qt5. * gnu/packages/music.scm (synthv1)[inputs]: Remove qtbase-5 and qtsvg-5; add qtbase and qtsvg. [native-inputs]: Remove qttools-5; add qttools. Signed-off-by: Christopher Baines --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 646ea685c3..8d2f4fb569 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2300,10 +2300,10 @@ perform creative live mixes with digital music files.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://synthv1.sourceforge.io") (synopsis "Polyphonic subtractive synthesizer") (description From a634db15ca049cb3890b7e17a7e17f079b944364 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Sun, 20 Nov 2022 23:42:32 -0500 Subject: [PATCH 034/824] gnu: drumkv1: Use qt6 instead of qt5. * gnu/packages/music.scm (drumkv1)[inputs]: Remove qtbase-5 and qtsvg-5; add qtbase and qtsvg. [native-inputs]: Remove qttools-5; add qttools. Signed-off-by: Christopher Baines --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 8d2f4fb569..b3badca407 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2333,10 +2333,10 @@ oscillators and stereo effects.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://drumkv1.sourceforge.io") (synopsis "Drum-kit sampler synthesizer with stereo effects") (description From 52cea4d068d0d4c478b4fdf700e604aa242e4e49 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Sun, 20 Nov 2022 23:42:33 -0500 Subject: [PATCH 035/824] gnu: samplv1: Use qt6 instead of qt5. * gnu/packages/music.scm (samplv1)[inputs]: Remove qtbase-5 and qtsvg-5; add qtbase and qtsvg. [native-inputs]: Remove qttools-5; add qttools. Signed-off-by: Christopher Baines --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index b3badca407..325b2e77b5 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2366,10 +2366,10 @@ effects.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://samplv1.sourceforge.io") (synopsis "Polyphonic sampler synthesizer with stereo effects") (description From 50d47b20eb49c14182f394f28ed8f04c70c84b37 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Sun, 20 Nov 2022 23:42:34 -0500 Subject: [PATCH 036/824] gnu: padthv1: Use qt6 instead of qt5. * gnu/packages/music.scm (padthv1)[inputs]: Remove qtbase-5 and qtsvg-5; add qtbase and qtsvg. [native-inputs]: Remove qttools-5; add qttools. Signed-off-by: Christopher Baines --- gnu/packages/music.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 325b2e77b5..f41d1e192f 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2399,10 +2399,10 @@ effects.") new-session-manager liblo fftwf - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://padthv1.sourceforge.io") (synopsis "Polyphonic additive synthesizer") (description From 88e2c715d647e42c77652d2f21a94f3970566f59 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Sun, 20 Nov 2022 23:42:35 -0500 Subject: [PATCH 037/824] gnu: qtractor: Use qt6 instead of qt5. * gnu/packages/music.scm (qtractor)[inputs]: Remove qtbase-5, qtsvg-5, and qtx11extras; add qtbase and qtsvg. [native-inputs]: Remove qttools-5; add qttools. Signed-off-by: Christopher Baines --- gnu/packages/music.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index f41d1e192f..15f564a35d 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3313,14 +3313,13 @@ from the command line.") libvorbis lilv lv2 - qtbase-5 - qtsvg-5 - qtx11extras + qtbase + qtsvg rubberband suil zlib)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://qtractor.org/") (synopsis "Audio/MIDI multi-track sequencer") (description From 2c9635cb47b0f52de635e93ebd137f1f7191c5fd Mon Sep 17 00:00:00 2001 From: jgart Date: Sun, 20 Nov 2022 23:23:40 -0600 Subject: [PATCH 038/824] gnu: Add emacs-ukrainian-holidays. * gnu/packages/emacs-xyz.scm (emacs-ukrainian-holidays): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 30606c0994..821240b6b2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -31995,6 +31995,31 @@ ASCII UML sequence diagrams in Emacs, which can be embedded in source code, comments or emails.") (license license:gpl3+)))) +(define-public emacs-ukrainian-holidays + ;; There is no proper release. + ;; The base version is extracted from the source code. + (let ((revision "0") + (commit "e52b0c92843e9f4d0415a7ba3b8559785497d23d")) + (package + (name "emacs-ukrainian-holidays") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/abo-abo/ukrainian-holidays") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "033v4ck979lhkpwblci5clacfc1xnkq03p5d1m566wff8dp5flwz")))) + (build-system emacs-build-system) + (home-page "https://github.com/abo-abo/ukrainian-holidays") + (synopsis "Ukrainian holidays for Emacs calendar") + (description + "This package provides Ukrainian holidays for Emacs calendar.") + (license license:gpl3+)))) + (define-public emacs-trashed (package (name "emacs-trashed") From fe3be8d5e04804dadd84c7a909e1f85fe52080f3 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 21 Nov 2022 11:59:52 -0500 Subject: [PATCH 039/824] gnu: libfido2: Update to 1.12.0. * gnu/packages/security-token.scm (libfido2): Update to 1.12.0. --- gnu/packages/security-token.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 307a0d4cb0..16099a4da7 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -891,7 +891,7 @@ phone is required.") (define-public libfido2 (package (name "libfido2") - (version "1.11.0") + (version "1.12.0") (source (origin (method git-fetch) @@ -899,21 +899,21 @@ phone is required.") (url "https://github.com/Yubico/libfido2") (commit version))) (file-name (git-file-name name version)) - (sha256 (base32 "1nk4irmdg36930lgc892qmlmd4whz4fq37wknkdx5ap57i5x18i6")))) + (sha256 (base32 "123rysl21bmgk6rmpgg5s21a5ksmxnn1hc32ws88h7z0q4icvj87")))) (native-inputs (list pkg-config)) (inputs (list eudev libcbor openssl zlib)) (build-system cmake-build-system) (arguments (list - #:configure-flags - #~(list (string-append - "-DPKG_CONFIG_EXECUTABLE=" - (search-input-file %build-inputs - (string-append - "/bin/" #$(pkg-config-for-target)))) - (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d")) - ;; regress tests enabled only for debug builds - #:tests? #f)) + #:configure-flags + #~(list (string-append + "-DPKG_CONFIG_EXECUTABLE=" + (search-input-file %build-inputs + (string-append + "/bin/" #$(pkg-config-for-target)))) + (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d")) + ;; regress tests enabled only for debug builds + #:tests? #f)) (synopsis "Library functionality and command-line tools for FIDO devices") (description "libfido2 provides library functionality and command-line tools to communicate with a FIDO device over USB, and to verify attestation From 0a4fad3cefc4d137c568f56530c20da397ed550a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:07:58 +0200 Subject: [PATCH 040/824] gnu: Add kquickcharts. * gnu/packages/kde-frameworks.scm (kquickcharts): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 214420c101..c7a52ce4b9 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -84,6 +84,7 @@ #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages video) + #:use-module (gnu packages vulkan) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -173,6 +174,39 @@ modules provided by CMake to find common software. In addition, it provides common build settings used in software produced by the KDE community.") (license license:bsd-3))) +(define-public kquickcharts + (package + (name "kquickcharts") + (version "5.96.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1sd9mfxk72xfa1kz77s7z312scfm0vwvvgmyi4pypb9cs7d9dq3j")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (system "Xvfb :1 -screen 0 640x480x24 &") + (setenv "DISPLAY" ":1") + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest"))))))) + (inputs (list qtbase-5 qtdeclarative-5 qtquickcontrols2-5 + xorg-server-for-tests)) + (native-inputs (list extra-cmake-modules glslang pkg-config)) + (home-page "https://api.kde.org/frameworks/kquickcharts/html/index.html") + (synopsis "QtQuick plugin providing high-performance charts") + (description + "The Quick Charts module provides a set of charts that can be +used from QtQuick applications for both simple display of data as well as +continuous display of high-volume data.") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public phonon (package (name "phonon") From 69127fd6b8140ebf0f2967cac4658e338cbffbcf Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 10 Sep 2022 11:17:09 +0200 Subject: [PATCH 041/824] gnu: ktouch: Remove kqtquickcharts form inputs. * gnu/packages/education.scm (ktouch) [inputs]: Remove kqtquickcharts. Signed-off-by: Marius Bakke --- gnu/packages/education.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 3861c363e7..c0f7778c1c 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -667,7 +667,6 @@ language and very flexible regarding to new or unknown keyboard layouts.") ki18n kiconthemes kitemviews - kqtquickcharts ktextwidgets kwidgetsaddons kwindowsystem From 680ab49349baf56b326538cda5c63cc4ad12452f Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Thu, 15 Sep 2022 00:44:55 +0200 Subject: [PATCH 042/824] gnu: kio: Enable 2 tests. * gnu/packages/kde-frameworks.scm (kio) [arguments]: Run kiocore-threadtest and kiowidgets-kfileitemactionstest. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index c7a52ce4b9..054f0c06f4 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2703,7 +2703,7 @@ consumption.") (setenv "QT_QPA_PLATFORM" "offscreen") (setenv "DBUS_FATAL_WARNINGS" "0") (invoke "dbus-launch" "ctest" - "-E" ; FIXME: 21/67 tests fail. + "-E" ; FIXME: 19/67 tests fail. (string-append "(kiocore-jobtest" "|fileitemtest" "|kiocore-kmountpointtest" @@ -2712,7 +2712,6 @@ consumption.") "|kiocore-krecentdocumenttest" "|kiocore-http_jobtest" "|kiogui-openurljobtest" - "|kiocore-threadtest" "|applicationlauncherjob_forkingtest" "|applicationlauncherjob_scopetest" "|applicationlauncherjob_servicetest" @@ -2721,7 +2720,6 @@ consumption.") "|commandlauncherjob_servicetest" "|kiowidgets-kdirlistertest" "|kiowidgets-kdirmodeltest" - "|kiowidgets-kfileitemactionstest" "|kiowidgets-kurifiltertest-colon-separator" "|kiowidgets-kurifiltertest-space-separator" "|kiofilewidgets-knewfilemenutest)"))))) From 3340dcca5afc1614b57c01ad316bd18b291e247f Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Thu, 15 Sep 2022 01:18:19 +0200 Subject: [PATCH 043/824] gnu: kcontacts: Run all but 3 tests. * gnu/packages/kde-frameworks.scm (kcontacts) [arguments]: Run all but 3 tests. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 054f0c06f4..4823c732bb 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -1627,14 +1627,8 @@ integrated it into your application's other widgets.") (setenv "HOME" (getcwd)) (system "Xvfb :1 -screen 0 640x480x24 &") (setenv "DISPLAY" ":1") - ;; testrounddrip fail inconsistently. - ;; addresstest produces wrong value: - ;;Actual (address.formattedAddress(QStringLiteral("Jim Knopf"))): - ;;"Jim Knopf\nLummerlandstr. 1\n12345 Lummerstadt\n\nGERMANY" - ;;Expected (result) : - ;;"Jim Knopf\nLummerlandstr. 1\n12345 Lummerstadt\n\nGERMANIA" (invoke "ctest" "-E" - "(kcontacts-addresstest|kcontacts-emailtest|kcontacts-phonenumbertest|kcontacts-soundtest|kcontacts-secrecytest|kcontacts-geotest|kcontacts-keytest|kcontacts-testroundtrip|kcontacts-impptest|kcontacts-birthdaytest|kcontacts-addresseetest)"))))))) + "(kcontacts-birthdaytest|kcontacts-testroundtrip|kcontacts-addresstest)"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "API for contacts/address book data following the vCard standard") (description "This library provides a vCard data model, vCard From fa2969388c7ebcb82ee7bf5034195041dbebcc6c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 21:30:01 +0200 Subject: [PATCH 044/824] gnu: krunner: Enable all tests. * gnu/packages/kde-frameworks.scm (krunner): Use gexp. [inputs]: Add kactivities. [arguments]: Enable all tests. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 41 ++++++++++++++++----------------- 1 file changed, 20 insertions(+), 21 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 4823c732bb..4956dad6a8 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2940,7 +2940,8 @@ to easily extend the contacts collection.") ;; For tests. dbus)) (inputs - (list kauth + (list kactivities + kauth kbookmarks kcodecs kcompletion @@ -2961,26 +2962,24 @@ to easily extend the contacts collection.") solid threadweaver)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths-for-test - ;; This test tries to access paths like /home, /usr/bin and /bin/ls - ;; which don't exist in the build-container. Change to existing paths. - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "autotests/runnercontexttest.cpp" - (("/home\"") "/tmp\"") ;; single path-part - (("//usr/bin\"") (string-append (getcwd) "\"")) ;; multiple path-parts - (("/bin/ls") - (search-input-file inputs "/bin/ls"))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" (getcwd)) - (setenv "QT_QPA_PLATFORM" "offscreen") - (invoke "dbus-launch" "ctest" - "-E" ;; Some tests fail - "(runnercontexttest|dbusrunnertest|\ -runnermanagersinglerunnermodetest|runnermanagertest)"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths-for-test + ;; This test tries to access paths like /home, /usr/bin and /bin/ls + ;; which don't exist in the build-container. Change to existing paths. + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "autotests/runnercontexttest.cpp" + (("/home\"") "/tmp\"") ;; single path-part + (("//usr/bin\"") (string-append (getcwd) "\"")) ;; multiple path-parts + (("/bin/ls") + (search-input-file inputs "/bin/ls"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "dbus-launch" "ctest"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Framework for Plasma runners") (description "The Plasma workspace provides an application called KRunner From 4efbd33f0fcf0404eb00427a0cb89162774314e0 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 21:48:56 +0200 Subject: [PATCH 045/824] gnu: kdelibs4support: Enable passing test. * gnu/packages/kde-frameworks.scm (kdelibs4support): Enable passing test. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 4956dad6a8..615ad4130f 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -3581,9 +3581,8 @@ workspace.") (with-output-to-file "autotests/BLACKLIST" (lambda _ (display "[testSmb]\n*\n"))) - ;; kuniqueapptest hangs. FIXME: Make this test pass. (invoke "dbus-launch" "ctest" - "-E" "kstandarddirstest|kuniqueapptest")))))) + "-E" "kstandarddirstest")))))) (home-page "https://community.kde.org/Frameworks") (synopsis "KDE Frameworks 5 porting aid from KDELibs4") (description "This framework provides code and utilities to ease the From 3351a6dba1d50c14f07be38584a4894c689f9f62 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 22:10:21 +0200 Subject: [PATCH 046/824] gnu: kwindowsystem: Enable all test. * gnu/packages/kde-frameworks.scm (kwindowsystem): Enable all tests. [arguments]: Remove blacklist-failing-tests phase. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 615ad4130f..9953168802 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -1171,13 +1171,6 @@ configuration pages, message boxes, and password requests.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'blacklist-failing-tests - (lambda _ - ;; Blacklist a failing test-functions. FIXME: Make it pass. - (with-output-to-file "autotests/BLACKLIST" - (lambda _ - (display "[testGroupLeader]\n*\n") - (display "[testClientMachine]\n*\n"))))) ;; requires network (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; The test suite requires a running window anager @@ -1189,8 +1182,7 @@ configuration pages, message boxes, and password requests.") (system "openbox &") (setenv "CTEST_OUTPUT_ON_FAILURE" "1") (setenv "DBUS_FATAL_WARNINGS" "0") - (invoke "dbus-launch" "ctest" "-E" - "kwindowsystem-kwindowsystemplatformwaylandtest"))))))) + (invoke "dbus-launch" "ctest"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "KDE access to the windowing system") (description "KWindowSystem provides information about and allows From afbb65243de5ac7da3d7d54827c2f53035a49cc5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 22:24:58 +0200 Subject: [PATCH 047/824] gnu: kfilemetadata: Add inputs. * gnu/packages/kde-frameworks.scm (kfilemetadata)[inputs]: Add ebook-tools, kconfig and kdegraphics-mobipocket. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 9953168802..5cdda92bc4 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages docbook) + #:use-module (gnu packages ebook) #:use-module (gnu packages flex) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) @@ -65,6 +66,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages iso-codes) #:use-module (gnu packages kerberos) + #:use-module (gnu packages kde) #:use-module (gnu packages kde-plasma) #:use-module (gnu packages libcanberra) #:use-module (gnu packages libreoffice) @@ -1735,9 +1737,11 @@ from DocBook files.") (native-inputs (list extra-cmake-modules pkg-config)) (inputs (list attr - ;; TODO: EPub http://sourceforge.net/projects/ebook-tools + ebook-tools karchive + kconfig kcoreaddons + kdegraphics-mobipocket ki18n qtmultimedia-5 qtbase-5 From 5f3c3d53eb711684ea3dad651689d506e61fb8e2 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 23:14:34 +0200 Subject: [PATCH 048/824] gnu: kio: Add more inputs. * gnu/packages/kde-frameworks.scm (kio)[inputs]: Add kded and qtdeclarative-5. [propagated-inputs]: Add libacl. [arguments]: Enable 2 passing tests. Use gexp. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 5cdda92bc4..b4760bfa30 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2641,7 +2641,8 @@ consumption.") (patches (search-patches "kio-search-smbd-on-PATH.patch")))) (build-system cmake-build-system) (propagated-inputs - (list kbookmarks + (list acl + kbookmarks kconfig kcompletion kcoreaddons @@ -2653,14 +2654,14 @@ consumption.") solid)) (native-inputs (list extra-cmake-modules dbus kdoctools qttools-5)) - (inputs (list ;; TODO: LibACL , - mit-krb5 + (inputs (list mit-krb5 karchive kauth kcodecs kconfigwidgets kcrash kdbusaddons + kded kguiaddons kiconthemes ki18n @@ -2671,14 +2672,15 @@ consumption.") libxml2 libxslt qtbase-5 + qtdeclarative-5 qtscript qtx11extras sonnet `(,util-linux "lib") ; libmount zlib)) (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-after 'unpack 'patch (lambda _ ;; Better error message (taken from NixOS) @@ -2693,10 +2695,10 @@ consumption.") (setenv "QT_QPA_PLATFORM" "offscreen") (setenv "DBUS_FATAL_WARNINGS" "0") (invoke "dbus-launch" "ctest" - "-E" ; FIXME: 19/67 tests fail. + "-E" ; FIXME: 17/69 tests fail. (string-append "(kiocore-jobtest" - "|fileitemtest" "|kiocore-kmountpointtest" + "|kiocore-kfileitemtest" "|kiocore-ktcpsockettest" "|kiocore-mimetypefinderjobtest" "|kiocore-krecentdocumenttest" @@ -2708,18 +2710,15 @@ consumption.") "|commandlauncherjob_forkingtest" "|commandlauncherjob_scopetest" "|commandlauncherjob_servicetest" - "|kiowidgets-kdirlistertest" "|kiowidgets-kdirmodeltest" "|kiowidgets-kurifiltertest-colon-separator" - "|kiowidgets-kurifiltertest-space-separator" - "|kiofilewidgets-knewfilemenutest)"))))) + "|kiowidgets-kurifiltertest-space-separator)"))))) (add-after 'install 'add-symlinks ;; Some package(s) (e.g. bluedevil) refer to these service types by ;; the wrong name. I would prefer to patch those packages, but I ;; cannot find the files! (lambda* (#:key outputs #:allow-other-keys) - (let ((kst5 (string-append (assoc-ref outputs "out") - "/share/kservicetypes5/"))) + (let ((kst5 (string-append #$output "/share/kservicetypes5/"))) (symlink (string-append kst5 "kfileitemactionplugin.desktop") (string-append kst5 "kfileitemaction-plugin.desktop")))))))) (home-page "https://community.kde.org/Frameworks") From 27eb4944bb140cf4832c44c8fd11397622b3d69e Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 23:30:05 +0200 Subject: [PATCH 049/824] gnu: ktexteditor: Add more inputs. * gnu/packages/kde-frameworks.scm (ktexteditor)[arguments]: Use gexp. Enable passing test. [inputs]: Add editorconfig-core-c and kparts Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index b4760bfa30..4d05689e82 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -84,6 +84,7 @@ #:use-module (gnu packages qt) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) + #:use-module (gnu packages text-editors) #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (gnu packages vulkan) @@ -3054,7 +3055,7 @@ types or handled by application specific code.") (native-inputs (list extra-cmake-modules pkg-config)) (inputs - (list ;; TODO: editor-config + (list editorconfig-core-c karchive kauth kbookmarks @@ -3069,6 +3070,7 @@ types or handled by application specific code.") kitemviews ki18n kjobwidgets + kparts kservice ktextwidgets kwidgetsaddons @@ -3082,23 +3084,23 @@ types or handled by application specific code.") solid sonnet)) (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-after 'unpack 'setup (lambda* (#:key inputs #:allow-other-keys) (setenv "XDG_DATA_DIRS" ; FIXME build phase doesn't find parts.desktop - (string-append (assoc-ref inputs "kparts") "/share")))) + (string-append #$(this-package-input "kparts") "/share")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? ;; Maybe locale issues with tests? (setenv "QT_QPA_PLATFORM" "offscreen") - (invoke "ctest" "-E" "(completion_test|kateview_test|movingrange_test)")))) + (invoke "ctest" "-E" "(kateview_test|movingrange_test)")))) (add-after 'install 'add-symlinks ;; Some package(s) (e.g. plasma-sdk) refer to these service types ;; by the wrong name. I would prefer to patch those packages, but ;; I cannot find the files! (lambda* (#:key outputs #:allow-other-keys) - (let ((kst5 (string-append (assoc-ref outputs "out") + (let ((kst5 (string-append #$output "/share/kservicetypes5/"))) (symlink (string-append kst5 "ktexteditorplugin.desktop") (string-append kst5 "ktexteditor-plugin.desktop")))))))) From d92e4f59bbb276e40c1dfffa35f5e6ed8dae8bab Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 08:36:22 +0200 Subject: [PATCH 050/824] gnu: kxmlgui: Enable tests. * gnu/packages/kde-frameworks.scm (kxmlgui): Use gexp. [arguments]: Enable all but 2 tests. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 4d05689e82..d1356931a1 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -3209,7 +3209,7 @@ the passwords on KDE work spaces.") (propagated-inputs (list kconfig kconfigwidgets)) (native-inputs - (list extra-cmake-modules qttools-5)) + (list extra-cmake-modules qttools-5 xorg-server-for-tests)) (inputs (list attica kauth @@ -3226,14 +3226,15 @@ the passwords on KDE work spaces.") qtbase-5 sonnet)) (arguments - `(#:tests? #f ; FIXME: 1/5 tests fail. - #:phases - (modify-phases %standard-phases - (add-before 'check 'check-setup - (lambda _ - (setenv "HOME" (getcwd)) - ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") ;; These tests fail + (invoke "ctest" "-E" + "(ktoolbar_unittest|kxmlgui_unittest)"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Framework for managing menu and toolbar actions") (description "KXMLGUI provides a framework for managing menu and toolbar From f487618b13fcc336ad25fe9a299867ee12b11a3b Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 08:40:00 +0200 Subject: [PATCH 051/824] gnu: phonon: Use gexp. * gnu/packages/kde-frameworks.scm (phonon): Use gexp. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index d1356931a1..f9e43583de 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -231,18 +231,18 @@ continuous display of high-volume data.") (inputs (list qtbase-5)) (arguments - `(#:configure-flags - '("-DCMAKE_CXX_FLAGS=-fPIC" - "-DPHONON_BUILD_PHONON4QT5=ON") - #:phases - (modify-phases %standard-phases - (add-before 'install 'patch-installdir - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((regex (string-append "(INSTALL DESTINATION \")" - (assoc-ref inputs "qtbase")))) - (substitute* "cmake_install.cmake" - ((regex all dest) - (string-append dest (assoc-ref outputs "out")))))))))) + (list #:configure-flags + #~'("-DCMAKE_CXX_FLAGS=-fPIC" + "-DPHONON_BUILD_PHONON4QT5=ON") + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'patch-installdir + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((regex (string-append "(INSTALL DESTINATION \")" + #$(this-package-input "qtbase")))) + (substitute* "cmake_install.cmake" + ((regex all dest) + (string-append dest #$output))))))))) (home-page "https://community.kde.org/Phonon") (synopsis "KDE's multimedia library") (description "KDE's multimedia library.") From d650f9c5a44cf1e6d9e368384a6d871be84050c5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 08:40:42 +0200 Subject: [PATCH 052/824] gnu: phonon-backend-gstreamer: Remove duplicate qtbase-5 in inputs. * gnu/packages/kde-frameworks.scm (phonon-backend-gstreamer)[inputs]: Remove duplicate qtbase-5. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index f9e43583de..bae5fc53ee 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -265,8 +265,7 @@ continuous display of high-volume data.") (native-inputs (list extra-cmake-modules pkg-config qttools-5)) (inputs - (list qtbase-5 - phonon + (list phonon qtbase-5 qtx11extras gstreamer From 37161b83d061fb9371cbc99bed77e29c1e697633 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 08:42:40 +0200 Subject: [PATCH 053/824] gnu: plasma-framework: Remove 'apply-fix' phase. * gnu/packages/kde-frameworks.scm (plasma-framework): Remove 'apply-fix' phase. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 5 ----- 1 file changed, 5 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index bae5fc53ee..1e3c407483 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -3340,11 +3340,6 @@ setUrl, setUserAgent and call.") (arguments `(#:phases (modify-phases %standard-phases - ;; Fix based on https://invent.kde.org/frameworks/plasma-framework/-/issues/13 - (add-after 'unpack 'apply-fix - (lambda* _ - (substitute* "src/scriptengines/qml/CMakeLists.txt" - (("KF5::ConfigQml") "")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From f841c98a4f8b7a750fc3244174d744f491448cfe Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 1 Oct 2022 19:59:09 +0200 Subject: [PATCH 054/824] gnu: knotifications: Add pkg-config to native-inputs. * gnu/packages/kde-frameworks.scm (knotifications)[native-input]: Add pkg-config. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 1e3c407483..f35b2c0471 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -1851,7 +1851,7 @@ asynchronous jobs.") "11fbqylchzvm0pfw8bvy03px5zcg4jbch39vzcvnl6si7vikm4qj")))) (build-system cmake-build-system) (native-inputs - (list extra-cmake-modules dbus qttools-5)) + (list extra-cmake-modules dbus pkg-config qttools-5)) (inputs (list kcodecs kconfig From e67c908c62384d385fae1d56023a97bf9393151e Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 11 Sep 2022 20:56:58 +0200 Subject: [PATCH 055/824] gnu: akregator: Remove kqtquickcharts form inputs. * gnu/packages/kde.scm (akregator) [inputs]: Remove kqtquickcharts. Add kquickcharts. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index f4d36c0f3a..a3d8cc3161 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -195,7 +195,7 @@ This package contains GUI widgets for baloo.") kontactinterface kpimcommon kpimtextedit - kqtquickcharts + kquickcharts ktexteditor kuserfeedback libkdepim From adee50f33f634a06ad1f870b4ab3907c511b4be4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:19:36 +0200 Subject: [PATCH 056/824] gnu: Remove kqtquickcharts. * gnu/packages/kde.scm (kqtquickcharts): Remove variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index a3d8cc3161..1ee2b936cf 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -847,30 +847,6 @@ to perform data analysis.") (license (list license:gpl2+ ;labplot license:gpl3+)))) ;liborigin -(define-public kqtquickcharts - (package - (name "kqtquickcharts") - (version "22.04.3") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://kde/stable/release-service/" - version "/src/kqtquickcharts-" version ".tar.xz")) - (sha256 - (base32 - "0bm7rdysvlfnfnvy87ii3kxl238q83vw0ia58zsnwjmkxmlgf6mp")))) - (build-system cmake-build-system) - (native-inputs - (list extra-cmake-modules)) - (inputs - (list qtbase-5 qtdeclarative-5)) - (home-page "https://phabricator.kde.org/source/kqtquickcharts/") - (synopsis "Interactive charts for Qt Quick") - (description - "Kqtquickcharts is a QtQuick plugin to render beautiful and interactive -charts.") - (license license:lgpl2.1+))) - (define-public kdf (package (name "kdf") From 2b2d28467c6575497b5cc5509987c9a1e5ba9f09 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:26:42 +0200 Subject: [PATCH 057/824] gnu: libksysguard: Update to 5.25.4. * gnu/packages/kde-plasma.scm (libksysguard): Update to 5.25.4. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 2b88ea2afe..073a6b5f4b 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -283,14 +283,14 @@ basic needs and easy to configure for those who want special setups.") (define-public libksysguard (package (name "libksysguard") - (version "5.25.3") + (version "5.25.4") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/libksysguard-" version ".tar.xz")) (sha256 - (base32 "1mrrrxjvqmrnkjwafvqrd2hlvl9gr9y4hn7dv0gf70lp5bl06i89")))) + (base32 "1kzpimhkagsmqj0cky4cfav1kbzyfjaj2l5xdapnmaygbm6r8086")))) (native-inputs (list extra-cmake-modules pkg-config qttools-5)) (inputs From 18de6150a710d9acabf8641ecce566461bad6080 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 20:11:33 +0200 Subject: [PATCH 058/824] gnu: libkscreen: Update to 5.25.4. * gnu/packages/kde-plasma.scm (libkscreen): Update to 5.24.4. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 073a6b5f4b..a4e35e36f7 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -255,14 +255,14 @@ call it if it is not associated to a terminal.") (define-public libkscreen (package (name "libkscreen") - (version "5.25.3") + (version "5.25.4") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1mxkrk04wcyw4xbfiyxbp5iwnhqr10yk39zx5bbjd9zag0vdi7z5")))) + (base32 "17ib0sgrhmmf3f8w3fni0825xz5581av5vnz8gca41vyf12css25")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules From c3c7e8fc9a22954dcf5ab8a15b4d29193dfa8d98 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 09:50:36 +0200 Subject: [PATCH 059/824] gnu: libksysguard: Enable all tests. * gnu/packages/kde-plasma.scm (libksysguard): Enable all tests. [arguments]: Substitute bash shell. [native-inputs]: Add bash-minimal. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index a4e35e36f7..967568c538 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -30,6 +30,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system qt) #:use-module (gnu packages admin) + #:use-module (gnu packages bash) #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) @@ -292,7 +293,7 @@ basic needs and easy to configure for those who want special setups.") (sha256 (base32 "1kzpimhkagsmqj0cky4cfav1kbzyfjaj2l5xdapnmaygbm6r8086")))) (native-inputs - (list extra-cmake-modules pkg-config qttools-5)) + (list bash-minimal extra-cmake-modules pkg-config qttools-5)) (inputs (list kauth kcompletion @@ -323,13 +324,12 @@ basic needs and easy to configure for those who want special setups.") zlib)) (build-system qt-build-system) (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; TODO: Fix this failing test-case - (invoke "ctest" "-E" "processtest"))))))) + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda* _ + (substitute* "autotests/processtest.cpp" + (("/bin/sh") + (which "bash")))))))) (home-page "https://userbase.kde.org/KSysGuard") (synopsis "Network enabled task and system monitoring") (description "KSysGuard can obtain information on system load and From 1e2d29ec719bae23bfd4f1d10a290f2bdad8bf2e Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 09:55:08 +0200 Subject: [PATCH 060/824] gnu: libkscreen: Add pkg-config to native-inputs. * gnu/packages/kde-plasma.scm (libkscreen)[native-inputs]: Add pkg-config. Fixes cmake warining with missing 'wayland.xml' file. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 967568c538..8d80a4686a 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -267,6 +267,7 @@ call it if it is not associated to a terminal.") (build-system qt-build-system) (native-inputs (list extra-cmake-modules + pkg-config ;; For testing. dbus)) (inputs From 2ecb9af51c601287523b11c5f3c85d23d1d8fe9a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 10:32:48 +0200 Subject: [PATCH 061/824] gnu: libkscreen: Enable all tests except for 5 failing. * gnu/packages/kde-plasma.scm (libkscreen): Enable all tests except for 5 failing. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 8d80a4686a..f7bc601ffb 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -265,6 +265,17 @@ call it if it is not associated to a terminal.") (sha256 (base32 "17ib0sgrhmmf3f8w3fni0825xz5581av5vnz8gca41vyf12css25")))) (build-system qt-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (setenv "WAYLAND_DISPLAY" "libkscreen-test-wayland-backend-0") + (invoke "ctest" "-E" + "(kscreen-testscreenconfig|kscreen-testqscreenbackend|kscreen-testkwaylandbackend|kscreen-testkwaylandconfig|kscreen-testkwaylanddpms)"))))))) (native-inputs (list extra-cmake-modules pkg-config @@ -273,8 +284,6 @@ call it if it is not associated to a terminal.") (inputs (list kwayland libxrandr plasma-wayland-protocols qtbase-5 qtwayland-5 wayland qtx11extras)) - (arguments - '(#:tests? #f)) ; FIXME: 55% tests passed, 5 tests failed out of 11 (home-page "https://community.kde.org/Solid/Projects/ScreenManagement") (synopsis "KDE's screen management software") (description "KScreen is the new screen management software for KDE Plasma From 430df96a9cb7927705d3d3d774d6fa9d3e568e55 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Thu, 22 Sep 2022 21:31:26 +0200 Subject: [PATCH 062/824] gnu: KDE Framework: Update 5.98.0. * gnu/packages/kde-frameworks.scm(extra-cmake-modules, attica, bluez-qt, breeze-icons, kapidox, karchive, kcalendarcore, kcodecs, kconfig, kcoreaddons, kdbusaddons, kdnssd, kguiaddons, kholidays, ki18n, kidletime, kirigami, kitemmodels, kitemviews, kplotting, ksyntaxhighlighting, kwayland, kwidgetsaddons, kwindowsystem, modemmanager-qt, networkmanager-qt, oxygen-icons, prison, qqc2-desktop-style, solid, sonnet, threadweaver, kactivities, kauth, kcompletion, kcontacts, kcrash, kdoctools, kfilemetadata, kimageformats, kjobwidgets, knotifications, kpackage, kpty, kunitconversion, syndication, baloo, kactivities-stats, kbookmarks, kcmutils, kconfigwidgets, kdeclarative, kded, kdesignerplugin, kdesu, kdewebkit, kemoticons, kglobalaccel, kiconthemes, kinit, kio, knewstuff, knotifyconfig, kparts, kpeople, krunner, kservice, ktexteditor, ktextwidgets,kwallet, kxmlgui, kxmlrpcclient, plasma-framework, purpose, kde-frameworkintegration, kdelibs4support, khtml, kjs, kjsembed, kmediaplayer, kross, kdav): Update to 5.96.0. (kwayland)[inputs]: Add libxkbcommon. (kcontacts)[arguments]: Enable old test, disable new failing tests. (kiconthemes)[inputs]: Add qtdeclarative-5. (kwallet)[inputs]: Add qca. [arguments]: Disable failing test. (kcontacts)[arguments]: Enable tests. [source](patches): Add patch. * gnu/packages/patches/kcontacts-incorrect-country-name.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly Signed-off-by: Marius Bakke --- gnu/local.mk | 1 + gnu/packages/kde-frameworks.scm | 342 +++++++++--------- .../kcontacts-incorrect-country-name.patch | 85 +++++ 3 files changed, 266 insertions(+), 162 deletions(-) create mode 100644 gnu/packages/patches/kcontacts-incorrect-country-name.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5fad380bbf..6bccbc2dc4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1387,6 +1387,7 @@ dist_patch_DATA = \ %D%/packages/patches/lightdm-vncserver-check.patch \ %D%/packages/patches/lightdm-vnc-color-depth.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ + %D%/packages/patches/kcontacts-incorrect-country-name.patch \ %D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ %D%/packages/patches/kiki-makefile.patch \ diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index f35b2c0471..b9610f3de1 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -90,6 +90,7 @@ #:use-module (gnu packages vulkan) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1)) @@ -290,7 +291,7 @@ Phonon-GStreamer is a backend based on the GStreamer multimedia library.") (define-public attica (package (name "attica") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -299,7 +300,7 @@ Phonon-GStreamer is a backend based on the GStreamer multimedia library.") name "-" version ".tar.xz")) (sha256 (base32 - "1xlg2sbfd45p9dw0sprpk0fancasp4idxacsf5xksf2ddn2crzp7")))) + "0w1w6w2jia1q32jnn2dhyxmkq64ha1dcbsqj233v4f224rp3aknp")))) (build-system cmake-build-system) (arguments `(#:phases @@ -330,7 +331,7 @@ http://freedesktop.org/wiki/Specifications/open-collaboration-services/") (define-public bluez-qt (package (name "bluez-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -339,7 +340,7 @@ http://freedesktop.org/wiki/Specifications/open-collaboration-services/") name "-" version ".tar.xz")) (sha256 (base32 - "0yc7mq9bnanp5dfv43vp8wpqw5l8qh4aahqpi9sid7jmd6sbywl2")))) + "0h2k2qiskn921cpni5rs7x5ahric6dlllwsrk77akpi4xcsrip2g")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules)) @@ -368,7 +369,7 @@ Bluetooth stack. It is used by the KDE Bluetooth stack, BlueDevil.") (define-public breeze-icons (package (name "breeze-icons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -377,7 +378,7 @@ Bluetooth stack. It is used by the KDE Bluetooth stack, BlueDevil.") name "-" version ".tar.xz")) (sha256 (base32 - "1ij723qy6xfkys8a9vp2ll2z2yp7667hfw559gi8cxn825hjx823")))) + "0a3zvmhcfsnxv0jpyjny3sl769p99psadl1872v0qlkax47pvsjp")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules fdupes @@ -398,7 +399,7 @@ It is the default icon theme for the KDE Plasma 5 desktop.") (define-public kapidox (package (name "kapidox") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -407,7 +408,7 @@ It is the default icon theme for the KDE Plasma 5 desktop.") name "-" version ".tar.xz")) (sha256 (base32 - "1w5h4xwscix0yjn8d0rcjd7hlmrnbmkjg20diqjabb5wcxsrjiwi")))) + "1k2qk8ibv5dqdhkn2992n8rlmslpmngz83hxb7zrh3pkphdg8v2n")))) (build-system python-build-system) (arguments `(#:tests? #f ; has no test target @@ -438,7 +439,7 @@ documentation.") (define-public karchive (package (name "karchive") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -447,7 +448,7 @@ documentation.") name "-" version ".tar.xz")) (sha256 (base32 - "1bra1q225xhh8dilwmzc0jgnj5m3dmi4nkz4y8f42si97b4xxxf5")))) + "1ipj7j1iw6g56z0qppji38h6qwbs05piiqqbsw8hdbf96l6cdiq2")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -471,7 +472,7 @@ GZip format, via a subclass of QIODevice.") (define-public kcalendarcore (package (name "kcalendarcore") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -480,7 +481,7 @@ GZip format, via a subclass of QIODevice.") name "-" version ".tar.xz")) (sha256 (base32 - "181yif830v4gg7nw9s15pvgfm98rmm6xwi2xxy3nxg7nkp14vs5k")))) + "16kclspsjzld9n07z1i8li2pc91ihpqhbk46a4s92nsihs2dkayk")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl tzdata-for-tests)) @@ -511,7 +512,7 @@ and the older vCalendar.") (define-public kcodecs (package (name "kcodecs") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -520,7 +521,7 @@ and the older vCalendar.") name "-" version ".tar.xz")) (sha256 (base32 - "05266wjxmzf3qpb2xwlm40cr9h266l5r9dqww81m8bq856pf8ivi")))) + "0n10r7s9r25xp7vlym41qi421kld00niig73yark7yghj0r41jcz")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules gperf qttools-5)) @@ -545,7 +546,7 @@ Internet).") (define-public kconfig (package (name "kconfig") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -554,7 +555,7 @@ Internet).") name "-" version ".tar.xz")) (sha256 (base32 - "1xa8xxm2x9783fqb26wyvg1mp6ybjikngznqdhsk9slhaca73yhz")))) + "15m2bggfr682q68dym7nzmvz7q7pwarzijad1wj0r5cs62l3bkjy")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules inetutils qttools-5 @@ -650,7 +651,7 @@ many more.") (define-public kdbusaddons (package (name "kdbusaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -659,7 +660,7 @@ many more.") name "-" version ".tar.xz")) (sha256 (base32 - "1y0fd0a1nwgchsk3vx8hvvkw96f0l0533g57xakq4j4xkvxd8l3y")))) + "0fwdmlnci2xn5pi1ywgia3xka3zsh6gl6xpx1gvql7lczk1y490a")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus qttools-5)) @@ -693,7 +694,7 @@ as well as an API to create KDED modules.") (define-public kdnssd (package (name "kdnssd") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -702,7 +703,7 @@ as well as an API to create KDED modules.") name "-" version ".tar.xz")) (sha256 (base32 - "1d3jq64gyj3bc3sf46gnpbmjrm809hva47z7fkwkk9i2lmnmy70w")))) + "0wcjq0g1cdjz9npy31i4rqbx85a95f15w71aamhm8x82l8nysv4g")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -748,7 +749,7 @@ replace the other outdated Graphviz tools.") (define-public kguiaddons (package (name "kguiaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -757,7 +758,7 @@ replace the other outdated Graphviz tools.") name "-" version ".tar.xz")) (sha256 (base32 - "028kn9lcvzv8f8b17a3clki7013dmhhcp1l9svvf6hydv97vkfbv")))) + "022qf858khdqklq117i223ihpw8mvdcbcfn8cwqmn2cv9qnfxnqj")))) (build-system qt-build-system) ;; TODO: Build packages for the Python bindings. Ideally this will be ;; done for all versions of python guix supports. Requires python, @@ -776,7 +777,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.") (define-public kholidays (package (name "kholidays") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -784,7 +785,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "0rcd8k2x1w6jszxj18pkzimn5q4v2k7zs9x1pfwszn7xl59b3n4k")))) + (base32 "0ysw52wiyxrkprn0gis85nphpfl1wdb4439i66dfmg7s9nyqpzp0")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -799,7 +800,7 @@ other special events for a geographical region.") (define-public ki18n (package (name "ki18n") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -808,7 +809,7 @@ other special events for a geographical region.") name "-" version ".tar.xz")) (sha256 (base32 - "1jry8bdjgxkcqln7awkj3k8996lh76vya2mf5kwpyxagk6vmr0gy")))) + "0b3r53v2ybhlyqpkjv98dv2w9q49yqqxk9qzbyc4mm7ypq4hvl47")))) (build-system cmake-build-system) (propagated-inputs (list gettext-minimal python)) @@ -840,7 +841,7 @@ translation scripting.") (define-public kidletime (package (name "kidletime") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -849,7 +850,7 @@ translation scripting.") name "-" version ".tar.xz")) (sha256 (base32 - "13piv607n9hmlbd7kkhl7b1wcxj1jq2b5386c6pxrz5caxjwgnmd")))) + "1jdbjkishqnlzz1qrzyg92xnlsl7w89dmrh0zhzaj9bnr5a3icck")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -869,7 +870,7 @@ or user activity.") ;; plasma-framework which is tier 3. (package (name "kirigami") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -878,7 +879,7 @@ or user activity.") "kirigami2-" version ".tar.xz")) (sha256 (base32 - "12ir4q9njl60b242j9raj1xsjs0cizsk7bixwb1hssfn6fzpzqkv")))) + "1l0ggwrprmg5n5y3gxv7h4593fg87d7naxkf30603kkavq0hgks6")))) (properties `((upstream-name . "kirigami2"))) (build-system cmake-build-system) (native-inputs @@ -904,7 +905,7 @@ of applications that follow the Kirigami Human Interface Guidelines.") (define-public kitemmodels (package (name "kitemmodels") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -913,7 +914,7 @@ of applications that follow the Kirigami Human Interface Guidelines.") name "-" version ".tar.xz")) (sha256 (base32 - "1j6kffvgbd07zzzv0kab8mbwa69fmw4b8jczd0wzvmp56idsfc2v")))) + "1z9swjmll833jxy2ym63zzgi9vl8ld79mgypndqszsrd4mfsbs16")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -954,7 +955,7 @@ model to observers (define-public kitemviews (package (name "kitemviews") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -963,7 +964,7 @@ model to observers name "-" version ".tar.xz")) (sha256 (base32 - "1wr62z6jwlg40m8kl9bpiyzkyjmsqx0fhgwc01192k58nl2696lb")))) + "176gqlinsvdgkbg7kr4qd97mnvcnbymrkcs9kg6hm75qzxcaj8dj")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -979,7 +980,7 @@ to flat and hierarchical lists.") (define-public kplotting (package (name "kplotting") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -988,7 +989,7 @@ to flat and hierarchical lists.") name "-" version ".tar.xz")) (sha256 (base32 - "1yqx260r3dzcinp8s685yzp5f2ihc0s1csckb9zv7z1bzljkn3h9")))) + "0hnzyl1x6acv1psdgsa9prpvnm12j71x6w6wbs1b0fl9bv5zw222")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1006,7 +1007,7 @@ pixel units.") (define-public ksyntaxhighlighting (package (name "ksyntaxhighlighting") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1015,7 +1016,7 @@ pixel units.") "syntax-highlighting-" version ".tar.xz")) (sha256 (base32 - "176prghxfrb7i68jacmq9vkl7j9arsn6gnkzyc2hlkph35js3zqs")))) + "092ilbhhs8xaqblc9w1xksapdzvqyazz8lj011wz4762p1nagiq2")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl qttools-5 @@ -1073,7 +1074,7 @@ protocols used in KDE Plasma.") (define-public kwayland (package (name "kwayland") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1083,12 +1084,17 @@ protocols used in KDE Plasma.") (patches (search-patches "kwayland-skip-flaky-test.patch")) (sha256 (base32 - "0dcnsiippwxvwvf1gvp75lx97c4nydzn3x1l8lfy86w9lfslw7zb")))) + "0c0953gm63xhrqb7aspvf28wi7x31mrgaid23dw5gqphkbgis5qw")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) (inputs - (list qtbase-5 plasma-wayland-protocols qtwayland-5 wayland wayland-protocols)) + (list libxkbcommon + plasma-wayland-protocols + qtbase-5 + qtwayland-5 + wayland + wayland-protocols)) (arguments (list ;; Tests spawn Wayland sessions that cannot run in parallel. @@ -1111,7 +1117,7 @@ represented by a QPoint or a QSize.") (define-public kwidgetsaddons (package (name "kwidgetsaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1120,7 +1126,7 @@ represented by a QPoint or a QSize.") name "-" version ".tar.xz")) (sha256 (base32 - "1igbkrn8qaalan0lyn8r2gqv5v3rwbmb3xv3w26yw77vwp0n789r")))) + "117wki4w2bs1d2pjhi5qpb2b3qhhva6fq9gikba5fb6980kmdayr")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5 xorg-server-for-tests)) @@ -1146,7 +1152,7 @@ configuration pages, message boxes, and password requests.") (define-public kwindowsystem (package (name "kwindowsystem") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1155,7 +1161,7 @@ configuration pages, message boxes, and password requests.") name "-" version ".tar.xz")) (sha256 (base32 - "1ilb3zl3mlndfrqz6gi28x6qqqs45l65d0wmy3lk07lppcw3wxzx")))) + "02l7xmxcilmrxpkkid4m9srl0d8ymqgwpw5j80w3g57p0rahwjl1")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules @@ -1202,7 +1208,7 @@ lower level classes for interaction with the X Windowing System.") (define-public modemmanager-qt (package (name "modemmanager-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1211,7 +1217,7 @@ lower level classes for interaction with the X Windowing System.") name "-" version ".tar.xz")) (sha256 (base32 - "1rbiqh1sj328cy7flz9pw6vbvgiy3vyv6xp3fk4xv91sxviz1mhd")))) + "0gk4jy3r1451a2dajhnz6lin4lfawc4qdlxp7n7m43ca4d89h13k")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus pkg-config)) @@ -1239,7 +1245,7 @@ messages.") (define-public networkmanager-qt (package (name "networkmanager-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1248,7 +1254,7 @@ messages.") name "-" version ".tar.xz")) (sha256 (base32 - "1gyvgy0wl00asg9bkhjgvqnz32xmazvazcarh3p0640jy2fjrzfz")))) + "0s1h02v9k8nyl30mw7gayzvpb8bnzzp9crcfqpry7rf02rxv9idw")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus pkg-config)) @@ -1277,7 +1283,7 @@ which are used in DBus communication.") (define-public oxygen-icons (package (name "oxygen-icons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1286,7 +1292,7 @@ which are used in DBus communication.") name "5" "-" version ".tar.xz")) (sha256 (base32 - "1f3fj6zr5iygb3s6f8vq2ayy749gxlx5j9h6v2zmkbf4m96sfmq5")))) + "03wk52hqrgj0r73nb4yiq7rnmdn4rrqzrj3cdzbg3flkw5r7wbbq")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules fdupes)) @@ -1301,7 +1307,7 @@ which are used in DBus communication.") (define-public prison (package (name "prison") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -1309,7 +1315,7 @@ which are used in DBus communication.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "1kzl8rbyj9ik83p1qb8jl32vr06vkzzvr1hpasj50sg3ajq8a9xs")))) + (base32 "1ppqm1f06q8fc1ncvzn9a133npmvlh1qxgvvbpwn6m0a8cr7ac6w")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1351,7 +1357,7 @@ libpulse.") (define-public qqc2-desktop-style (package (name "qqc2-desktop-style") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1360,7 +1366,7 @@ libpulse.") name "-" version ".tar.xz")) (sha256 (base32 - "0ff9vd34wss9na2m3gzm8wc2bwq0flda6bv6yqygv5iallw2lz88")))) + "1af7izd4k220dzngf1nwgcw0bi7vl772lpjrqd9fp9rijh74dx7d")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -1384,7 +1390,7 @@ feel.") (define-public solid (package (name "solid") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1393,7 +1399,7 @@ feel.") name "-" version ".tar.xz")) (sha256 (base32 - "0j64glc1g7mwy2ysaj09w5f7sd2992h91ncknk9gpfsrxhpm814i")))) + "14bf2k40skhyhrmgyyscg7psm1a8klf4z696pimlwjjhnawjfr06")))) (build-system cmake-build-system) (arguments `(#:phases @@ -1418,7 +1424,7 @@ system.") (define-public sonnet (package (name "sonnet") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1427,7 +1433,7 @@ system.") name "-" version ".tar.xz")) (sha256 (base32 - "0i0gksdkfyl8hfbqgrgklqanbvfm3h9gjnv42p2qq40b0zjj0sh4")))) + "0j4p91xx1scg3jmvq6km7bwfjz5ihafk76yf1byb6aqyw50h3bm3")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config qttools-5)) @@ -1446,7 +1452,7 @@ ASpell and HUNSPELL.") (define-public threadweaver (package (name "threadweaver") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1455,7 +1461,7 @@ ASpell and HUNSPELL.") name "-" version ".tar.xz")) (sha256 (base32 - "0ljjnbwmc2zz4q0q1njqny43cj6xdf976vrvijcsqdsril5wzdbq")))) + "1pwinpz5kscx64kc7dn4qf76m64kxzp92zjk8j2a2s1mx0s0vk2s")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1476,7 +1482,7 @@ uses a job-based interface to queue tasks and execute them in an efficient way." (define-public kactivities (package (name "kactivities") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1485,7 +1491,7 @@ uses a job-based interface to queue tasks and execute them in an efficient way." name "-" version ".tar.xz")) (sha256 (base32 - "0g16k3v6i20rc6h0js4pk00d6yg236bs0kxj88q21d5c934hbksk")))) + "0n7r88y1b8mph5al2xh8fbw5ckdzdmdzjipf205y20ib35bskd9i")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1521,7 +1527,7 @@ with other frameworks.") (define-public kauth (package (name "kauth") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1530,7 +1536,7 @@ with other frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "1hi36504bbr0266wl08kqiq61xysl3dw3kpgjfbgx169m0m3gmx9")))) + "0nzdvx2mibpq1cgzpll9ffjr46vch1qvriaywyqih0iybx6mx5z6")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules qttools-5)) @@ -1565,7 +1571,7 @@ utilities.") (define-public kcompletion (package (name "kcompletion") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1574,7 +1580,7 @@ utilities.") name "-" version ".tar.xz")) (sha256 (base32 - "1jmrd2mfz27qfn6dq1mk6bcqlagmifbf9vnayi1mkqa9jsj4dwdj")))) + "191vid00zskvhl6dgj6yz9iyvwdcmg35l5gq68ggjr17cj59acsf")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1590,16 +1596,18 @@ integrated it into your application's other widgets.") (define-public kcontacts (package (name "kcontacts") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/frameworks/" (version-major+minor version) "/" name "-" version ".tar.xz")) + (patches + (search-patches "kcontacts-incorrect-country-name.patch")) (sha256 (base32 - "075mw7clqf7qycngly21q3m0js3g8pcgqc2x3alp28f4zq3c8m21")))) + "0g3lg1i9rg7hjw7xjx9228sy54dy35lgwghcjds5cawszl5yi106")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules xorg-server)) ; for the tests @@ -1634,7 +1642,7 @@ localized country name to ISO 3166-1 alpha 2 code mapping and vice verca. (define-public kcrash (package (name "kcrash") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1643,7 +1651,7 @@ localized country name to ISO 3166-1 alpha 2 code mapping and vice verca. name "-" version ".tar.xz")) (sha256 (base32 - "05sw3lh4lw5jgl7gvxvpyl6nims9j4b1hjsn365fa2p48qmsx6v5")))) + "03ba3x9jgp15dxgwbjnv5s98f5di2z4ncp4hiv1qkyiibqqfx6kf")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1658,7 +1666,7 @@ application crashes.") (define-public kdoctools (package (name "kdoctools") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1667,7 +1675,7 @@ application crashes.") name "-" version ".tar.xz")) (sha256 (base32 - "04nk87dbmnf9840401s40mxlsfh9is1l1mqky9xi5mcghbp0308b")))) + "0ygpjasdynsmb3c8rdwnc5jminl5f34cmqnihsig831xsq8z6chs")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1713,7 +1721,7 @@ from DocBook files.") (define-public kfilemetadata (package (name "kfilemetadata") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1722,7 +1730,7 @@ from DocBook files.") name "-" version ".tar.xz")) (sha256 (base32 - "0sh3malq6007fp5m4hica20ha8z5abqzq5ifcmrpm8zqmm5aa2bq")))) + "1nsvslhs2kiff3r5ji8z931lh6srvjzzvwnv9cs0j74sr46c6rkn")))) (build-system cmake-build-system) (arguments `(#:phases @@ -1763,7 +1771,7 @@ by applications to write metadata.") (define-public kimageformats (package (name "kimageformats") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1772,7 +1780,7 @@ by applications to write metadata.") name "-" version ".tar.xz")) (sha256 (base32 - "0dbl2varirp5f1bd8173jlhmkc3ql16yg0d6w04nc56hy973bkm5")))) + "0v4jr1lh2qjk453q8mpz94cd98k4kmjrykn8kxrd7zvrkaa4snfy")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -1815,7 +1823,7 @@ formats.") (define-public kjobwidgets (package (name "kjobwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1824,7 +1832,7 @@ formats.") name "-" version ".tar.xz")) (sha256 (base32 - "1w1h9vnlq1j72812558cl5dlq7f80nnh5i30qmkpbvv49xhhq2dl")))) + "0f87n5d3h2f9y1z2imfd0jj9108wbcxg7dg4k1c53zar2lrfx4wc")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1839,7 +1847,7 @@ asynchronous jobs.") (define-public knotifications (package (name "knotifications") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1848,7 +1856,7 @@ asynchronous jobs.") name "-" version ".tar.xz")) (sha256 (base32 - "11fbqylchzvm0pfw8bvy03px5zcg4jbch39vzcvnl6si7vikm4qj")))) + "10whr3wjldaxdvbj6i250rqgsy2m1n606ja1yka571f1fz7laqcd")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus pkg-config qttools-5)) @@ -1882,7 +1890,7 @@ covers feedback and persistent events.") (define-public kpackage (package (name "kpackage") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1891,7 +1899,7 @@ covers feedback and persistent events.") name "-" version ".tar.xz")) (sha256 (base32 - "0gsxizpqa47apbvchga3f0w86v4jh8z1vyf0kifipz17fay4ws8d")))) + "1234jq9qqhq2z5afkkniz6w5s1ab9r4x9wamq3c9y08nzjq634py")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1938,7 +1946,7 @@ were traditional plugins.") (define-public kpty (package (name "kpty") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1947,7 +1955,7 @@ were traditional plugins.") name "-" version ".tar.xz")) (sha256 (base32 - "15swvv6qhvc654wyvxzbjbnzrd2vwn0mr4lby1x6x5f4c9br0cip")))) + "0arxbdxldwnrcg5x1vpvkwdd4hayrpqvn08jz6r7zb4s9h1582ww")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1973,7 +1981,7 @@ and communicating with them using a pty.") (define-public kunitconversion (package (name "kunitconversion") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1982,7 +1990,7 @@ and communicating with them using a pty.") name "-" version ".tar.xz")) (sha256 (base32 - "1qls3319gwn1nzaq04wrqjhbchk0s0pfx97m4za63yzvapvym73g")))) + "0lhyg1d1k25kqk94lzy8mb06p4c17limmcrzirnsnxjvhjrc6r05")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;; Requires network. (native-inputs @@ -2000,7 +2008,7 @@ gallons).") (define-public syndication (package (name "syndication") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2009,7 +2017,7 @@ gallons).") name "-" version ".tar.xz")) (sha256 (base32 - "1q60dznlkbncqqgjnp3lq3x0f6r7wvz141ajkymmxlgfq3wdpcd4")))) + "04py880hxkvidydsqcyjbkq0wv9cp42d7svkdgf74fmzfyfrmrax")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2032,7 +2040,7 @@ between feed formats.") (define-public baloo (package (name "baloo") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2041,7 +2049,7 @@ between feed formats.") name "-" version ".tar.xz")) (sha256 (base32 - "1icpxmmxhvgdr6zxpz0wybc82nyy595cmr09067i82kh7v5dj66l")))) + "0x515lnvrzlnsv5i924q17mzi88k00krj90myad17s0g7p5pi1rw")))) (build-system cmake-build-system) (propagated-inputs (list kcoreaddons kfilemetadata)) @@ -2094,7 +2102,7 @@ maintaining an index of the contents of your files.") (define-public kactivities-stats (package (name "kactivities-stats") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2103,7 +2111,7 @@ maintaining an index of the contents of your files.") name "-" version ".tar.xz")) (sha256 (base32 - "0lfanv55b7zx5s0a7gh4r41w9yb641j1zjjcvdjfrj7pdh52576s")))) + "0zvw3km1wf91wl9xbjvawjia0847kbs3js4nbf3d0z87l5h6rbx8")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2120,7 +2128,7 @@ by which applications, and what documents have been linked to which activity.") (define-public kbookmarks (package (name "kbookmarks") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2129,7 +2137,7 @@ by which applications, and what documents have been linked to which activity.") name "-" version ".tar.xz")) (sha256 (base32 - "131yng8wmxrnf3x1i6gg60q3rrya19yk4jnzi5ylafvaw7q2r8b4")))) + "1rpjqz2xnpb2wp2k3pjdclbkb0p96y48x6h8l056nr93alxyrqvi")))) (build-system cmake-build-system) (propagated-inputs (list kwidgetsaddons)) @@ -2161,7 +2169,7 @@ using the XBEL format.") (define-public kcmutils (package (name "kcmutils") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2170,7 +2178,7 @@ using the XBEL format.") name "-" version ".tar.xz")) (sha256 (base32 - "0vff93kja9dq8rf1aapxpfgjxsinm75f5nydxqcihskp8girz0c8")))) + "0jqkg4i16jnxricrhi1cbvv7gjjj7ry3z36mzh11h48ml7rl05qx")))) (build-system cmake-build-system) (propagated-inputs (list kconfigwidgets kservice)) @@ -2216,7 +2224,7 @@ KCModules can be created with the KConfigWidgets framework.") (define-public kconfigwidgets (package (name "kconfigwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2225,7 +2233,7 @@ KCModules can be created with the KConfigWidgets framework.") name "-" version ".tar.xz")) (sha256 (base32 - "045j6gkp5sf1lc12zwlkr1dz0fd89yrg5b31j4ybk3dyc8jz90hl")))) + "05bwldqc5k6dlzsxjby5565sch6i0mh7jg5cbyjz24xb1fpj0d7b")))) (build-system qt-build-system) (propagated-inputs (list kauth kcodecs kconfig kwidgetsaddons)) @@ -2248,7 +2256,7 @@ KCModules can be created with the KConfigWidgets framework.") (("^\\s*(QDirIterator it\\(.*, QDirIterator::Subdirectories)(\\);)" _ a b) (string-append a " | QDirIterator::FollowSymlinks" b))) (substitute* "CMakeLists.txt" - (("5\\.90\\.0") "5.96.0")))) + (("5\\.90\\.0") "5.98.0")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -2264,7 +2272,7 @@ their settings.") (define-public kdeclarative (package (name "kdeclarative") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2273,7 +2281,7 @@ their settings.") name "-" version ".tar.xz")) (sha256 (base32 - "1x4r231g0l5im4ala21m5fz5q6nixbx0z6lfia5zjinzlp7x5534")))) + "0y5scmcnzhwvyb7x6fdb59xgdhghw8v9i3r05gx1x7g1gfsw0wh6")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kpackage qtdeclarative-5)) @@ -2327,7 +2335,7 @@ that offer bindings to some of the Frameworks.") (define-public kded (package (name "kded") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2336,7 +2344,7 @@ that offer bindings to some of the Frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "0x40yvcx2gjb4pngyk2vfrn3z7dbyvksbj1h3ck04fyyma8z3gb3")))) + "1k8yxdnihfvvdjmw7lmd62vi5k1hpvjdcwd7njqxz6178iq7dd75")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -2359,7 +2367,7 @@ started on demand.") (define-public kdesignerplugin (package (name "kdesignerplugin") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2368,7 +2376,7 @@ started on demand.") name "-" version ".tar.xz")) (sha256 (base32 - "0cddad1rdi06l28iiwizfds78dplbvv7j40vphww0ix7cmsh3rh9")))) + "17b0javl6k5zcmx04aqzmh3qdgwvzhf62x603m4pg6xbl3zns67g")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -2388,7 +2396,7 @@ ini-style description files.") (define-public kdesu (package (name "kdesu") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2397,7 +2405,7 @@ ini-style description files.") name "-" version ".tar.xz")) (sha256 (base32 - "1wjjjwpfjr7sx10x0236zqjx3jrw6mz60724s5qg269dwfbpahvj")))) + "15fbb7zifk4lhnlwvqhs9svzb80qwms03zbrjfnsc1n1wyyfk7v2")))) (build-system cmake-build-system) (propagated-inputs (list kpty)) @@ -2415,7 +2423,7 @@ with su and ssh respectively.") (define-public kdewebkit (package (name "kdewebkit") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2424,7 +2432,7 @@ with su and ssh respectively.") name "-" version ".tar.xz")) (sha256 (base32 - "0l8nnar4s84igxih5w0fhwd9nvccp7zm53jy2gk6lfbj6gqarfbf")))) + "03bwwgzh1xfj4w7q2cvr7712yrjgf9qhqkqgzypcdb49gpvaq164")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -2447,7 +2455,7 @@ engine WebKit via QtWebKit.") (define-public kemoticons (package (name "kemoticons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2456,7 +2464,7 @@ engine WebKit via QtWebKit.") name "-" version ".tar.xz")) (sha256 (base32 - "03b5axwvd6ayw1kbl1jv6h04cihp1y1pa835gs3m1qx2ivgj7f75")))) + "0f3d0jmpnqkrjn95sbvjzda923rfdgrlxd4k58pmzd0bblxkcxh2")))) (build-system cmake-build-system) (propagated-inputs (list kservice)) @@ -2483,7 +2491,7 @@ emoticons coming from different providers.") (define-public kglobalaccel (package (name "kglobalaccel") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2492,7 +2500,7 @@ emoticons coming from different providers.") name "-" version ".tar.xz")) (sha256 (base32 - "1sx4fmy8xy22im0i3dw0xdmxrgw2jhnk2wsfy2xw74dsj3adg2iq")))) + "1vr6k7lpxsxa6in60ld2wcdqfpaan5xgbmwm3xyr584x6pv737cl")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config qttools-5)) @@ -2516,7 +2524,7 @@ window does not need focus for them to be activated.") (define-public kiconthemes (package (name "kiconthemes") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2525,7 +2533,7 @@ window does not need focus for them to be activated.") name "-" version ".tar.xz")) (sha256 (base32 - "0w9m956xfpfxp7a63a5v2y10lb9zp2gqfjyfvq3ksxfl961g4hsg")))) + "1qmld8xgabmwx2dh5395pll0a0jgirxhlbqv6aph76jg4lvynkqx")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5 shared-mime-info)) @@ -2540,6 +2548,7 @@ window does not need focus for them to be activated.") kitemviews kwidgetsaddons qtbase-5 + qtdeclarative-5 qtsvg-5)) (arguments `(#:phases @@ -2561,7 +2570,7 @@ in applications using the KDE Frameworks.") (define-public kinit (package (name "kinit") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2570,7 +2579,7 @@ in applications using the KDE Frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "1y7x80icm2jv9c8917481w1hs1vm2rvvvnc9drw4q7vrjzfx73dq")) + "04654hz3yipnlhy5gz3bkh988fcfl1lv7608k4xa5qnbsxaqh141")) ;; Use the store paths for other packages and dynamically loaded ;; libs (patches (search-patches "kinit-kdeinit-extra_libs.patch")))) @@ -2628,7 +2637,7 @@ consumption.") (define-public kio (package (name "kio") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2637,7 +2646,7 @@ consumption.") name "-" version ".tar.xz")) (sha256 (base32 - "0xmvgq7cp1kkicmngxjj4cmijaah91jmfqdzzxziphq1rl23k64m")) + "0z1ikpa3an3qmd26h2v48kxxw1jph21i12x4nawvc4x1dp4vkm1d")) (patches (search-patches "kio-search-smbd-on-PATH.patch")))) (build-system cmake-build-system) (propagated-inputs @@ -2735,7 +2744,7 @@ KIO enabled infrastructure.") (define-public knewstuff (package (name "knewstuff") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2744,7 +2753,7 @@ KIO enabled infrastructure.") name "-" version ".tar.xz")) (sha256 (base32 - "0kls40wlqkqirfjhf8kn83saxwahlh4rkm7iypqd81h93gi81fgc")))) + "09mxzpv0l1i5ml963gdnji8rskmi8b2f0hp4rn6ibkcj00z48fgy")))) (build-system cmake-build-system) (propagated-inputs (list attica kservice kxmlgui)) @@ -2789,7 +2798,7 @@ specification.") (define-public knotifyconfig (package (name "knotifyconfig") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2798,7 +2807,7 @@ specification.") name "-" version ".tar.xz")) (sha256 (base32 - "09bcw47zp6rsnk7f83gkmlpylg428a7phn7bbi9mpkdpzc6zvfd2")))) + "1qlmgr5rifygp8zk8qfjwm6k72kfyj8x6hvqwy2a59lfi3wgbm07")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2831,7 +2840,7 @@ notifications which can be embedded in your application.") (define-public kparts (package (name "kparts") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2840,7 +2849,7 @@ notifications which can be embedded in your application.") name "-" version ".tar.xz")) (sha256 (base32 - "0b68kyi7l3ndw798sll2hrzf6qq6w875n48sc11q6882xilzinh2")))) + "01gcnywbzrgwlk4cws2rr139r95r201yfal1af3jkd7g2x499vgr")))) (build-system qt-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -2881,7 +2890,7 @@ widgets with a user-interface defined in terms of actions.") (define-public kpeople (package (name "kpeople") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2890,7 +2899,7 @@ widgets with a user-interface defined in terms of actions.") name "-" version ".tar.xz")) (sha256 (base32 - "0q3c0ghxa9km5xcq6h0cwa7swfd18h491jpfafy4qgq3nwp0115b")))) + "0wxy8pxkbfqbb4i9v3q912shzck56bk6xra3blhwva82qm9rps0f")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -2917,7 +2926,7 @@ to easily extend the contacts collection.") (define-public krunner (package (name "krunner") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2926,7 +2935,7 @@ to easily extend the contacts collection.") name "-" version ".tar.xz")) (sha256 (base32 - "0wd2nmhw9mb09mm88cnkmirwgxdnvkrkyjvaiqh9k74xqsggnplk")))) + "0kch839xw09h1lddqgdcfwniq6rza5wdyyzcx99hcasn7l60nhsj")))) (build-system cmake-build-system) (propagated-inputs (list plasma-framework)) @@ -2986,7 +2995,7 @@ typed.") (define-public kservice (package (name "kservice") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2995,7 +3004,7 @@ typed.") name "-" version ".tar.xz")) (sha256 (base32 - "1zg3a35my8ba5ikmlg9s3wc9r0s5a2x0rggiiv9znhfi3snvi6gd")))) + "0lgwpcdkkbxwq84zp5aymrdwy0iacqxz5ckc89pymcm0bacyhl31")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kcoreaddons kdoctools)) @@ -3037,7 +3046,7 @@ types or handled by application specific code.") (define-public ktexteditor (package (name "ktexteditor") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3046,7 +3055,7 @@ types or handled by application specific code.") "ktexteditor-" version ".tar.xz")) (sha256 (base32 - "071jx26ycyk31bh167cq5fwx8xkr4ldjg8zlhn9dh7wa3rjpp183")))) + "1pazi9rz4v95g31s7d26yla8rcb0cgd08mlmdcasywsaxc8nn7vw")))) (build-system cmake-build-system) (propagated-inputs (list kparts @@ -3114,7 +3123,7 @@ library.") (define-public ktextwidgets (package (name "ktextwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3123,7 +3132,7 @@ library.") name "-" version ".tar.xz")) (sha256 (base32 - "1vab4qmqq9268bwzx6xia2bcz8rdmiwlgjkbkk8nci2pnmhjrzpj")))) + "14ivmpng7x9rsk3x6kyd86jabzqxgjcdrma1im44wacnvisi4llk")))) (build-system qt-build-system) (propagated-inputs (list ki18n sonnet)) @@ -3152,7 +3161,7 @@ It supports rich text as well as plain text.") (define-public kwallet (package (name "kwallet") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3161,8 +3170,16 @@ It supports rich text as well as plain text.") name "-" version ".tar.xz")) (sha256 (base32 - "0rj610c7i66fbv1x0i0sfn9mac8fkqir4vwgaq1ad5i9ca36h1jq")))) + "0kwxkxlk0xlxkjgpjpb40xfl2l9hnhpymb4lxw4zwlxjn81r6sab")))) (build-system cmake-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? ;; Seems to require network. + (invoke "ctest" "-E" + "(fdo_secrets_test)"))))))) (native-inputs (list extra-cmake-modules kdoctools)) (inputs @@ -3183,6 +3200,7 @@ It supports rich text as well as plain text.") libgcrypt phonon qgpgme + qca qtbase-5)) (home-page "https://community.kde.org/Frameworks") (synopsis "Safe desktop-wide storage for passwords") @@ -3194,7 +3212,7 @@ the passwords on KDE work spaces.") (define-public kxmlgui (package (name "kxmlgui") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3203,7 +3221,7 @@ the passwords on KDE work spaces.") name "-" version ".tar.xz")) (sha256 (base32 - "1hiz2fgwpc4mgh2zzir0qi18pjsc3052lf888rc1pgql90faxb1k")))) + "08n5l3zgkh0fxaqwrfx5mk4j5wq9ylkpxd37751qcivpag7l0x45")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kconfigwidgets)) @@ -3246,7 +3264,7 @@ descriptions for integrating actions from plugins.") (define-public kxmlrpcclient (package (name "kxmlrpcclient") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3255,7 +3273,7 @@ descriptions for integrating actions from plugins.") name "-" version ".tar.xz")) (sha256 (base32 - "1jrmrzcvnnw7q7pxgfpcz8608jmxqxf89habmgwv71b8kjz3vgaw")))) + "09apfrkgvvzv8zwxyjbi5qb145a9awirk02nx474bshgypfqslpb")))) (build-system cmake-build-system) (propagated-inputs (list kio)) @@ -3289,7 +3307,7 @@ setUrl, setUserAgent and call.") (define-public plasma-framework (package (name "plasma-framework") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3298,7 +3316,7 @@ setUrl, setUserAgent and call.") name "-" version ".tar.xz")) (sha256 (base32 - "14myvv70pixygb20c136sk7prv5f5dca53fgc74dk6c28hwyldh2")))) + "1bmwvk0pj0bnb8qhcl0bz82r63nls6h7lzzmkfkdwcwmjifmiqg4")))) (build-system cmake-build-system) (propagated-inputs (list kpackage kservice)) @@ -3359,7 +3377,7 @@ script engines.") (define-public purpose (package (name "purpose") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3368,7 +3386,7 @@ script engines.") name "-" version ".tar.xz")) (sha256 (base32 - "0gji3dsccbii1gm83dpwry02cqmjrimhj8gnkb6nzvzrnq5xfh3r")))) + "0g9ykhsn9dl3y3qp4wm3r7bkdhpl9mcbg671wa26qx3ba8a2jynr")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -3425,7 +3443,7 @@ need.") (define-public kde-frameworkintegration (package (name "kde-frameworkintegration") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3434,7 +3452,7 @@ need.") "frameworkintegration-" version ".tar.xz")) (sha256 (base32 - "19piq6h51qh64nbkqnpy6jg91vbl67vg2sh4hlwzsb2lcrmwxgk9")))) + "1mrangjj8lhm4njpkhqna2zwnidkd9crs23gj6kdlwzmiknypi6q")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -3479,7 +3497,7 @@ workspace.") (define-public kdelibs4support (package (name "kdelibs4support") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3488,7 +3506,7 @@ workspace.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "18f99g1g1z1mrkgq3l8kgxjxi60a632p0sg8d46r67b9n008w9m7")))) + (base32 "0hyyrxic1rkw2jrr92rnmbk6bqkfrcnpc917vs7xyansk9799b8f")))) (build-system cmake-build-system) (native-inputs (list dbus @@ -3595,7 +3613,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (define-public khtml (package (name "khtml") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3604,7 +3622,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0lc933z4568962xj7grzy44aj97h76s5vvv1cnj351dzwr5qahpx")))) + (base32 "0bflwrp6i2w6a3fq2m2df655495rpnsmqcm7w1f1dzfndc6yd9i5")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules perl)) @@ -3645,7 +3663,7 @@ technology and using KJS for JavaScript support.") (define-public kjs (package (name "kjs") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3654,7 +3672,7 @@ technology and using KJS for JavaScript support.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0jhfjjpv5hzbib3p30ngn6ic023fnrvnr8jrbjdzyacjywj69vvp")))) + (base32 "03is1a5b1sfh1nd011lchgir9nrywvax06ilg9y7z0vsn0ick7ik")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools perl pkg-config)) @@ -3674,7 +3692,7 @@ support.") (define-public kjsembed (package (name "kjsembed") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3683,7 +3701,7 @@ support.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "1z8h0n4v1qgs2lsxflrzhdfb91jna3y2dxal1qz7i3szjvrf63h0")))) + (base32 "0zb4vr0hp73lzc1gfnpq1grwmlpdvnp8awf3ydx4vqjh9n6jbaf2")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3698,7 +3716,7 @@ QObjects, so you can script your applications.") (define-public kmediaplayer (package (name "kmediaplayer") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3707,7 +3725,7 @@ QObjects, so you can script your applications.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0qqlah4zi0b7b6yb4009kkjqw7fkp1lgvp2mcpxs8vbbshs3376c")))) + (base32 "0wcv99xgg9pxijbjl4cmsgmpwb893ira6wd3ys5ihk2nakbvd09x")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3734,7 +3752,7 @@ KParts instead.") (define-public kross (package (name "kross") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3743,7 +3761,7 @@ KParts instead.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "03dvg2jh9587kcp2f9nir727z0qvkcywrgxfi1p1hxq1bx6y8fm2")))) + (base32 "0yjn66r44jxlrm4vz1nf8s64kcw7lmarjpqz1mcgb1n4jc28hs60")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3776,7 +3794,7 @@ offers abstract functionality to deal with scripts.") (define-public kdav (package (name "kdav") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3784,7 +3802,7 @@ offers abstract functionality to deal with scripts.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "1zqib8km4fg9aj4gmhx4hm7n7bbrz62l41qb48nz1pc3qia2x1wl")))) + (base32 "02474a3k7yqgnb1sbxbnm6l4cahn88y2631jvkq9xlmcx7xs2dzi")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) diff --git a/gnu/packages/patches/kcontacts-incorrect-country-name.patch b/gnu/packages/patches/kcontacts-incorrect-country-name.patch new file mode 100644 index 0000000000..7e15f9f5eb --- /dev/null +++ b/gnu/packages/patches/kcontacts-incorrect-country-name.patch @@ -0,0 +1,85 @@ +From 5fc2ce8b9f34ea3218a030aeede01b70bedb2546 Mon Sep 17 00:00:00 2001 +From: Petr Hodina +Date: Wed, 28 Sep 2022 20:58:43 +0200 +Subject: [PATCH] autotests: Fix incorrect name of country in comparison. + + +diff --git a/autotests/addresstest.cpp b/autotests/addresstest.cpp +index fc6a9bc7..01e474b6 100644 +--- a/autotests/addresstest.cpp ++++ b/autotests/addresstest.cpp +@@ -157,7 +157,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Jim Knopf\nLummerlandstr. 1\n" +- "12345 Lummerstadt\n\nGERMANIA")); ++ "12345 Lummerstadt\n\nGERMANY")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Jim Knopf")), result); + #if KCONTACTS_BUILD_DEPRECATED_SINCE(5, 92) +@@ -175,7 +175,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Huck Finn\n457 Foobar Ave\nNERVOUSBREAKTOWN," +- " DC 1A2B3C\n\nSTATI UNITI")); ++ " DC 1A2B3C\n\nUNITED STATES")); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Huck Finn")), result); + } + +@@ -188,7 +188,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Jim Knopf\nLummerlandstr. 1\n" +- "12345 Lummerstadt\n\nGERMANIA")); ++ "12345 Lummerstadt\n\nGERMANY")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Jim Knopf")), result); + } +@@ -214,7 +214,7 @@ void AddressTest::formatTest() + address.setCountry(QStringLiteral("Schweiz")); + + // we want the Italian variant of the Swiss format for it_CH +- const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSVIZZERA")); ++ const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSWITZERLAND")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Dr. Konqui")), result); + } +@@ -228,14 +228,14 @@ void AddressTest::formatTest() + address.setCountry(QStringLiteral("CH")); + + // we want the Italian variant of the Swiss format for it_CH +- const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSVIZZERA")); ++ const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSWITZERLAND")); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Dr. Konqui")), result); + } + + { + KContacts::Address address; + address.setCountry(QStringLiteral("CH")); +- QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QString()), QLatin1String("SVIZZERA")); ++ QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QString()), QLatin1String("SWITZERLAND")); + } + + { +@@ -257,14 +257,14 @@ void AddressTest::formatTest() + address.setLocality(QStringLiteral("Minato-ku")); + address.setPostalCode(QStringLiteral("106-0047")); + address.setStreet(QStringLiteral("4-6-28 Minami-Azabu")); +- auto result = QString::fromUtf8("4-6-28 Minami-Azabu, Minato-ku\nTOKYO 106-0047\n\nGIAPPONE"); ++ auto result = QString::fromUtf8("4-6-28 Minami-Azabu, Minato-ku\nTOKYO 106-0047\n\nJAPAN"); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal), result); + + address.setRegion(QStringLiteral("東京")); + address.setLocality(QStringLiteral("都港区")); + address.setPostalCode(QStringLiteral("106-0047")); + address.setStreet(QStringLiteral("南麻布 4-6-28")); +- result = QString::fromUtf8("〒106-0047\n東京都港区南麻布 4-6-28\n\nGIAPPONE"); ++ result = QString::fromUtf8("〒106-0047\n東京都港区南麻布 4-6-28\n\nJAPAN"); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal), result); + } + } + +base-commit: 1d757eba019718cab5d3b33a231d19daf31eb8ba +-- +2.37.2 + From 6d5d7902c21a683000ca665c416ce367bcb63a19 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 20:11:39 +0200 Subject: [PATCH 063/824] gnu: kinit: Use gexp. * gnu/packages/kde-frameworks.scm (kinit): Use gexp. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index b9610f3de1..ee4ba95263 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2585,15 +2585,17 @@ in applications using the KDE Frameworks.") (patches (search-patches "kinit-kdeinit-extra_libs.patch")))) (build-system cmake-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Set patched-in values: - (substitute* "src/kdeinit/kinit.cpp" - (("GUIX_PKGS_KF5_KIO") (assoc-ref inputs "kio")) - (("GUIX_PKGS_KF5_PARTS") (assoc-ref inputs "kparts")) - (("GUIX_PKGS_KF5_PLASMA") (assoc-ref inputs "plasma-framework")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set patched-in values: + (substitute* "src/kdeinit/kinit.cpp" + (("GUIX_PKGS_KF5_KIO") #$(this-package-input "kio")) + (("GUIX_PKGS_KF5_PARTS") #$(this-package-input "kparts")) + (("GUIX_PKGS_KF5_PLASMA") + #$(this-package-input "plasma-framework")))))))) (native-search-paths (list (search-path-specification (variable "KDEINIT5_LIBRARY_PATH") From b776efe1e4e8fdd2d08dcf83362a032f34994c72 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 17:16:44 +0200 Subject: [PATCH 064/824] gnu: grantleetheme: Update to 22.08.1. * gnu/packages/kde.scm (grantleetheme): Update to 22.08.1. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 1ee2b936cf..ff50cb6c9f 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -123,14 +123,14 @@ This package contains GUI widgets for baloo.") (define-public grantleetheme (package (name "grantleetheme") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/grantleetheme-" version ".tar.xz")) (sha256 - (base32 "50c6s1g3vp5sdhpiciz1j6rsryld7hcc6lvmxdlsvms2bbcmnj7l")))) + (base32 "01ls16x6ngi43lcwffav9qig3afakrs04v4wvyfb8lm7sd65hgf9")))) (build-system qt-build-system) (arguments `(#:tests? #f)) ; unexpected error in the test suite. (native-inputs From fd5d0309ea1ce58dc8403bcd0a41f7f0febba504 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 11:14:35 +0200 Subject: [PATCH 065/824] gnu: materialdecoration: Remove input labels. * gnu/packages/qt.scm (materialdecoration): Remove input labels. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 8cbb2c6a07..c37e718ba1 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -219,10 +219,10 @@ window managers, that don't provide Qt integration by themselves.") (native-inputs (list cmake-shared extra-cmake-modules pkg-config)) (inputs - `(("qtbase" ,qtbase-5) - ("qtwayland" ,qtwayland-5) - ("wayland" ,wayland) - ("xkbcommon" ,libxkbcommon))) + (list qtbase-5 + qtwayland-5 + wayland + libxkbcommon)) (synopsis "Material Decoration for Qt") (description "MaterialDecoration is a client-side decoration for Qt applications on Wayland.") From c48f2ea27b719471698e904cb6a3235ebb90c38d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 11:22:15 +0200 Subject: [PATCH 066/824] gnu: QT: Remove trailing booleans. * gnu/packages/qt.scm (qite, grantlee, single-application-qt5, python-pyqt, python-pyqtwebengine, python-qscintilla, python-pyqt+qscintilla, qtsolutions, qwt, python-shiboken-2, python-shiboken-6, python-pyside-2, python-pyside-6 python-pyside-2-tools, kdsoap): Remove trailing booleans. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 56 ++++++++++++++++----------------------------- 1 file changed, 20 insertions(+), 36 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index c37e718ba1..faac5e75d4 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -140,8 +140,7 @@ (modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ - (chdir "libqite") - #t))))) + (chdir "libqite")))))) (inputs (list qtbase-5 qtmultimedia-5)) (home-page "https://github.com/Ri0n/qite/") @@ -254,8 +253,7 @@ applications on Wayland.") (add-before 'check 'check-setup (lambda _ ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen") - #t))))) + (setenv "QT_QPA_PLATFORM" "offscreen")))))) (home-page "https://github.com/steveire/grantlee") (synopsis "Libraries for text templating with Qt") (description "Grantlee Templates can be used for theming and generation of @@ -2941,8 +2939,7 @@ system libraries.") (string-append source "/" file) (string-append out "/include"))) '("SingleApplication" - "singleapplication.h" "singleapplication_p.h")) - #t)))))) + "singleapplication.h" "singleapplication_p.h")))))))) (inputs (list qtbase-5)) (home-page "https://github.com/itay-grudev/SingleApplication") @@ -3088,9 +3085,7 @@ module provides support functions to the automatically generated code.") (let* ((qtbase (assoc-ref inputs "qtbase")) (qtprinter.h (string-append "\"" qtbase "/include/qt5/QtPrintSupport/qprinter.h\""))) (substitute* "sip/QtPrintSupport/qprinter.sip" - (("") - qtprinter.h)) - #t))) + (("") qtprinter.h))))) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -3215,8 +3210,7 @@ contain over 620 classes.") (lambda _ (display " from pkgutil import extend_path __path__ = extend_path(__path__, __name__) -"))) - #t)))))) +"))))))))) (home-page "https://www.riverbankcomputing.com/software/pyqtwebengine/intro") (synopsis "Python bindings for QtWebEngine") (description @@ -3376,8 +3370,7 @@ indicators, code completion and call tips.") (string-append out "/lib"))) ;; And fix the installed.txt file (substitute* "installed.txt" - (("/gnu/store/[^/]+") out))) - #t))))) + (("/gnu/store/[^/]+") out)))))))) (inputs `(("qscintilla" ,qscintilla) ("python" ,python) @@ -3405,8 +3398,7 @@ This package provides the Python bindings."))) (match %build-inputs (((names . directories) ...) (union-build (assoc-ref %outputs "out") - directories) - #t))))) + directories)))))) (inputs `(("python-pyqt" ,python-pyqt) ("python-qscintilla" ,python-qscintilla))) @@ -3484,8 +3476,7 @@ securely. It will not store any data unencrypted unless explicitly requested.") (("#include \"qtlockedfile.*\\.cpp\"") "") ;; Unwrap namespace added in the vendoring process. (("QtLP_Private::QtLockedFile") - "QtLockedFile"))) - #t)))) + "QtLockedFile"))))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; No target @@ -3509,8 +3500,7 @@ securely. It will not store any data unencrypted unless explicitly requested.") (("SUBDIRS\\+=examples") "")) ;; Fix deprecated functions. (substitute* "qtsoap/src/qtsoap.cpp" - (("toAscii") "toUtf8")) - #t)) + (("toAscii") "toUtf8")))) (replace 'configure (lambda _ (for-each (lambda (solution) @@ -3518,16 +3508,14 @@ securely. It will not store any data unencrypted unless explicitly requested.") (invoke "./configure" "-library") (invoke "qmake"))) '("qtlockedfile" "qtpropertybrowser" "qtservice" - "qtsingleapplication" "qtsoap")) - #t)) + "qtsingleapplication" "qtsoap")))) (replace 'build (lambda _ (for-each (lambda (solution) (with-directory-excursion solution (invoke "make"))) '("qtlockedfile" "qtpropertybrowser" "qtservice" - "qtsingleapplication" "qtsoap")) - #t)) + "qtsingleapplication" "qtsoap")))) (replace 'install (lambda args (for-each (lambda (solution) @@ -3607,8 +3595,7 @@ that can be only started once per user. ;; Remove some incomplete manual pages. (for-each delete-file (find-files "doc/man/man3" "^_tmp.*")) (mkdir-p man) - (copy-recursively "doc/man" man) - #t)))))) + (copy-recursively "doc/man" man))))))) (home-page "http://qwt.sourceforge.net") (synopsis "Qt widgets for plots, scales, dials and other technical software GUI components") @@ -3850,7 +3837,7 @@ color-related widgets.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'use-shiboken-dir-only - (lambda _ (chdir "sources/shiboken2") #t)) + (lambda _ (chdir "sources/shiboken2"))) (add-before 'configure 'make-files-writable-and-update-timestamps (lambda _ ;; The build scripts need to modify some files in @@ -3861,13 +3848,11 @@ color-related widgets.") (for-each (lambda (file) (make-file-writable file) (utime file circa-1980 circa-1980)) - (find-files "."))) - #t)) + (find-files "."))))) (add-before 'configure 'set-build-env (lambda _ (let ((llvm #$(this-package-input "clang-toolchain"))) - (setenv "CLANG_INSTALL_DIR" llvm) - #t)))))) + (setenv "CLANG_INSTALL_DIR" llvm))))))) (home-page "https://wiki.qt.io/Qt_for_Python") (synopsis "Shiboken generates bindings for C++ libraries using CPython source code") @@ -3905,7 +3890,7 @@ color-related widgets.") ((#:phases p) #~(modify-phases #$p (replace 'use-shiboken-dir-only - (lambda _ (chdir "sources/shiboken6") #t)))) + (lambda _ (chdir "sources/shiboken6"))))) ((#:configure-flags flags) #~(cons* ;; The RUNPATH of shibokenmodule contains the entry in build @@ -3959,7 +3944,7 @@ color-related widgets.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside2") #t)) + (lambda _ (chdir "sources/pyside2"))) (add-after 'go-to-source-dir 'fix-qt-module-detection (lambda _ ;; Activate qt module support even if it not in the same @@ -4054,7 +4039,7 @@ generate Python bindings for your C or C++ code.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside6") #t)) + (lambda _ (chdir "sources/pyside6"))) (add-after 'go-to-source-dir 'fix-qt-module-detection (lambda _ (substitute* "cmake/PySideHelpers.cmake" @@ -4114,7 +4099,7 @@ generate Python bindings for your C or C++ code."))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside2-tools") #t))))) + (lambda _ (chdir "sources/pyside2-tools")))))) (home-page "https://wiki.qt.io/Qt_for_Python") (synopsis "Command line tools for PySide2") @@ -4291,8 +4276,7 @@ and import their menus over DBus.") (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "ctest" "-E" ;; These tests try connect to the internet. - "(kdsoap-webcalls|kdsoap-webcalls_wsdl|kdsoap-test_calc)")) - #t))))) + "(kdsoap-webcalls|kdsoap-webcalls_wsdl|kdsoap-test_calc)"))))))) (home-page "https://www.kdab.com/development-resources/qt-tools/kd-soap/") (synopsis "Qt SOAP component") (description "KD SOAP is a tool for creating client applications for web From 75236e98a3e9178951ffda4509b99197417c0272 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 13:30:00 +0200 Subject: [PATCH 067/824] gnu: qtgamepad: Remove input labels. * gnu/packages/qt.scm (qtgamepad): Remove input labels. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index faac5e75d4..9d1c0f6b5f 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1915,12 +1915,12 @@ coloring, and many more."))) (native-inputs (list perl pkg-config)) (inputs - `(("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("libxrender" ,libxrender) - ("sdl2" ,sdl2) - ("qtbase" ,qtbase-5) - ("qtdeclarative-5" ,qtdeclarative-5))) + (list fontconfig + freetype + libxrender + sdl2 + qtbase-5 + qtdeclarative-5)) (synopsis "Qt Gamepad module") (description "The Qt Gamepad module is an add-on library that enables Qt applications to support the use of gamepad hardware and in some cases remote From 060251a00e5a20a025a1dfdb6fb93d105a1ae009 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 28 Sep 2022 21:25:19 +0200 Subject: [PATCH 068/824] gnu: KDE PIM: Update to 22.08.1. * gnu/packages/kde-pim.scm (akonadi, akonadi-calendar, akonadi-contacts, akonadi-mime, akonadi-notes, akonadi-search, kincidenceeditor, kaddressbook, kcalendarsupport, kcalutils, kdepim-runtime, keventviews, kgpg, kidentitymanagement, kimap, kldap, kleopatra, kmail, kmailcommon, kmailimporter, kmailtransport, kmbox, kmessagelib, kmime, knotes, kontactinterface, korganizer, kpimcommon, libgravatar, kpimtextedit, ksmtp, ktnef, libkdepim, libkgapi, libkleo, libksieve): Update to 22.08.1. (kmailcommon)[inputs]: Add qtwebchannel-5 and qtwebengine-5. (libkleo)[inputs]: Add kconfigwidgets. (libksieve)[arguments]: Fix disabling of test. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 149 ++++++++++++++++++++------------------- 1 file changed, 76 insertions(+), 73 deletions(-) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 73edce6c33..881385e279 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -45,14 +45,14 @@ (define-public akonadi (package (name "akonadi") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-" version ".tar.xz")) (sha256 - (base32 "0g277jl2ay00p4yhkadvzjn1k2rkriz90ql2qcp5d4fjgs0220ky")) + (base32 "1yfy0b6kyiq82zkfkx9ldgjlbwg3lgg4di53fqjllmqhzaj1xy91")) (patches (search-patches "akonadi-paths.patch" "akonadi-timestamps.patch" @@ -117,14 +117,14 @@ programs.") (define-public akonadi-calendar (package (name "akonadi-calendar") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-calendar-" version ".tar.xz")) (sha256 - (base32 "0hcc2hpyhpd7219my7hpjcl24gsr9g8d2bwhlc66da96ray0pzg4")))) + (base32 "1xcnlkipy2rq0bsm811y9khw7dmsgkqxgw18b3lmy29xs7wcsiv5")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -164,14 +164,14 @@ collection and item views.") (define-public akonadi-contacts (package (name "akonadi-contacts") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-contacts-" version ".tar.xz")) (sha256 - (base32 "080ba08sxb79il7na97m56k3gpwc8pj4bljca3qgw5kwhswj6gnx")))) + (base32 "1mzlv124wa135xfbxl2ghl4n8pi1a6zd64195px1v90qnhjljw28")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -219,14 +219,14 @@ to list and filter contacts.") (define-public akonadi-mime (package (name "akonadi-mime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-mime-" version ".tar.xz")) (sha256 - (base32 "1qggacdhj5b5vrhwp1srlrhapl13hcc5d1ff5wlsdip87in4jad1")))) + (base32 "19wbfkvhkyzlz5r49y7rzbn4ay7rm8zyj7d4j3x9j79nprjr4zw0")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules libxslt ;; xslt for generating interface descriptions @@ -269,14 +269,14 @@ with emails through Akonadi easier.") (define-public akonadi-notes (package (name "akonadi-notes") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-notes-" version ".tar.xz")) (sha256 - (base32 "0ps99717hvsq62fh3zagn5xgw5sc99naiiay5ym9wmfjvhr5slml")))) + (base32 "05sx7h1aw4mx93l4krv4574zpjf63vdrhaiwayqz11wrdpvdq7ww")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -294,14 +294,14 @@ wrapping notes into KMime::Message objects.") (define-public akonadi-search (package (name "akonadi-search") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-search-" version ".tar.xz")) (sha256 - (base32 "0jpirnnpab6ki2gf5vlzklp04rwm05l8phlzajp2apcddb84lqvm")))) + (base32 "06apb5lx7bs0lfvsnbf8kyxk7yyjrzb1f1wfckfsjaysf0xmdvfg")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules @@ -349,14 +349,14 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (define-public kincidenceeditor (package (name "kincidenceeditor") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/incidenceeditor-" version ".tar.xz")) (sha256 - (base32 "0bm25r3l9d1qhlkxz7pd5hmg6xd0y651q8any4q71bd6a023ps0b")))) + (base32 "1znbpqpxkbn79pzhcg5v77bqr345lcmy2h0a6d90rzdmnlh303ln")))) (properties `((upstream-name . "incidenceeditor"))) (build-system qt-build-system) (native-inputs @@ -410,14 +410,14 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (define-public kaddressbook (package (name "kaddressbook") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kaddressbook-" version ".tar.xz")) (sha256 - (base32 "18f6xjcmqgslrw12dik9immw3mw0krvzi6y6f0ryr2ry1shqvivb")))) + (base32 "177zgbpgignvglpvbis1q9d36pi1dvyckv3q2gcgd9425gpm0vmb")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -499,14 +499,14 @@ one of the APIs mentioned above.") (define-public kcalendarsupport (package (name "kcalendarsupport") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/calendarsupport-" version ".tar.xz")) (sha256 - (base32 "05x5ps15hkbv0cm4am859wzf6r5yiyaadidw3617qcim4sh5smqd")))) + (base32 "09fs15qckydmbs6idl5k1b6gyhjkygsa1r8frlysn1ahhfmxr33p")))) (properties `((upstream-name . "calendarsupport"))) (build-system qt-build-system) (native-inputs @@ -544,14 +544,14 @@ calendaring applications.") (define-public kcalutils (package (name "kcalutils") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kcalutils-" version ".tar.xz")) (sha256 - (base32 "1vv2nv4yc2hwi31b9k0jcxmxgbpaalmdc06jhbcq8qbi20pj70kh")))) + (base32 "1y25csn37lp14ba18gqmw9ssimy4dqi55irx8c89p4p1lypjwfzq")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules libxml2)) ;; xmllint required for tests @@ -582,14 +582,14 @@ functions for accessing calendar data using the kcalcore API.") (define-public kdepim-runtime (package (name "kdepim-runtime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdepim-runtime-" version ".tar.xz")) (sha256 - (base32 "1lhkcfdjnxlm8amfczw4pi41grlq951pd67cj1z51whs6b84an27")))) + (base32 "1g6bq27s7nf9rmrbl5kwycl4lzjpp3m088mji3p7qrrv01ywp4mn")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus kdoctools libxslt shared-mime-info)) @@ -677,14 +677,14 @@ package.") (define-public keventviews (package (name "keventviews") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/eventviews-" version ".tar.xz")) (sha256 - (base32 "1346k5fvjdgxhfjhf0mbc7s559ampxc2vfg0i4wk1a6n6d4jpmcr")))) + (base32 "0bkidva045q85z4ymhj4m9ayfbsckjl4cl7nncl48yk2dmanfg51")))) (properties `((upstream-name . "eventviews"))) (build-system qt-build-system) (native-inputs @@ -726,14 +726,14 @@ package.") (define-public kgpg (package (name "kgpg") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kgpg-" version ".tar.xz")) (sha256 - (base32 "196xgbvc68jzacal4wwxgdrwxyiyr49hq0h2dwpzq5yhpfh3fcrw")))) + (base32 "1xs0w6lxwq3hzs8r1cwmygcjilbgwa8zpjxwj6zz1wmbg04gqk36")))) (build-system qt-build-system) (arguments `(#:phases @@ -784,14 +784,14 @@ cryptography to the contents of the clipboard.") (define-public kidentitymanagement (package (name "kidentitymanagement") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kidentitymanagement-" version ".tar.xz")) (sha256 - (base32 "0z1ixwlrdm7dzfxszphf2wma0gjprr0143c46li79g5gzvcrid8w")))) + (base32 "1h76c8k6lvf4dlh9awd4z71hkikm7x71760gljybd6fkygxpm992")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -822,14 +822,14 @@ cryptography to the contents of the clipboard.") (define-public kimap (package (name "kimap") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kimap-" version ".tar.xz")) (sha256 - (base32 "1k5h7jmzxg8wq58iqk0f1gx5r45pr2895vl7y5ihyav9w0qfqcn0")))) + (base32 "1a3wwzwlp0zsj4brhs22sygfxh65slikapa4iipxjw78mkwhiq8h")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -853,14 +853,14 @@ easier to do so.") (define-public kldap (package (name "kldap") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kldap-" version ".tar.xz")) (sha256 - (base32 "024xgjffz5n8zz6js06i78pf8s3nd5sbmvhzz7bm3qc05xqxyp75")))) + (base32 "0hqvf939d2sqb2frizw9pnhgpc8vi627882d30ssymw5p5nm58il")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -878,14 +878,14 @@ protocol for querying and modifying directory services running over TCP/IP.") (define-public kleopatra (package (name "kleopatra") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kleopatra-" version ".tar.xz")) (sha256 - (base32 "1dp421hniyknggirpqqdb7pmsrbidz9qshmd3qnsqvcr9pz301d5")))) + (base32 "1vay6cdrx1l7qyg0rrc7z7rwv1jjpwksqzadka7rpshfqhf3r9y8")))) (build-system qt-build-system) (native-inputs (list dbus extra-cmake-modules gnupg ;; TODO: Remove after gpgme uses fixed path @@ -932,14 +932,14 @@ and retrieving certificates from LDAP servers.") (define-public kmail (package (name "kmail") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmail-" version ".tar.xz")) (sha256 - (base32 "0x2d8w8hlb62h9q9qkh3cwyg7pwwl7px1rf89vyfp9arfbs030dq")))) + (base32 "1q7d2jazc6792dhwxb2zx66bghdnn43sw6lvdg44a7d9zgik1qzb")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus kdoctools)) @@ -1032,14 +1032,14 @@ manager from KDE.") (define-public kmailcommon (package (name "kmailcommon") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/mailcommon-" version ".tar.xz")) (sha256 - (base32 "0vir2p7akihfzb86iwspz3k6j3psc6xxyak4x738dw3lhn22nfzb")))) + (base32 "1lpnfcj2p58lhgcjg6ray5b9ygz7gpb8xh8qkakn4m7cpjhgcj5j")))) (properties `((upstream-name . "mailcommon"))) (build-system qt-build-system) (native-inputs @@ -1086,6 +1086,8 @@ manager from KDE.") libxslt phonon qgpgme + qtwebchannel-5 + qtwebengine-5 qtbase-5)) (arguments `(#:tests? #f)) ;; TODO: 12/62 tests fail @@ -1099,14 +1101,14 @@ dealing with email.") (define-public kmailimporter (package (name "kmailimporter") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/mailimporter-" version ".tar.xz")) (sha256 - (base32 "0hb4ba8vr7wrw8mcrc7hicl8f9r6ihsbwkxxr1qkzk0310yjmcbf")))) + (base32 "1k7gwagcvhj733c48ayxwi1gf37y6w5g6n2b9fknhfs40kqpdri9")))) (properties `((upstream-name . "mailimporter"))) (build-system qt-build-system) (native-inputs @@ -1146,14 +1148,14 @@ e-mail client programs into KMail and KDE PIM.") (define-public kmailtransport (package (name "kmailtransport") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmailtransport-" version ".tar.xz")) (sha256 - (base32 "0fcgwln40d9h3r4m58mp4m79k425hianjz0ambqckdzp0aspkhzp")))) + (base32 "0hhd1m1kfagyiwwfmsxhpin5c25dsiwbzg188khppn6fp2dh79dg")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1188,14 +1190,14 @@ mail transport.") (define-public kmbox (package (name "kmbox") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmbox-" version ".tar.xz")) (sha256 - (base32 "0d3i36zkn3apcjqkbsq633mgrk382xgx8knfg6fkyyc8i55p3dig")))) + (base32 "0n49xqgyx40hml9554zvnycff26qki9fdy32awx9v9l8jbnrmm6p")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1210,14 +1212,14 @@ using a Qt/KMime C++ API.") (define-public kmessagelib (package (name "kmessagelib") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/messagelib-" version ".tar.xz")) (sha256 - (base32 "06vsba8r9sh94y59hmkh8nbg8xhib83sv80qnfw4g9fv5gfjppjh")))) + (base32 "0xq1a064g3h3igrqanfald9n21nnrsg16a4kmn9vn1k03qv1vlp2")))) (properties `((upstream-name . "messagelib"))) (build-system qt-build-system) (native-inputs @@ -1296,14 +1298,14 @@ kwebengineviewer.") (define-public kmime (package (name "kmime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmime-" version ".tar.xz")) (sha256 - (base32 "1k9lvq3a728015laj7rklg136hgg256l4snarnc5cw97ijqdm5ng")))) + (base32 "1vz5gw33ncc5lx8fx2nnp8ayxpdhfjwwx226gwa94vhxxkfcnmh4")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1331,14 +1333,14 @@ information in non-ASCII character sets.") (define-public knotes (package (name "knotes") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/knotes-" version ".tar.xz")) (sha256 - (base32 "1bbrcr2s5am7gq3im5s9kk63nrsgz0kfkm3qzhasafnz06zhf1vf")))) + (base32 "076rwgkwx67rn6z0mj0sj77h1jngcpbvrwka3ijg2309r9f2wg8h")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools libxslt)) @@ -1401,14 +1403,14 @@ Features: (define-public kontactinterface (package (name "kontactinterface") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kontactinterface-" version ".tar.xz")) (sha256 - (base32 "0npaxlrvgpg2p8wdaqs03k2gyppbid81k64q6cawin6wrn6zzc9m")))) + (base32 "0j7cck262j8z7m7fm55qa5i936x81ljn3cijrk5c5h881152h4fs")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1429,14 +1431,14 @@ application \"Parts\" to be embedded as a Kontact component (or plugin).") (define-public korganizer (package (name "korganizer") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/korganizer-" version ".tar.xz")) (sha256 - (base32 "0ypscdr0la4pdxz491mryjmg535d0g7c4r62y0l7an5g1ribrjq9")))) + (base32 "0pcyij50k96mrm9vkq0pzr7n0nrgy1d51zrcb3hly7fpl4gvkx4x")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus qttools-5 kdoctools)) @@ -1550,14 +1552,14 @@ Virtual Contact File}) files to the KPeople contact management library.") (define-public kpimcommon (package (name "kpimcommon") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/pimcommon-" version ".tar.xz")) (sha256 - (base32 "1xns3qc5n5fig898bsj3kzda6484n0r406km43gicnly1m7jpar9")))) + (base32 "00gxv1028xdp7ag44z9h6cpmlw55f3rk7i6msymga3pdq639c19y")))) (properties `((upstream-name . "pimcommon"))) (build-system qt-build-system) (native-inputs @@ -1613,14 +1615,14 @@ Virtual Contact File}) files to the KPeople contact management library.") (define-public libgravatar (package (name "libgravatar") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libgravatar-" version ".tar.xz")) (sha256 - (base32 "1zik4y1micgqyz2y6cj5w5sjccm69d49svl72bdjcj5n3r6xl9iq")))) + (base32 "1yhmxl2gqwrn5flr5qm56aqg6rgmqbgcr3pyb4d0vshdfksjr4rc")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) (inputs (list kconfig @@ -1644,14 +1646,14 @@ unnecessary network operations.") (define-public kpimtextedit (package (name "kpimtextedit") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kpimtextedit-" version ".tar.xz")) (sha256 - (base32 "1gb0n8nrx673ya3mgkjs6khjlz7472a932lgpy5pwir48mc57g1d")))) + (base32 "1dxdlspqssxnvha202bgh9yaszs77cph5qd9wcbd45xj07dqgbw1")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1685,14 +1687,14 @@ text in the text edit to all kinds of markup, like HTML or BBCODE.") (define-public ksmtp (package (name "ksmtp") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksmtp-" version ".tar.xz")) (sha256 - (base32 "1l0w7yxmmvkj2wbv49yf73b2ca7k0yxrishkdqgm3q5crahg8l4z")))) + (base32 "13ybnr39pim3r83p56wj98fwj0yk1rspd9g24a8d0qykmnbx57l3")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1724,14 +1726,14 @@ standard protocols for e-mail transmission.") (define-public ktnef (package (name "ktnef") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/ktnef-" version ".tar.xz")) (sha256 - (base32 "0nvvaakjhciqdn0v1697d559p0py5v41iyd0ix2z8sqgw7lb7nkh")))) + (base32 "05rcs0m4dr4p4wxigcnhjmmp15nlf36ka85v8b8gd8630v61w6y6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1756,14 +1758,14 @@ and allows one to view/extract message formatted text in Rich Text Format.") (define-public libkdepim (package (name "libkdepim") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkdepim-" version ".tar.xz")) (sha256 - (base32 "1r6hbj3rgma1q1fxmi982widvnq1dajslhwmd21aknnnryspfx7s")))) + (base32 "07ihnps983x3sp74yq5glsq3h3jw4k80mnc4xxzm6ps2vgswah12")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1803,14 +1805,14 @@ and allows one to view/extract message formatted text in Rich Text Format.") (define-public libkgapi (package (name "libkgapi") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkgapi-" version ".tar.xz")) (sha256 - (base32 "0m47wqr2m147csypzm38i29msm1mcnn6mx3l0nwfhwsmycf6lsr7")))) + (base32 "065441mbl67wyp4nz03jdygkn5wmnmkj4fiql4mnq99k2v80y0ka")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1838,14 +1840,14 @@ various Google services.") (define-public libkleo (package (name "libkleo") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkleo-" version ".tar.xz")) (sha256 - (base32 "0nk6bi2z4s0rf0qim00xcmvxyzwax4bjn1f4f6iyw5qdfkc6yvnp")))) + (base32 "05ypgrwynm1hr32hj35faj3sxabi46x8slnbs3pxwz2f2z2ry58a")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -1855,6 +1857,7 @@ various Google services.") kcodecs kcompletion kconfig + kconfigwidgets kcoreaddons kcrash ki18n @@ -1885,7 +1888,7 @@ KDE using certificate-based crypto.") (define-public libksieve (package (name "libksieve") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) @@ -1893,7 +1896,7 @@ KDE using certificate-based crypto.") "/src/libksieve-" version ".tar.xz")) (sha256 (base32 - "0s5c49vgsqmbpyk1bhwjb04v6v6vb9xlcms8dvc6f3gyjdchk5lc")))) + "1ia1gjx8x9ym3dml3y403kif50jhcsrqmhivn3j5yxf8abc3rnk6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1930,7 +1933,7 @@ KDE using certificate-based crypto.") ;; sieveeditorhelphtmlwidgettest fails with `sigtrap` (substitute* "src/ksieveui/editor/webengine/autotests/CMakeLists.txt" - (("^\\s*(add_test|ecm_mark_as_test)\\W" line) + (("^\\s*(add_test|ecm_mark_as_test|set_tests_properties)\\W" line) (string-append "# " line)))))))) (home-page "https://invent.kde.org/pim/libksieve") (synopsis "KDE Sieve library") From e8ddc727d89177fae4d5a9eb40395853ecce53b3 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 21:13:13 +0200 Subject: [PATCH 069/824] gnu: KDE: Update to 22.08.1. * gnu/packages/kde.scm (baloo-widgets, grantleetheme, akregator, kdenlive, kdevelop, libkomparediff2, kpmcore, kdeconnect, labplot, kdf, kcachegrind, libkdegames, marble-qt, okular, poxml, kdegraphics-mobipocket, libkexiv2): Update to 22.08.1. (kdeconnect)[inputs]: Add plasma-wayland-protocols. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 61 ++++++++++++++++++++++---------------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index ff50cb6c9f..61ffd1830b 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -99,14 +99,14 @@ (define-public baloo-widgets (package (name "baloo-widgets") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/baloo-widgets-" version ".tar.xz")) (sha256 - (base32 "0084bnrlbdypdwzxi9gfxcywhyjd1z2cmh7p6gv0zhc9f7h6ffnp")))) + (base32 "02p4v8g4syk908mg7f0l5fpqn7ddsxqji1n8jqghsdkkdsvry7mn")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -151,14 +151,14 @@ This package contains GUI widgets for baloo.") (define-public akregator (package (name "akregator") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akregator-" version ".tar.xz")) (sha256 - (base32 "08n713271i7ifnbrgwrqmxvcpvj45wfqjiidw8zf9rpwxg2m2m9g")))) + (base32 "01rgyl2hwjprq4z5yjc99j6jk9vrhjy608ha72j470pw6g47ac5s")))) (build-system qt-build-system) (arguments `(#:phases @@ -220,7 +220,7 @@ browser for easy news reading.") (define-public kdenlive (package (name "kdenlive") - (version "22.04.3") + (version "22.08.1") (source (origin (method git-fetch) @@ -229,7 +229,7 @@ browser for easy news reading.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0v545kd5rm5isy4cx21fp3pi49mvsv1r1ahp0jhim8s6b7ghrh64")))) + (base32 "0xnasi8s8zxh2s4vnn51pc8ni58q8pk70bwh9dfxp1wdmpv3zsrx")))) (build-system qt-build-system) (arguments ;; XXX: there is a single test that spawns other tests and @@ -304,14 +304,14 @@ projects.") (define-public kdevelop (package (name "kdevelop") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdevelop-" version ".tar.xz")) (sha256 - (base32 "03dwllxy96sy20kdsc3sll0n6bhh6gdmpjl821flsxv0jb5naplv")))) + (base32 "14a80z4sahxyzssrz605zp7ah5xdjbc22ccv0vwcnhr5lzr76v31")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config shared-mime-info qttools-5)) @@ -584,14 +584,14 @@ compressed massif files can also be opened transparently.") (define-public libkomparediff2 (package (name "libkomparediff2") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkomparediff2-" version ".tar.xz")) (sha256 - (base32 "1vaxbx7c6r7skh3452blxyrngfcsdyjmmvcg6j2wcsn04m01mw8k")))) + (base32 "0hjxxhfv0ds05l821avq787sfdy0afr595xx266c20x8fxgm6kv9")))) (native-inputs (list extra-cmake-modules pkg-config)) (inputs @@ -639,7 +639,7 @@ cards.") (define-public kpmcore (package (name "kpmcore") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append @@ -647,7 +647,7 @@ cards.") "/src/" name "-" version ".tar.xz")) (sha256 (base32 - "04qslli4vnbnl329zynbinlwaigxr9xpswra5n0v710p92as0qif")))) + "1y28dnmbnkkjar4kl033fkmcnazgczc3pgdac2q1ry2hjzkcbnpa")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -703,7 +703,7 @@ different notification systems.") (define-public kdeconnect (package (name "kdeconnect") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) @@ -712,7 +712,7 @@ different notification systems.") version ".tar.xz")) (sha256 (base32 - "015gxglclds2vmjr4bv51yfv840bafzgrl71cnwgnwwy8rrh9x4x")))) + "1yzx49gcm7x2wdk53iznyjz09y2a6mrrhh68xilbcsafyiw3l3zr")))) (build-system qt-build-system) (arguments `(#:configure-flags '("-DBUILD_TESTING=ON" @@ -741,6 +741,7 @@ different notification systems.") kpeoplevcard kwayland libfakekey + plasma-wayland-protocols pulseaudio-qt qca qqc2-desktop-style @@ -850,14 +851,14 @@ to perform data analysis.") (define-public kdf (package (name "kdf") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdf-" version ".tar.xz")) (sha256 (base32 - "1m0dwk3inqzk9kjjzgsaam15lnpbhzjfmwrzv8sazfk44scnr2v1")))) + "0p7iqld2phc74pmhyb8bqqg9clnc7l2rh6hd0i6jcsp266cgg205")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -910,14 +911,14 @@ timers for each task can be started, stopped, changed, or looped.") (define-public kcachegrind (package (name "kcachegrind") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kcachegrind-" version ".tar.xz")) (sha256 (base32 - "12ckn90hqm2c5c58xqkzgcih64jk4kwkgz4q0f5ns1rxv3pidz5n")))) + "05wcnfqs0fdfhfpagn0pqky0l7014nblv8r9fv1khy4g5mdlm4hs")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl python qttools-5 kdoctools)) @@ -944,14 +945,14 @@ Python, PHP, and Perl.") (define-public libkdegames (package (name "libkdegames") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkdegames-" version ".tar.xz")) (sha256 - (base32 "0igq87anam9x2mclb0lkvwhrxk62y1f4xl14a4dhd97mqsc5pbzn")))) + (base32 "1aihbha073fw2bxmdk4l768716kvrlyjd72x2nfx0vvr0ngc5wx9")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -990,7 +991,7 @@ Python, PHP, and Perl.") (define-public marble-qt (package (name "marble-qt") - (version "22.04.3") + (version "22.08.1") (source (origin (method git-fetch) @@ -1000,7 +1001,7 @@ Python, PHP, and Perl.") (file-name (git-file-name name version)) (sha256 (base32 - "1saacnrl0hkl32nq96l1bgn9yrsz455q96jdxzp7ax8iaa5nmdiz")))) + "0pn0mjh5cg7mgjj82bsj8zikzdyq2fmzckdcav2y0msxwi859crl")))) (build-system qt-build-system) (arguments ;; FIXME: libmarblewidget-qt5.so.28 not found. Also enable the @@ -1047,14 +1048,14 @@ creating routes by drag and drop and more.") (define-public okular (package (name "okular") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "03jpwgrhjgyx14g1h3lxhnyib88ck0qkqcxh4fpc398xwdr3amkw")))) + (base32 "0f98kfsb6sirpym27j2wwz4qr4p5vl4pbnckxd3gmgyfpz8mszln")))) (build-system qt-build-system) ;; The tests fail because they can't find the proper mimetype plugins: ;; "org.kde.okular.core: No plugin for mimetype '"image/jpeg"'." @@ -1112,7 +1113,7 @@ a variety of formats, including PDF, PostScript, DejaVu, and EPub.") (define-public poxml (package (name "poxml") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri @@ -1120,7 +1121,7 @@ a variety of formats, including PDF, PostScript, DejaVu, and EPub.") "/src/poxml-" version ".tar.xz")) (sha256 (base32 - "1nrp0i3a39pw4pzcanpmjyks3pl1lyfj3zq61ii8xx402xw1ip2w")))) + "13jp5g5la3kq9i3qybdvwfl4vgqz3hxf64qzmh7kl71ykas7s5vi")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1137,14 +1138,14 @@ PO template files.") (define-public kdegraphics-mobipocket (package (name "kdegraphics-mobipocket") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "12yrwa22c4qxsf10fv76fzaaj5xlv5lmrwcqvf6qhgr6f9qsw7sj")))) + (base32 "1kxvzgmq83hml10pc4j66r59dsar7h92w2i0cs1nhar781mz666n")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1159,14 +1160,14 @@ Mobipocket e-books in Dolphin and other KDE apps.") (define-public libkexiv2 (package (name "libkexiv2") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "0p43z69yh5jk8m1hn3xynjpgzxpkc89h0dafj5964qx4xp4vxl19")))) + (base32 "0iwpy79ppv4bbsqrszp9kmghgjvkl13gdpnafsbikh4wy1ch4cv9")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) From 158126fada5cac1dbaf504aec6b742c6d5bd7c37 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 11:01:41 +0200 Subject: [PATCH 070/824] gnu: KDE Plasma: Update to 5.25.5. * gnu/packages/kde-plasma.scm (breeze, breeze-gtk, kdecoration, ksshaskpass, layer-shell-qt, kscreenlocker, libkscreen, libksysguard): Update to 5.25.5. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index f7bc601ffb..af623e2250 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -47,14 +47,14 @@ (define-public breeze (package (name "breeze") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) (sha256 (base32 - "0za75ckgfcdxrh2qxgyl2c1273g2xqwmd55njsis1yvwryadypqw")))) + "0m3ggv5znzfcp25afgl7v5w7m27v5hdvv6jw9vrvwbqj8lzq1hlx")))) (build-system qt-build-system) ;; TODO: Warning at /gnu/store/…-kpackage-5.34.0/…/KF5PackageMacros.cmake: ;; warnings during generation of metainfo for org.kde.breezedark.desktop: @@ -94,7 +94,7 @@ the Plasma Desktop. Breeze is the default theme for the KDE Plasma desktop.") (define-public breeze-gtk (package (name "breeze-gtk") - (version "5.19.5") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" @@ -102,7 +102,7 @@ the Plasma Desktop. Breeze is the default theme for the KDE Plasma desktop.") "-" version ".tar.xz")) (sha256 (base32 - "1j2nq9yw1ragmgwrz9f6ca4ifpi86qv1bbprdgd2qm2yh7vb44sj")))) + "0wj8qzy2104ggczxagxm45zwsvvpwd6jjnbv1893mhlr6f2zrbmh")))) (build-system qt-build-system) (arguments '(#:tests? #f)) ;no 'test' target @@ -118,14 +118,14 @@ Breeze is the default theme for the KDE Plasma desktop.") (define-public kdecoration (package (name "kdecoration") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/kdecoration-" version ".tar.xz")) (sha256 (base32 - "0b6ynqkndmlac89hv339k365m7wykp9y238df62jlq4vpr1r9x9y")))) + "1x3scszz5nfwqciwc3bv0r04wgqlxs0c9j1090zvn6mjjg2nsyb7")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -141,14 +141,14 @@ manager which re-parents a Client window to a window decoration frame.") (define-public ksshaskpass (package (name "ksshaskpass") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/ksshaskpass-" version ".tar.xz")) (sha256 (base32 - "0sfl77szvfq9c7v0gsv5nnf7h5kxigyy2z2p1cwmhm1pq4n606nk")))) + "0z8pp2mh4s98jh8jkf6r8v014gb6svapmp0m1npzw7zcmr6jvpn6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -165,14 +165,14 @@ call it if it is not associated to a terminal.") (define-public layer-shell-qt (package (name "layer-shell-qt") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/layer-shell-qt-" version ".tar.xz")) (sha256 (base32 - "06rxqm4wh4mcszrwb2dbgpxj3dqfx0rccyyjp091lbsncqm1gib0")))) + "1mvhklq7n9hhjing704jr3ybq58ixwr9fdg3phnqhmdnqc2q3w0l")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -191,14 +191,14 @@ call it if it is not associated to a terminal.") (define-public kscreenlocker (package (name "kscreenlocker") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/kscreenlocker-" version ".tar.xz")) (sha256 (base32 - "1kii3r3j89avwyb00wrw80k5sj0q4wqgmy1q0yxfps9jk729k3wc")))) + "0mivx0l266310iy52qi94b6wi8w2a8nl7cjn5750x66dz81jl3yj")))) (build-system qt-build-system) (arguments `(#:tests? #f ;; TODO: make tests pass @@ -256,14 +256,14 @@ call it if it is not associated to a terminal.") (define-public libkscreen (package (name "libkscreen") - (version "5.25.4") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "17ib0sgrhmmf3f8w3fni0825xz5581av5vnz8gca41vyf12css25")))) + (base32 "17f2pbbkpmw3a32nsqlwd0x5xb71l6dzrh7ldwcqv46nvb54yhfa")))) (build-system qt-build-system) (arguments '(#:phases @@ -294,14 +294,14 @@ basic needs and easy to configure for those who want special setups.") (define-public libksysguard (package (name "libksysguard") - (version "5.25.4") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/libksysguard-" version ".tar.xz")) (sha256 - (base32 "1kzpimhkagsmqj0cky4cfav1kbzyfjaj2l5xdapnmaygbm6r8086")))) + (base32 "1gqsjsdkp25abqqp4f6cv6ih199q9ad7q1a4lkhjgsh4h8jq1856")))) (native-inputs (list bash-minimal extra-cmake-modules pkg-config qttools-5)) (inputs @@ -395,4 +395,3 @@ wayland-server API.") (license (list license:lgpl2.1 license:lgpl3 ;; src/server/drm_fourcc.h carries the MIT license. license:expat)))) - From 6d98b42ca537b3016a60b14dee3978b1b1c62b7a Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Wed, 2 Mar 2022 08:29:54 +1100 Subject: [PATCH 071/824] gnu: Add libaccounts-glib. * gnu/packages/glib.scm (libaccounts-glib): New variable. Co-authored-by: Marius Bakke --- gnu/packages/glib.scm | 56 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 61040c91e7..f85d5e3225 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen ;;; Copyright © 2020 Arthur Margerit ;;; Copyright © 2021 Maxime Devos +;;; Copyright © 2022 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,6 +68,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages sqlite) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -76,6 +78,7 @@ #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -758,6 +761,59 @@ translated.") by GDBus included in Glib.") (license license:gpl2))) ; or Academic Free License 2.1 +(define-public libaccounts-glib + (package + (name "libaccounts-glib") + (version "1.25") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libaccounts-glib") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19rhk9f97m736d5ia26vfcbjp5kgi454558yhf9mrwm4iw5d9pk4")))) + (build-system meson-build-system) + (native-inputs (list dbus + `(,glib "bin") + gobject-introspection + gtk-doc + pkg-config + vala)) + (inputs (list check python python-pygobject)) + (propagated-inputs (list glib libxml2 sqlite)) + (arguments + (list #:tests? #f ;one test fails. + #:imported-modules `((guix build python-build-system) + ,@%meson-build-system-modules) + #:modules '(((guix build python-build-system) + #:select (python-version)) + (guix build meson-build-system) + (guix build utils)) + ;; don't try installing to python store path. + #:configure-flags + #~(list (string-append "-Dpy-overrides-dir=" + #$output "/lib/python" + (python-version #$(this-package-input + "python")) + "/site-packages/gi/overrides")) + #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-run-session" "--" "meson" "test" + "--print-errorlogs"))))))) + (home-page "https://accounts-sso.gitlab.io/") + (synopsis "Accounts SSO (Single Sign-On) management library for GLib +applications") + (description + "Accounts SSO is a framework for application developers who +wish to acquire, use and store web account details and credentials. It +handles the authentication process of an account and securely stores the +credentials and service-specific settings.") + (license license:lgpl2.1+))) + (define libsigc++ (package (name "libsigc++") From 293ab255b24d9a3abb709611af604a59249322f9 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Thu, 18 Aug 2022 01:52:33 +0200 Subject: [PATCH 072/824] gnu: Add signond. * gnu/packages/qt.scm (signond): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 9d1c0f6b5f..757a920056 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -4284,6 +4284,51 @@ services using the XML based SOAP protocol and without the need for a dedicated web server.") (license (list license:gpl2 license:gpl3)))) +(define-public signond + (package + (name "signond") + (version "8.61") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/signond") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0k6saz5spys4a4p6ws0ayrjks2gqdqvz7zfmlhdpz5axha0gbqq4")))) + (build-system qt-build-system) + (native-inputs (list doxygen pkg-config qtbase-5 qttools-5)) + (inputs (list dbus glib libaccounts-glib)) + (arguments + (list #:tests? #f ; Figure out how to run tests + #:phases + #~(modify-phases %standard-phases + (delete 'validate-runpath) + (replace 'configure + (lambda _ + (substitute* "src/signond/signond.pro" + (("/etc/") + (string-append #$output "/etc/"))) + (substitute* + '("tests/extensions/extensions.pri" + "tests/signond-tests/mock-ac-plugin/plugin.pro" + "tests/signond-tests/identity-tool.pro" + "tests/signond-tests/mock-ac-plugin/identity-ac-helper.pro" + "tests/libsignon-qt-tests/libsignon-qt-tests.pro" + "tests/signond-tests/signond-tests.pri") + (("QMAKE_RPATHDIR = \\$\\$\\{QMAKE_LIBDIR\\}") + (string-append "QMAKE_RPATHDIR = " + #$output "/lib:" + #$output "/lib/signon"))) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + (home-page "http://accounts-sso.gitlab.io/signond/index.html") + (synopsis "Perform user authentication over D-Bus") + (description "This package provides a D-Bus service which performs user +authentication on behalf of its clients.") + (license license:lgpl2.1+))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar From c7b97cb44b1f55c9317b86f2a894eb1f9da5cff6 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:54:23 +0200 Subject: [PATCH 073/824] gnu: Add signon-plugin-oauth2. * gnu/packages/qt.scm (signon-plugin-oauth2): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 757a920056..925bcc8f35 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -4329,6 +4329,42 @@ web server.") (description "This package provides a D-Bus service which performs user authentication on behalf of its clients.") (license license:lgpl2.1+))) + +(define-public signon-plugin-oauth2 + (package + (name "signon-plugin-oauth2") + (version "0.25") + (home-page "https://gitlab.com/accounts-sso/signon-plugin-oauth2") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16aslnyk8jdg03zcg97rp6qzd0gmclj14hyhliksz8jgfz1l0w7c")))) + (build-system qt-build-system) + (native-inputs (list doxygen pkg-config)) + (inputs (list signond)) + (arguments + (list #:tests? #f ;no tests + #:make-flags #~(list (string-append "INSTALL_ROOT=" #$output)) + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "common-project-config.pri" + (("-Werror") + "")) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + (synopsis "OAuth 2 plugin for signon") + (description + "This plugin for the Accounts-SSO SignOn daemon handles the OAuth +1.0 and 2.0 authentication protocols.") + (license license:lgpl2.1+))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar From 527f2c6a871d532dbab1e9fedbb54f83985ab50d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 14 Aug 2022 01:57:34 +0200 Subject: [PATCH 074/824] gnu: Add kpublictransport. * gnu/packages/kde-utils.scm (kpublictransport): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 61ffd1830b..9a855712f6 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -674,6 +674,37 @@ cards.") (description "Library for managing partitions.") (license license:gpl3+))) +(define-public kpublictransport + (package + (name "kpublictransport") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kde/stable/release-service/" version + "/src/kpublictransport-" version ".tar.xz")) + (sha256 + (base32 + "0z7zyyiq4815m74s6p841k1c4pxbrss7hnkag8kr5qa3q4264kg9")))) + (build-system qt-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(mergeutiltest|departuretest|journeytest|networkconfigtest|locationhistorymodeltest|navitiaparsertest|otpparsertest|ivvassparsertest|cachetest)"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + ;; TODO: clipper and osmctools are not detected + (inputs (list clipper osmctools protobuf qtdeclarative-5 zlib)) + (home-page "https://api.kde.org/kdepim/kpublictransport/html/index.html") + (synopsis "Library for accessing realtime public transport data") + (description + "This package provides a library for accessing realtime public +transport data and for performing public transport journey queries.") + (license (list license:lgpl2.0+)))) + (define-public snorenotify (package (name "snorenotify") From df66bede3e5beba471ec95a916fa63c3fa464918 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Sat, 5 Mar 2022 11:46:47 +1100 Subject: [PATCH 075/824] gnu: Add libaccounts-qt. * gnu/packages/qt.scm (libaccounts-qt): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 925bcc8f35..bbfb4759c2 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -25,6 +25,7 @@ ;;; Copyright © 2021 Nicolò Balzarotti ;;; Copyright © 2022 Foo Chuan Wei ;;; Copyright © 2022 Zhu Zihao +;;; Copyright © 2022 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -4284,6 +4285,47 @@ services using the XML based SOAP protocol and without the need for a dedicated web server.") (license (list license:gpl2 license:gpl3)))) +(define-public libaccounts-qt + (package + (name "libaccounts-qt") + (version "1.16") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libaccounts-qt") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vmpjvysm0ld8dqnx8msa15hlhrkny02cqycsh4k2azrnijg0xjz")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;TODO + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "tests/tst_libaccounts.pro" + (("QMAKE_RPATHDIR = \\$\\$\\{QMAKE_LIBDIR\\}") + (string-append "QMAKE_RPATHDIR =" + #$output "/lib"))) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + ;; * SignOnQt5 (required version >= 8.55), D-Bus service which performs + ;; user authentication on behalf of its clients, + ;; + (native-inputs (list doxygen pkg-config qtbase-5 qttools-5)) + (inputs (list glib signond libaccounts-glib)) + (home-page "https://accounts-sso.gitlab.io/") + (synopsis "Qt5 bindings for libaccounts-glib") + (description + "Accounts SSO is a framework for application developers who +wish to acquire, use and store web account details and credentials. It +handles the authentication process of an account and securely stores the +credentials and service-specific settings.") + (license license:lgpl2.1+))) + (define-public signond (package (name "signond") From 7bc1fe06560ae1e74d42deee23df85d805870be4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Thu, 18 Aug 2022 01:53:40 +0200 Subject: [PATCH 076/824] gnu: Add libsignon-glib. * gnu/packages/qt.scm (libsignon-glib): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 48 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index bbfb4759c2..e6afbf4ac4 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -49,6 +49,7 @@ #:use-module (guix git-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system meson) #:use-module (guix build-system trivial) #:use-module (guix build-system python) #:use-module (guix build-system qt) @@ -60,6 +61,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages base) #:use-module (gnu packages bison) + #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cups) @@ -4326,6 +4328,52 @@ handles the authentication process of an account and securely stores the credentials and service-specific settings.") (license license:lgpl2.1+))) +(define-public libsignon-glib + (package + (name "libsignon-glib") + (version "2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libsignon-glib") + (commit (string-append "VERSION_" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gnx9gqsh0hcfm1lk7w60g64mkn1iicga5f5xcy1j9a9byacsfd0")))) + (build-system meson-build-system) + (arguments + (list #:tests? #f ;TODO: ninja: no work to do. + #:imported-modules `((guix build python-build-system) + ,@%meson-build-system-modules) + #:modules '(((guix build python-build-system) + #:select (python-version)) + (guix build meson-build-system) + (guix build utils)) + #:configure-flags + #~(list "-Dtests=true" + (string-append "-Dpy-overrides-dir=" + #$output "/lib/python" + (python-version #$(this-package-input + "python")) + "/site-packages/gi/overrides")))) + (native-inputs (list dbus + dbus-test-runner + `(,glib "bin") + gobject-introspection + gtk-doc + pkg-config + vala)) + (inputs (list check signond python python-pygobject)) + (propagated-inputs (list glib)) + (home-page "https://accounts-sso.gitlab.io/libsignon-glib/") + (synopsis "Single signon authentication library for GLib applications") + (description + "This package provides single signon authentication library for +GLib applications.") + (license license:lgpl2.1+))) + (define-public signond (package (name "signond") From 431f34ec02f5cee7ac030dc2502a534d94765b10 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 23 Sep 2022 16:15:32 +0200 Subject: [PATCH 077/824] gnu: Add kaccounts-integration. * gnu/packages/kde-pim.scm (kaccounts-integration): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 881385e279..a24964f208 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -496,6 +496,34 @@ modern blogging web application that provides an XML data interface supports one of the APIs mentioned above.") (license license:lgpl2.0+))) +(define-public kaccounts-integration + (package + (name "kaccounts-integration") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1q1d2a1qknfkgm63gji6ijji35d0b1jy1kvf10a7ac4l1z1fvnpl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcmutils + ki18n + kcoreaddons + kdbusaddons + kdeclarative + kwallet + kio + libaccounts-qt + signond)) + (home-page "https://invent.kde.org/network/kaccounts-integration") + (synopsis "Online account management system") + (description "The Kaccounts Integration library provides online account +management system and its Plasma integration components.") + (license license:lgpl2.0+))) + (define-public kcalendarsupport (package (name "kcalendarsupport") From 2c6b4872fc7bd4429f2d34bbf98758d348c5d2ec Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 23 Sep 2022 16:20:01 +0200 Subject: [PATCH 078/824] gnu: akonadi: Add dbus and pkg-config to native-inputs. * gnu/packages/kde-pim.scm (akonadi)[native-inputs]: Add dbus and pkg-config. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index a24964f208..6c5e73bb07 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages openldap) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages qt) #:use-module (gnu packages search) #:use-module (gnu packages sqlite) @@ -59,7 +60,7 @@ "akonadi-not-relocatable.patch")))) (build-system qt-build-system) (native-inputs - (list extra-cmake-modules qttools-5 shared-mime-info)) + (list dbus extra-cmake-modules qttools-5 shared-mime-info pkg-config)) (inputs (list boost kconfig From 98fd85c0320f849ad174e4e45c5c86dd81cfcbd2 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 17:11:04 +0200 Subject: [PATCH 079/824] gnu: akonadi: Enable tests. * gnu/packages/kde-pim.scm (akonadi)[arguments]: Enable tests and use gexp. [inputs]: Add LIBACCOUNTS-QT and SIGNOND. Co-authored-by: Marius Bakke --- gnu/packages/kde-pim.scm | 83 +++++++++++++++++++++++----------------- 1 file changed, 47 insertions(+), 36 deletions(-) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 6c5e73bb07..11b6acdc7c 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -23,6 +23,7 @@ (define-module (gnu packages kde-pim) #:use-module (guix build-system qt) #:use-module (guix download) + #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -47,22 +48,26 @@ (package (name "akonadi") (version "22.08.1") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://kde/stable/release-service/" version - "/src/akonadi-" version ".tar.xz")) - (sha256 - (base32 "1yfy0b6kyiq82zkfkx9ldgjlbwg3lgg4di53fqjllmqhzaj1xy91")) - (patches (search-patches - "akonadi-paths.patch" - "akonadi-timestamps.patch" - "akonadi-not-relocatable.patch")))) + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/akonadi-" version ".tar.xz")) + (sha256 + (base32 + "1yfy0b6kyiq82zkfkx9ldgjlbwg3lgg4di53fqjllmqhzaj1xy91")) + (patches (search-patches "akonadi-paths.patch" + "akonadi-timestamps.patch" + "akonadi-not-relocatable.patch")))) (build-system qt-build-system) (native-inputs - (list dbus extra-cmake-modules qttools-5 shared-mime-info pkg-config)) + (list dbus + extra-cmake-modules + qttools-5 + shared-mime-info + pkg-config)) (inputs (list boost + libaccounts-qt kconfig kconfigwidgets kcoreaddons @@ -80,33 +85,39 @@ ;; Do NOT add mysql or postgresql to the inputs. Otherwise the binaries ;; and wrapped files will refer to them, even if the user choices none ;; of these. Executables are searched on $PATH then. - qtbase-5 - sqlite)) + signond + qtbase-5)) + (propagated-inputs (list sqlite kaccounts-integration)) (arguments - `(#:tests? #f ;; TODO 135/167 tests fail - #:configure-flags '("-DDATABASE_BACKEND=SQLITE") ; lightweight - #:modules ((ice-9 textual-ports) - ,@%qt-build-system-modules) - #:phases - (modify-phases (@ (guix build qt-build-system) %standard-phases) - (add-before 'configure 'add-definitions - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (with-output-to-file "CMakeLists.txt.new" - (lambda _ - (display - (string-append - "add_compile_definitions(\n" - "NIX_OUT=\"" out "\"\n" - ;; pin binaries for mysql backend - ")\n\n")) - (display - (call-with-input-file "CMakeLists.txt" - get-string-all)))) - (rename-file "CMakeLists.txt.new" "CMakeLists.txt"))))))) + (list #:tests? #f + #:configure-flags #~'("-DDATABASE_BACKEND=SQLITE") ;lightweight + #:modules `((ice-9 textual-ports) + ,@%qt-build-system-modules) + #:phases + #~(modify-phases (@ (guix build qt-build-system) %standard-phases) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "PATH" + (string-append (getcwd) "/bin" ":" + (getenv "PATH"))) + (invoke "dbus-launch" "ctest" "-E" + "(AkonadiServer-dbconfigtest|mimetypecheckertest|entitytreemodeltest|akonadi-sqlite-testenvironmenttest|akonadi-sqlite-autoincrementtest|akonadi-sqlite-attributefactorytest|akonadi-sqlite-collectionpathresolvertest|akonadi-sqlite-collectionattributetest|akonadi-sqlite-itemfetchtest|akonadi-sqlite-itemappendtest|akonadi-sqlite-itemstoretest|akonadi-sqlite-itemdeletetest|akonadi-sqlite-entitycachetest|akonadi-sqlite-monitortest|akonadi-sqlite-changerecordertest|akonadi-sqlite-resourcetest|akonadi-sqlite-subscriptiontest|akonadi-sqlite-transactiontest|akonadi-sqlite-itemcopytest|akonadi-sqlite-itemmovetest|akonadi-sqlite-invalidatecachejobtest|akonadi-sqlite-collectioncreatetest|akonadi-sqlite-collectioncopytest|akonadi-sqlite-collectionmovetest|akonadi-sqlite-collectionsynctest|akonadi-sqlite-itemsynctest)")))) + (add-before 'configure 'add-definitions + (lambda* (#:key outputs inputs #:allow-other-keys) + (with-output-to-file "CMakeLists.txt.new" + (lambda _ + (display (string-append + "add_compile_definitions(\n" + "NIX_OUT=\"" + #$output "\"\n" ")\n\n")) + (display (call-with-input-file "CMakeLists.txt" + get-string-all)))) + (rename-file "CMakeLists.txt.new" "CMakeLists.txt")))))) (home-page "https://kontact.kde.org/components/akonadi/") (synopsis "Extensible cross-desktop storage service for PIM") - (description "Akonadi is an extensible cross-desktop Personal Information + (description + "Akonadi is an extensible cross-desktop Personal Information Management (PIM) storage service. It provides a common framework for applications to store and access mail, calendars, addressbooks, and other PIM data. From 8b60547c2306b0bddfe904bb7a6d96cc8695a7d9 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 23:43:36 +0200 Subject: [PATCH 080/824] gnu: bluez-qt: Add qtdeclarative-5 to inputs. * gnu/packages/kde-frameworks.scm (qtdeclarative-5)[inputs]: Add qtdeclarative-5. [arguments]: Disable failing test. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index ee4ba95263..3632b61334 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -345,21 +345,19 @@ http://freedesktop.org/wiki/Specifications/open-collaboration-services/") (native-inputs (list dbus extra-cmake-modules)) (inputs - ;; TODO: qtdeclarative-5 (yields one failing test) - (list qtbase-5)) + (list qtdeclarative-5 + qtbase-5)) (arguments (list #:configure-flags #~(list (string-append "-DUDEV_RULES_INSTALL_DIR=" #$output "/lib/udev/rules.d")) - ;; TODO: Make tests pass: DBUS_FATAL_WARNINGS=0 still yields 7/8 tests - ;; failing. When running after install, tests hang. - #:phases - '(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "DBUS_FATAL_WARNINGS" "0") - (invoke "dbus-launch" "ctest"))))))) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "DBUS_FATAL_WARNINGS" "0") + (invoke "dbus-launch" "ctest" "-E" "bluezqt-qmltests"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "QML wrapper for BlueZ") (description "bluez-qt is a Qt-style library for accessing the bluez From 7f8e838a9a1c56b98143acf34b5dda71f8636f8f Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 23:53:41 +0200 Subject: [PATCH 081/824] gnu: breeze-icons: Enable tests. Update icons cache. * gnu/packages/kde-frameworks.scm (breeze-icons)[arguments]: Enable tests. Add phase to update icons. [native-inputs]: Add gtk+:bin. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 30 ++++++++++++++++++++---------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 3632b61334..d1542dc7d1 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -63,6 +63,7 @@ #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) + #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages iso-codes) #:use-module (gnu packages kerberos) @@ -370,21 +371,30 @@ Bluetooth stack. It is used by the KDE Bluetooth stack, BlueDevil.") (version "5.98.0") (source (origin (method url-fetch) - (uri (string-append - "mirror://kde/stable/frameworks/" - (version-major+minor version) "/" - name "-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) (sha256 (base32 "0a3zvmhcfsnxv0jpyjny3sl769p99psadl1872v0qlkax47pvsjp")))) (build-system cmake-build-system) (native-inputs - (list extra-cmake-modules fdupes - python python-lxml)) ;; For 24x24 icon generation - (inputs - (list qtbase-5)) - (arguments ;; fails because duplicate icons exist. TODO: try fix this. - `(#:tests? #f)) + (list extra-cmake-modules + fdupes + `(,gtk+ "bin") + python + python-lxml)) ;for 24x24 icon generation + (inputs (list qtbase-5)) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'install 'update-cache + (lambda* _ + (invoke "gtk-update-icon-cache" + (string-append #$output + "/share/icons/breeze")) + (invoke "gtk-update-icon-cache" + (string-append #$output + "/share/icons/breeze-dark"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Default KDE Plasma 5 icon theme") (description "Breeze provides a freedesktop.org compatible icon theme. From de3829816d7a49dfa06b6fb080446f1d0be6f657 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 00:17:21 +0200 Subject: [PATCH 082/824] gnu: Add python-doxyqml. * gnu/packages/python-xyz.scm (python-doxyqml): New variable. Signed-off-by: Marius Bakke --- gnu/packages/python-xyz.scm | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 509d57964f..5f736f05ac 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -104,7 +104,7 @@ ;;; Copyright © 2021 Maxime Devos ;;; Copyright © 2021 Hugo Lecomte ;;; Copyright © 2021 Franck Pérignon -;;; Copyright © 2021 Petr Hodina +;;; Copyright © 2021, 2022 Petr Hodina ;;; Copyright © 2021 Simon Streit ;;; Copyright © 2021 Daniel Meißner ;;; Copyright © 2021, 2022 Pradana Aumars @@ -3075,6 +3075,23 @@ applications. dogtail scripts are written in Python and executed like any other Python program.") (license license:gpl2+))) +(define-public python-doxyqml + (package + (name "python-doxyqml") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "doxyqml" version)) + (sha256 + (base32 + "1f0jjqvamly4hn7f1palvq27z6yr694rfzyxrb6g0ysbbawxkvq9")))) + (build-system python-build-system) + (home-page "http://agateau.com/projects/doxyqml") + (synopsis "Doxygen input filter for QML files") + (description + "This package provides a Doxygen input filter for QML files.") + (license license:bsd-3))) + (define-public python-empy (package (name "python-empy") From 2c65a197fc22edf83cc095e5fd766e3234fdba0c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 00:19:17 +0200 Subject: [PATCH 083/824] gnu: Add python-doxypypy. * gnu/packages/python-xyz.scm (python-doxypypy): New variable. Signed-off-by: Marius Bakke --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5f736f05ac..eaad292a7f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3092,6 +3092,24 @@ other Python program.") "This package provides a Doxygen input filter for QML files.") (license license:bsd-3))) +(define-public python-doxypypy + (package + (name "python-doxypypy") + (version "0.8.8.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "doxypypy" version)) + (sha256 + (base32 + "06z0vbh975g42z5szbfvn9i3bif3xwr5pncqd4fvjzjkbi2p2xb2")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ;no test suite + (home-page "https://github.com/Feneric/doxypypy") + (synopsis "Doxygen filter for Python") + (description + "This package provides a Doxygen filter for Python.") + (license license:gpl2+))) + (define-public python-empy (package (name "python-empy") From 9206921aa3f6eacb2056bca5a0ac1b1d4b9a2522 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 00:38:35 +0200 Subject: [PATCH 084/824] gnu: karchive: Enable zstd support. * gnu/packages/kde-frameworks.scm (karchive)[native-inputs]: Add pkg-config. [inputs]: Add zstd:lib. [arguments]: Disable karchivetest. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index d1542dc7d1..dece10f4db 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -450,23 +450,27 @@ documentation.") (version "5.98.0") (source (origin (method url-fetch) - (uri (string-append - "mirror://kde/stable/frameworks/" - (version-major+minor version) "/" - name "-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) (sha256 (base32 "1ipj7j1iw6g56z0qppji38h6qwbs05piiqqbsw8hdbf96l6cdiq2")))) (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "karchivetest"))))))) (native-inputs - (list extra-cmake-modules)) - ;; pkg-config ;; For zstd + (list extra-cmake-modules pkg-config)) (inputs - (list bzip2 qtbase-5 xz zlib)) - ;; `(,zstd "lib") ;; FIXME: Tests fail with zstd + (list bzip2 qtbase-5 xz zlib `(,zstd "lib"))) (home-page "https://community.kde.org/Frameworks") (synopsis "Qt 5 addon providing access to numerous types of archives") - (description "KArchive provides classes for easy reading, creation and + (description + "KArchive provides classes for easy reading, creation and manipulation of @code{archive} formats like ZIP and TAR. It also provides transparent compression and decompression of data, like the From 5922ceabde5098912a718e835f4549659bbc12b4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 02:10:46 +0200 Subject: [PATCH 085/824] gnu: kiconthemes: Use gexp. * gnu/packages/kde-frameworks.scm (kiconthemes): Use gexp. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index dece10f4db..f1aae61a3c 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -2563,16 +2563,17 @@ window does not need focus for them to be activated.") qtdeclarative-5 qtsvg-5)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'check-setup - (lambda* (#:key inputs #:allow-other-keys) - (setenv "XDG_DATA_DIRS" - (string-append (assoc-ref inputs "shared-mime-info") - "/share")) - (setenv "HOME" (getcwd)) - ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (list #:phases + #~(modify-phases %standard-phases + (add-before 'check 'check-setup + (lambda* (#:key inputs #:allow-other-keys) + (setenv "XDG_DATA_DIRS" + (string-append #$(this-package-native-input + "shared-mime-info") + "/share")) + (setenv "HOME" (getcwd)) + ;; make Qt render "offscreen", required for tests + (setenv "QT_QPA_PLATFORM" "offscreen")))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Icon GUI utilities") (description "This library contains classes to improve the handling of icons From 2f68492d10940bd88e1bd662188d21ce76178676 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 27 Sep 2022 08:39:15 +0200 Subject: [PATCH 086/824] gnu: kdbusaddons: Use gexp. * gnu/packages/kde-frameworks.scm (kdbusadons, kdbusaddons-bootstrap): Use gexp. (kdbusaddons-bootstrap) [inputs]: Use modify-inputs. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index f1aae61a3c..dd6d1b303a 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -680,8 +680,8 @@ many more.") (list qtbase-5 qtx11extras kinit-bootstrap)) ;; kinit-bootstrap: kinit package which does not depend on kdbusaddons. (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-before 'configure 'patch-source (lambda* (#:key inputs #:allow-other-keys) ;; look for the kdeinit5 executable in kinit's store directory, @@ -689,7 +689,8 @@ many more.") (substitute* "src/kdeinitinterface.cpp" (("<< QCoreApplication::applicationDirPath..") (string-append - "<< QString::fromUtf8(\"" (assoc-ref inputs "kinit") "/bin\")" ))))) + "<< QString::fromUtf8(\"/" (dirname (search-input-file inputs + "bin/kdeinit5")) "\")" ))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -3437,11 +3438,11 @@ need.") (source (origin (inherit (package-source kdbusaddons)) (patches '()))) - (inputs (alist-delete "kinit" (package-inputs kdbusaddons))) + (inputs (modify-inputs (package-inputs kdbusaddons) (delete "kinit"))) (arguments (substitute-keyword-arguments (package-arguments kdbusaddons) ((#:phases phases) - `(modify-phases ,phases + #~(modify-phases #$phases (delete 'patch-source))))))) (define kinit-bootstrap From fb94d0a17d83d5f11a7c956d606018a23d504f84 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 07:50:23 +0200 Subject: [PATCH 087/824] gnu: Add kwayland-integration. * gnu/packages/kde-plasma.scm (kwayland-integration): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 45 +++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index af623e2250..31b143ab4e 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -395,3 +395,48 @@ wayland-server API.") (license (list license:lgpl2.1 license:lgpl3 ;; src/server/drm_fourcc.h carries the MIT license. license:expat)))) + +(define-public kwayland-integration + (package + (name "kwayland-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "10xl7yrj519b9s5vq0hqqfz3vvg1fdwggw96snzm44iwycqbgss8")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check-after-install + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + ;; https://bugs.gentoo.org/668872 + (invoke "ctest" "-E" "(idleTest-kwayland-test)")))) + (add-before 'check-after-install 'check-setup + (lambda* (#:key outputs #:allow-other-keys) + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH")))))))) + (native-inputs (list extra-cmake-modules wayland-protocols pkg-config)) + (inputs (list kguiaddons + kidletime + kwindowsystem + kwayland + libxkbcommon + wayland + qtbase-5 + qtwayland)) + (synopsis "KWayland runtime integration plugins") + (description "This package provides Wayland integration plugins for various +KDE Frameworks components.") + (home-page "https://invent.kde.org/plasma/kwayland-integration") + (license (list license:lgpl2.1 license:lgpl3)))) From 448df3cde19e648c8ac65472b10bc8011e5d4151 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 27 Aug 2022 17:01:13 +0200 Subject: [PATCH 088/824] gnu: Add ksysguard. * gnu/packages/kde-plasma.scm (ksysguard): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 31b143ab4e..14733c7c0a 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -253,6 +253,43 @@ call it if it is not associated to a terminal.") "@code{kscreenlocker} is a library for creating secure lock screens.") (license license:gpl2+))) +(define-public ksysguard + (package + (name "ksysguard") + (version "5.22.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/ksysguard/" version + "/ksysguard-" version ".tar.xz")) + (sha256 + (base32 "0bb2aj46v7ig0wn3ir68igryl2gblz2n75cddn8fwamvbx76570g")))) + (build-system qt-build-system) + ;; TODO: No tests found + (native-inputs + (list extra-cmake-modules kdoctools)) + (inputs + (list kconfig + kcoreaddons + kdbusaddons + ki18n + kiconthemes + kinit + kio + kitemviews + knewstuff + knotifications + kwindowsystem + libksysguard + `(,lm-sensors "lib") + qtbase-5)) + (home-page "https://www.kde.org/applications/system/ksysguard/") + (synopsis "Plasma process and performance monitor") + (description "KSysGuard is a program to monitor various elements of your +system, or any other remote system with the KSysGuard daemon (ksysgardd) +installed.") + (license license:gpl2+))) + (define-public libkscreen (package (name "libkscreen") From 263280fd64ef88522ac2cefdd3a2cbd5570c9f48 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:08:42 +0200 Subject: [PATCH 089/824] gnu: Add kio-extras. * gnu/packages/kde.scm (kio-extras): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 45 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 9a855712f6..fe76366b65 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -68,6 +68,7 @@ #:use-module (gnu packages ghostscript) #:use-module (gnu packages gimp) #:use-module (gnu packages gl) + #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gps) #:use-module (gnu packages graphics) @@ -443,6 +444,50 @@ a module for implementing ODF Gantt charts, which are bar charts that illustrate project schedules.") (license license:gpl2+))) +(define-public kio-extras + (package + (name "kio-extras") + (version "22.08.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0gzna2ps2qd2js28c97kjpcbah7zz8n4s4932faggc2nz5z5wnyn")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "TMPDIR" (getcwd)) + (invoke "ctest" "-E" "testkioarchive"))))))) + (native-inputs (list extra-cmake-modules dbus kdoctools qttools-5)) + (inputs (list karchive + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + ki18n + kdnssd + kio + solid + kbookmarks + kguiaddons + ksyntaxhighlighting + qtbase-5 + qtsvg-5)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Additional components to increase the functionality of KIO") + (description + "This package provides additional components to increase +the functionality of the KDE resource and network access abstractions.") + (license license:lgpl2.0+))) + + (define-public kseexpr (package (name "kseexpr") From dd2ba1a807378de4050d49904c377d66e3e42f0d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:09:53 +0200 Subject: [PATCH 090/824] gnu: Add kio-fuse. * gnu/packages/kde.scm (kio-fuse): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index fe76366b65..439a4b53f0 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -487,6 +487,34 @@ illustrate project schedules.") the functionality of the KDE resource and network access abstractions.") (license license:lgpl2.0+))) +(define-public kio-fuse + (package + (name "kio-fuse") + (version "5.0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name "/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1pb62h45c06dq3rml91xbf8j5y2c1l8z8j8lycchxrlgys5rlrv6")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "dbus-launch" "ctest" "-E" + "(fileopstest-cache|fileopstest-filejob)"))))))) + (native-inputs (list dbus extra-cmake-modules pkg-config)) + (inputs (list fuse-3 kio kcoreaddons qtbase-5)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "FUSE Interface for KIO") + (description "This package provides FUSE Interface for KIO.") + (license license:lgpl2.1+))) (define-public kseexpr (package From 605a6c87cb951aaad97e30b39fc8ff8bbf5f3531 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 10 Aug 2022 00:39:57 +0200 Subject: [PATCH 091/824] gnu: Add kpkpass. * gnu/packages/kde-pim.scm (kpkpass): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 11b6acdc7c..3cfd338a4e 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -1589,6 +1589,26 @@ and exchanging calendar data, vCalendar and iCalendar.") Virtual Contact File}) files to the KPeople contact management library.") (license license:lgpl2.1+))) +(define-public kpkpass + (package + (name "kpkpass") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/kpkpass-" version ".tar.xz")) + (sha256 + (base32 + "09l6c7nsgfnffgkm0yzjhsfkm79fv9izasislrlzdvca5xninrgb")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive qtbase-5 shared-mime-info)) + (home-page "https://invent.kde.org/pim/kpkpass") + (synopsis "Apple Wallet Pass reader") + (description "This package provides library to deal with Apple Wallet +pass files.") + (license license:lgpl2.0+))) + (define-public kpimcommon (package (name "kpimcommon") From 8ca39d7a125254a8bb6740bf29eb1404014b14ca Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 06:01:45 +0200 Subject: [PATCH 092/824] gnu: Add kgamma. * gnu/packages/kde-plasma.scm (kgamma): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 14733c7c0a..8b3e525b07 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -138,6 +138,32 @@ These window decorations can be used by for example an X11 based window manager which re-parents a Client window to a window decoration frame.") (license license:lgpl3+))) +(define-public kgamma + (package + (name "kgamma") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "5-" + version ".tar.xz")) + (sha256 + (base32 + "1c305bs50km7bsn0phz7yj4x2168sxwsw9zxbpcgw4q3r53c0ywz")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + kcoreaddons + kconfig + kconfigwidgets + kdoctools + ki18n)) + (synopsis "Adjust monitor gamma settings") + (description + "This package provides a tool to adjust your monitor gamma settings.") + (home-page "https://invent.kde.org/plasma/kgamma5") + (license license:gpl2+))) + (define-public ksshaskpass (package (name "ksshaskpass") From e528b5eea34a39d944cdb11900a49f68dd396c54 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 22 Aug 2022 18:13:10 +0200 Subject: [PATCH 093/824] gnu: Add kscreen. * gnu/packages/kde-plasma.scm (kscreen): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 42 +++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 8b3e525b07..32fd21da0d 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2020 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2022 Brendan Tildesley +;;; Copyright © 2022 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -164,6 +165,47 @@ manager which re-parents a Client window to a window decoration frame.") (home-page "https://invent.kde.org/plasma/kgamma5") (license license:gpl2+))) +(define-public kscreen + (package + (name "kscreen") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0361202n0366jiyv61w06jikh2i4s1fzr6x3chmdykx4fgvbqj7s")))) + (build-system cmake-build-system) + (arguments + ;; TODO: All tests fail + (list #:tests? #f)) + (native-inputs (list extra-cmake-modules qttools-5 pkg-config)) + (inputs (list kconfig + kdbusaddons + kdeclarative + kglobalaccel + ki18n + kwindowsystem + kiconthemes + kcoreaddons + kcmutils + kxmlgui + libkscreen + libxi + plasma-wayland-protocols + qtsensors + qtbase-5 + qtx11extras + xcb-util)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/plasma/kscreen") + (synopsis "Screen management software") + (description "This package provides the screen management software for +KDE Plasma Workspaces.") + (license license:gpl2+))) + (define-public ksshaskpass (package (name "ksshaskpass") From 10fdd4265cebf3e95a99e842a3741839a4982b74 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 07:55:01 +0200 Subject: [PATCH 094/824] gnu: Add kwrited. * gnu/packages/kde-plasma.scm (kwrited): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 32fd21da0d..4f4c882a32 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -545,3 +545,24 @@ wayland-server API.") KDE Frameworks components.") (home-page "https://invent.kde.org/plasma/kwayland-integration") (license (list license:lgpl2.1 license:lgpl3)))) + +(define-public kwrited + (package + (name "kwrited") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "03gw3czdgyf35n6x79x416rk6f7w1ayzmy5pb65v9733nx1j34mh")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons ki18n kpty knotifications)) + (home-page "https://invent.kde.org/plasma/kwrited") + (synopsis "System notification daemon") + (description + "This package provides a daemon that listens to system notifications.") + (license license:gpl2+))) From dff5235290cb48ce7bb755cbc4b156caa73ca195 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 21 Nov 2022 13:23:09 +0100 Subject: [PATCH 095/824] fxup kwayland-integration --- gnu/packages/kde-plasma.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 4f4c882a32..1e77ad3c9f 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -539,7 +539,7 @@ wayland-server API.") libxkbcommon wayland qtbase-5 - qtwayland)) + qtwayland-5)) (synopsis "KWayland runtime integration plugins") (description "This package provides Wayland integration plugins for various KDE Frameworks components.") From bcbfae94b2810c1895ce7c6066e0ace85eb937a2 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 07:09:44 +0200 Subject: [PATCH 096/824] gnu: Add kmenuedit. * gnu/packages/kde-plasma.scm (kmenuedit): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 1e77ad3c9f..cd95f03e9b 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -165,6 +165,34 @@ manager which re-parents a Client window to a window decoration frame.") (home-page "https://invent.kde.org/plasma/kgamma5") (license license:gpl2+))) +(define-public kmenuedit + (package + (name "kmenuedit") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0z85w7w207dnsinsz8yg6s408pwfy3l7wjkcsjpyg8aj8s9x6nl7")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list ki18n + kxmlgui + kdbusaddons + kiconthemes + kio + kitemviews + sonnet + kglobalaccel + kwindowsystem)) + (synopsis "Menu Editor for Plasma Workspaces") + (description "This package provides menu editor for Plasma Workspaces.") + (home-page "https://invent.kde.org/plasma/kmenuedit") + (license license:gpl2+))) + (define-public kscreen (package (name "kscreen") From ebd845c697799f0c3560fffe93297455ba2f7149 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 14 Aug 2022 01:56:33 +0200 Subject: [PATCH 097/824] gnu: Add kirigami-addons. * gnu/packages/kde.scm (kirigami-addons): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 439a4b53f0..422e85a553 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -516,6 +516,30 @@ the functionality of the KDE resource and network access abstractions.") (description "This package provides FUSE Interface for KIO.") (license license:lgpl2.1+))) +(define-public kirigami-addons + (package + (name "kirigami-addons") + (version "0.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://invent.kde.org/libraries/kirigami-addons/-/archive/v" + version "/kirigami-addons-v" version ".tar.gz")) + (sha256 + (base32 + "1zr8dpc7bzw6g3y0jaxsr2lqlxqwlcphchpk8iah6g1f3n9fq73r")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f)) ; failing test + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami ki18n qtdeclarative-5 qtquickcontrols2-5)) + (home-page "https://invent.kde.org/libraries/kirigami-addons") + (synopsis "Add-ons for the Kirigami framework") + (description + "This package provides Kirigami components usable by both touch +and desktop experiences.") + (license license:lgpl2.0+))) + (define-public kseexpr (package (name "kseexpr") From c71f599cff9e6dd719b7c43940d0a0fddb9a5c22 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 06:20:06 +0200 Subject: [PATCH 098/824] gnu: Add kactivitymanagerd. * gnu/packages/kde-plasma.scm (kactivitymanagerd): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index cd95f03e9b..27eaf735c5 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -32,6 +32,7 @@ #:use-module (guix build-system qt) #:use-module (gnu packages admin) #:use-module (gnu packages bash) + #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) @@ -116,6 +117,36 @@ Breeze is the default theme for the KDE Plasma desktop.") (license (list license:bsd-3 ;cmake/FindSass.cmake license:lgpl2.1+)))) ; +(define-public kactivitymanagerd + (package + (name "kactivitymanagerd") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0hsllhqi46n25sr27crnad053ghk3hni2w496g6d2qfmi20l3g4n")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list boost + kconfig + kcoreaddons + kwindowsystem + kglobalaccel + kio + kxmlgui + kdbusaddons + ki18n + kcrash)) + (synopsis "System service to manage user's activities") + (description "This package provides components for managing the KDE Activity +concept.") + (home-page "https://invent.kde.org/plasma/kactivitymanagerd") + (license (list license:gpl2 license:gpl3)))) + (define-public kdecoration (package (name "kdecoration") From c1c576ad7c6f4535d1f47870dda14b36590d93a5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 25 Mar 2022 11:38:20 +0100 Subject: [PATCH 099/824] gnu: Add maliit-framework. * gnu/pacakges/freedesktop.scm (maliit-framework): New variable. Signed-off-by: Marius Bakke --- gnu/packages/freedesktop.scm | 38 ++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index d74d6aa935..a965f4242d 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -78,6 +78,7 @@ #:use-module (gnu packages disk) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) + #:use-module (gnu packages fcitx) #:use-module (gnu packages file) #:use-module (gnu packages fontutils) #:use-module (gnu packages gawk) @@ -91,9 +92,12 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) + #:use-module (gnu packages ibus) #:use-module (gnu packages image) + #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages language) #:use-module (gnu packages libffi) + #:use-module (gnu packages libreoffice) #:use-module (gnu packages libunwind) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) @@ -386,6 +390,40 @@ inappropriate content.") license:gpl2+ license:lgpl2.1+)))) +(define-public maliit-framework + (package + (name "maliit-framework") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/maliit/framework") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dkjxvfxg56hfy70j6ibfklfyv57jiha4vgc3ggl60r5kjx65s5b")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules + wayland-protocols + pkg-config + doxygen + graphviz + `(,glib "bin"))) ;for gdbus-codegen)) + (inputs (list qtbase-5 + qtdeclarative-5 + qtwayland-5 + wayland + libxkbcommon + dbus + eudev + glib)) + (home-page "https://github.com/maliit/framework") + (synopsis "Core libraries of Maliit") + (description "This package provides Maliit provides a flexible input +method framework.") + (license license:lgpl2.1+))) + (define-public xdg-utils (package (name "xdg-utils") From e7a7e434375a4b6150323f6f6c8f6e8f6642b1f9 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 2 Oct 2022 15:08:52 +0200 Subject: [PATCH 100/824] gnu: Add maliit-keyboard. * gnu/pacakges/freedesktop.scm (maliit-keyboard): New variable. Signed-off-by: Marius Bakke --- gnu/packages/freedesktop.scm | 41 ++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index a965f4242d..61d959e03f 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -424,6 +424,47 @@ inappropriate content.") method framework.") (license license:lgpl2.1+))) +(define-public maliit-keyboard + (package + (name "maliit-keyboard") + (version "2.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/maliit/keyboard") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0g89lckl4wzwamc89hs8871fbiyrsjwzk5b6ic4vhc4d1clyqzaw")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-after 'install 'install-schemas + (lambda* (#:key source outputs #:allow-other-keys) + (with-directory-excursion (string-append #$output + "/share/glib-2.0/schemas") + (invoke "glib-compile-schemas" "."))))))) + (native-inputs (list extra-cmake-modules pkg-config gettext-minimal + `(,glib "bin"))) + (inputs (list hunspell + glib + libchewing + libpinyin + maliit-framework + presage + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtquickcontrols2-5)) + (home-page "https://github.com/maliit/keyboard") + (synopsis "Maliit Keyboard") + (description + "This package provides virtual keyboard for Wayland and X11 +display servers. It supports many different languages and emoji.") + (license license:gpl3+))) + (define-public xdg-utils (package (name "xdg-utils") From d15b931948184b967cb2882082ce587410e35bb5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 10 Aug 2022 00:39:14 +0200 Subject: [PATCH 101/824] gnu: Add kitinerary. * gnu/packages/kde-pim.scm (kitinerary): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 49 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 3cfd338a4e..90d124a053 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -22,6 +22,7 @@ (define-module (gnu packages kde-pim) #:use-module (guix build-system qt) + #:use-module (guix gexp) #:use-module (guix download) #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) @@ -29,6 +30,7 @@ #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) + #:use-module (gnu packages compression) #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages databases) #:use-module (gnu packages documentation) @@ -38,10 +40,12 @@ #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages openldap) + #:use-module (gnu packages pdf) #:use-module (gnu packages pkg-config) #:use-module (gnu packages qt) #:use-module (gnu packages search) #:use-module (gnu packages sqlite) + #:use-module (gnu packages tls) #:use-module (gnu packages xml)) (define-public akonadi @@ -890,6 +894,51 @@ easier to do so.") (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0+)))) +(define-public kitinerary + (package + (name "kitinerary") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://invent.kde.org/pim/kitinerary/-/archive/v" + version "/kitinerary-v" version ".tar.gz")) + (sha256 + (base32 + "1gpy5siaw9k4332ii6a87rq162dbmyfkqp1l1k8bmldg1755v3jz")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest" "-E" + "(jsonlddocumenttest|mergeutiltest|locationutiltest|knowledgedbtest|airportdbtest|extractorscriptenginetest|pkpassextractortest|postprocessortest|calendarhandlertest|extractortest)"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list kpkpass + kcalendarcore + karchive + ki18n + kcoreaddons + kcontacts + kmime + knotifications + shared-mime-info + openssl + poppler + qtbase-5 + qtdeclarative-5 + qtlocation + qtquickcontrols2-5 + libxml2 + zlib)) + (home-page "https://apps.kde.org/itinerary/") + (synopsis + "Data Model and Extraction System for Travel Reservation information") + (description "This package provides a library containing itinerary data +model and itinerary extraction code.") + (license license:lgpl2.0))) + (define-public kldap (package (name "kldap") From 4b39a8a55ffddfd069055d6a9c78ea7edbff9d44 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 10 Aug 2022 01:18:23 +0200 Subject: [PATCH 102/824] gnu: Add plasmatube. * gnu/packages/kde-plasma.scm (plasmatube): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 27eaf735c5..480f946aa8 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages video) #:use-module (gnu packages qt) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) @@ -625,3 +626,32 @@ KDE Frameworks components.") (description "This package provides a daemon that listens to system notifications.") (license license:gpl2+))) + +(define-public plasmatube + (package + (name "plasmatube") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + version "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "00w9p5fcpv4s406lmcdcbrxf19sgkvf9yy8pfjmf1asvvvi8bpnk")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs + (list kconfig + kirigami + ki18n + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtquickcontrols2-5 + qtsvg-5 + youtube-dl)) + (home-page "https://apps.kde.org/plasmatube/") + (synopsis "Kirigami YouTube video player") + (description "This package provides YouTube video player based +on QtMultimedia and @command{yt-dlp}.") + (license license:gpl3+))) From 3cdecf5f5e313f521e7770ca6a697baec0772eb4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Wed, 10 Aug 2022 01:20:21 +0200 Subject: [PATCH 103/824] gnu: Add latte-dock. * gnu/packages/kde-plasma.scm (latte-dock): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 42 +++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 480f946aa8..d0a12f88ac 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -290,6 +290,48 @@ directly, you need to tell @code{ssh-add} about it. @code{ssh-add} will then call it if it is not associated to a terminal.") (license license:gpl2+))) +(define-public latte-dock + (package + (name "latte-dock") + (version "0.10.8") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/latte-dock/" + "latte-dock-" version ".tar.xz")) + (sha256 + (base32 + "0ali9i0y0y1c5mdaps5ybhk4nqvzzs5jq27wj8rg8xxqjyfvbah0")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list qtbase-5 + qtdeclarative-5 + knotifications + kwindowsystem + kio + plasma-framework + kwayland + kactivities + kcrash + kiconthemes + knewstuff + karchive + kguiaddons + kdbusaddons + kglobalaccel + kirigami + ki18n + kdeclarative + kcoreaddons + xcb-util + qtx11extras + libsm)) + (synopsis "Latte is a dock based on plasma frameworks") + (description + "Latte is a dock based on plasma frameworks that provides +an elegant and intuitive experience for your tasks and plasmoids.") + (home-page "https://github.com/KDE/latte-dock") + (license license:gpl2+))) + (define-public layer-shell-qt (package (name "layer-shell-qt") From 4bc8c1ec9dccd5f9d36edea6a38422ff83148d8b Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 10:29:15 +0200 Subject: [PATCH 104/824] gnu: Add oxygen-sounds. * gnu/packages/kde-plasma.scm (oxygen-sounds): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index d0a12f88ac..87c6e7d87a 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -669,6 +669,25 @@ KDE Frameworks components.") "This package provides a daemon that listens to system notifications.") (license license:gpl2+))) +(define-public oxygen-sounds + (package + (name "oxygen-sounds") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "04rn3ccqszznknvblz2i8r406m32hk4d3yzma4vzq93jfk57hdf1")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Sounds for the KDE desktop") + (description "This package provides Oxygen sounds for the KDE desktop.") + (license license:lgpl3+))) + (define-public plasmatube (package (name "plasmatube") From b2a2f566aaed47eb61035c625bdfb3886f91c84d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 12:55:28 +0200 Subject: [PATCH 105/824] gnu: Add wacomtablet. * gnu/packages/kde-utils.scm (wacomtablet): New variable. Signed-off-by: Marius Bakke --- gnu/local.mk | 2 + gnu/packages/kde-utils.scm | 47 +++++++++++++++++++ .../wacomtablet-add-missing-includes.patch | 11 +++++ gnu/packages/patches/wacomtablet-qt5.15.patch | 23 +++++++++ 4 files changed, 83 insertions(+) create mode 100644 gnu/packages/patches/wacomtablet-add-missing-includes.patch create mode 100644 gnu/packages/patches/wacomtablet-qt5.15.patch diff --git a/gnu/local.mk b/gnu/local.mk index 6bccbc2dc4..68ea09cb91 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1990,6 +1990,8 @@ dist_patch_DATA = \ %D%/packages/patches/vtk-7-gcc-10-compat.patch \ %D%/packages/patches/vtk-7-hdf5-compat.patch \ %D%/packages/patches/vtk-7-python-compat.patch \ + %D%/packages/patches/wacomtablet-add-missing-includes.patch \ + %D%/packages/patches/wacomtablet-qt5.15.patch \ %D%/packages/patches/warsow-qfusion-fix-bool-return-type.patch \ %D%/packages/patches/webkitgtk-adjust-bubblewrap-paths.patch \ %D%/packages/patches/webrtc-audio-processing-big-endian.patch \ diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index b2295d184a..2d051c74f6 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -22,6 +22,7 @@ (define-module (gnu packages kde-utils) #:use-module (guix build-system qt) + #:use-module (guix gexp) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -30,6 +31,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages glib) ; dbus for tests #:use-module (gnu packages gnome) #:use-module (gnu packages imagemagick) #:use-module (gnu packages pkg-config) @@ -38,6 +40,7 @@ #:use-module (gnu packages kde-plasma) #:use-module (gnu packages qt) #:use-module (gnu packages samba) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg)) (define-public ark @@ -180,6 +183,50 @@ Kate's features include: (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0)))) +(define-public wacomtablet + (package + (name "wacomtablet") + (version "3.2.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" + name "/" version "/" + name "-" version ".tar.xz")) + (patches (search-patches + "wacomtablet-add-missing-includes.patch" + "wacomtablet-qt5.15.patch")) + (sha256 + (base32 + "197pwpl87gqlnza36bp68jvw8ww25znk08acmi8bpz7n84xfc368")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest" "-E" + "(Test.KDED.DBusTabletService|Test.KDED.TabletHandler|Test.KDED.XInputAdaptor|Test.KDED.XsetWacomAdaptor)"))))))) + (native-inputs (list dbus extra-cmake-modules kdoctools pkg-config)) + (inputs (list kcoreaddons + ki18n + kglobalaccel + kconfig + kxmlgui + kwidgetsaddons + kwindowsystem + knotifications + kdbusaddons + qtx11extras + qtdeclarative-5 + libwacom + xf86-input-wacom + libxi)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/system/wacomtablet") + (synopsis "KDE GUI for the Wacom Linux Drivers") + (description "Provides KDE GUI for the Wacom Linux Drivers.") + (license license:gpl2+))) + (define-public kmag (package (name "kmag") diff --git a/gnu/packages/patches/wacomtablet-add-missing-includes.patch b/gnu/packages/patches/wacomtablet-add-missing-includes.patch new file mode 100644 index 0000000000..cd93938075 --- /dev/null +++ b/gnu/packages/patches/wacomtablet-add-missing-includes.patch @@ -0,0 +1,11 @@ +diff -rup wacomtablet-3.1.0/src/kcmodule/styluspagewidget.cpp wacomtablet-3.1.0.new/src/kcmodule/styluspagewidget.cpp +--- wacomtablet-3.1.0/src/kcmodule/styluspagewidget.cpp 2018-06-22 15:07:58.000000000 +0200 ++++ wacomtablet-3.1.0.new/src/kcmodule/styluspagewidget.cpp 2018-07-10 17:38:09.239242847 +0200 +@@ -25,6 +25,7 @@ + #include "profilemanagement.h" + + // common includes ++#include "logging.h" + #include "property.h" + #include "deviceprofile.h" + #include "dbustabletinterface.h" diff --git a/gnu/packages/patches/wacomtablet-qt5.15.patch b/gnu/packages/patches/wacomtablet-qt5.15.patch new file mode 100644 index 0000000000..598ac939e8 --- /dev/null +++ b/gnu/packages/patches/wacomtablet-qt5.15.patch @@ -0,0 +1,23 @@ +From 4f73ff02b3efd5e8728b18fcf1067eca166704ee Mon Sep 17 00:00:00 2001 +From: Christophe Giboudeaux +Date: Thu, 4 Jun 2020 16:00:38 +0200 +Subject: [PATCH] Fix build with Qt 5.15 + +--- + src/kcmodule/pressurecurvewidget.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/kcmodule/pressurecurvewidget.cpp b/src/kcmodule/pressurecurvewidget.cpp +index 0c943b3..f047a6c 100644 +--- a/src/kcmodule/pressurecurvewidget.cpp ++++ b/src/kcmodule/pressurecurvewidget.cpp +@@ -22,6 +22,7 @@ + //Qt includes + #include + #include ++#include + #include + #include + #include +-- +GitLab From 2ee129f46c2478099c2edc41e13427088d41f9c0 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 15:28:01 +0200 Subject: [PATCH 106/824] gnu: Add plasma-vault. * gnu/packages/kde-plasma.scm (plasma-vault): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 87c6e7d87a..84633e9a86 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -716,3 +716,33 @@ KDE Frameworks components.") (description "This package provides YouTube video player based on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) + +(define-public plasma-vault + (package + (name "plasma-vault") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "15nf4myl6sry0930m8qiixpr1i8bh1g58cy2gf304h029vr2fn5j")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kio + ki18n + kconfigwidgets + kconfig + kactivities + kdbusaddons + kiconthemes + networkmanager-qt + libksysguard + plasma-framework + qtdeclarative-5)) + (home-page "https://invent.kde.org/plasma/plasma-vault") + (synopsis "Plasma applet and services for creating encrypted vaults") + (description "Provides Plasma applet and services for creating encrypted + vaults.") + (license (list license:gpl2 license:gpl3)))) From 05499412f56e7e5c16aa89313a65e357c3ca0ed5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 15:42:30 +0200 Subject: [PATCH 107/824] gnu: Add plasma-pass. * gnu/packages/kde-plasma.scm (plasma-pass): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 84633e9a86..18ffaec6cb 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -33,6 +33,8 @@ #:use-module (gnu packages admin) #:use-module (gnu packages bash) #:use-module (gnu packages boost) + #:use-module (gnu packages authentication) + #:use-module (gnu packages bash) #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) @@ -717,6 +719,27 @@ KDE Frameworks components.") on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) +(define-public plasma-pass + (package + (name "plasma-pass") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "107pd6cnkd46px83pm3q7vbw10g5pd0qsw77jmr0c774k4xv1w01")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n kitemmodels kwindowsystem oath-toolkit qtdeclarative-5)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/plasma/plasma-pass") + (synopsis "Plasma applet for the Pass password manager") + (description + "This package provides a Plasma applet for the Pass password manager.") + (license license:lgpl2.1+))) + (define-public plasma-vault (package (name "plasma-vault") From 848cd9950c2e85d4624de0d9fc854193ea300d72 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 20:13:56 +0200 Subject: [PATCH 108/824] gnu: Add plasma-nm. * gnu/packages/kde-plasma.scm (plasma-nm): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 51 +++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 18ffaec6cb..0bfbae8f5f 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -38,12 +38,15 @@ #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) + #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages video) + #:use-module (gnu packages vpn) #:use-module (gnu packages qt) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) @@ -719,6 +722,54 @@ KDE Frameworks components.") on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) +(define-public plasma-nm + (package + (name "plasma-nm") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "036bx0qjrjanfxy8aiy6ab7rmm2h8l7wlkvlwhzw2hgl1w03xjps")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "mobileproviderstest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (home-page "https://invent.kde.org/plasma/plasma-nm") + (inputs (list kconfigwidgets + kcompletion + kcoreaddons + kdeclarative + kdbusaddons + kio + ki18n + networkmanager-qt + knotifications + kirigami + plasma-framework + modemmanager-qt + network-manager + qca + kservice + solid + prison + kwallet + kwidgetsaddons + kwindowsystem + openconnect + qtdeclarative-5)) + (synopsis "Plasma applet for managing network connections") + (description "This package provides Plasma applet for managing network +connections.") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public plasma-pass (package (name "plasma-pass") From 7c4eaf02fc9dfff9585fed320860071486771f33 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 20:14:58 +0200 Subject: [PATCH 109/824] gnu: Add plasma-integration. * gnu/packages/kde-plasma.scm (plasma-integration): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 50 +++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 0bfbae8f5f..310642f7a1 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -722,6 +722,56 @@ KDE Frameworks components.") on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) +(define-public plasma-integration + (package + (name "plasma-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "1pab56cg2zi8fcaar53lhhh98iw7l07f5lkymkqhsh8a5crfc3yr")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;TODO: Failing tests + #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(frameworkintegration-kdeplatformtheme_unittest|frameworkintegration-kfontsettingsdata_unittest|frameworkintegration-kfiledialog_unittest|qmltests|frameworkintegration-kfiledialogqml_unittest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list breeze + kconfig + kio + ki18n + kwidgetsaddons + kconfigwidgets + kiconthemes + knotifications + libxcb + libxcursor + plasma-wayland-protocols + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland-5 + qtx11extras + wayland)) + (home-page "https://invent.kde.org/plasma/plasma-integration") + (synopsis + "Qt Platform Theme integration plugins for the Plasma workspaces") + (description + "This package provides a set of plugins responsible for better +integration of Qt applications when running on a KDE Plasma workspace.") + (license license:lgpl2.0))) + (define-public plasma-nm (package (name "plasma-nm") From eb1ec3b9cb31f7b14cccb117ac27017a16a63da4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 20:33:15 +0200 Subject: [PATCH 110/824] gnu: Add plasma-pa. * gnu/packages/kde-plasma.scm (plasma-pa): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 310642f7a1..b8e9210431 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -42,8 +42,10 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) + #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages video) #:use-module (gnu packages vpn) @@ -820,6 +822,37 @@ integration of Qt applications when running on a KDE Plasma workspace.") connections.") (license (list license:lgpl2.1 license:lgpl3)))) +(define-public plasma-pa + (package + (name "plasma-pa") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0g06pm1isnzx4hv6380rjpyr22s4j5iw9083s71vnl4npx28npvb")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools pkg-config)) + (inputs (list glib + kcoreaddons + kdeclarative + kglobalaccel + knotifications + kwindowsystem + kirigami + ki18n + qtdeclarative-5)) + (propagated-inputs (list libcanberra pulseaudio plasma-framework)) + (home-page "https://invent.kde.org/plasma/plasma-pa") + (synopsis "Plasma applet for audio volume management using PulseAudio") + (description + "This package provides Plasma applet for audio volume management using +PulseAudio.") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public plasma-pass (package (name "plasma-pass") From d113630f98c70e937e89f0b927756b11ea11c057 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:07:54 +0200 Subject: [PATCH 111/824] gnu: Add plasma-disks. * gnu/packages/kde-plasma.scm (plasma-disks): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index b8e9210431..8ee5999211 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -724,6 +724,35 @@ KDE Frameworks components.") on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) +(define-public plasma-disks + (package + (name "plasma-disks") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0vci2cf8vx2lclypys9rmvjb8haakv6ksrvqm5j28pazbq2kskvl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + kdbusaddons + knotifications + ki18n + solid + kservice + kio + kauth + kdeclarative + smartmontools)) + (synopsis "Monitors S.M.A.R.T. capable devices for imminent failure") + (description "This package provides interface to S.M.A.R.T. data of disks.") + (home-page "https://invent.kde.org/plasma/plasma-disks") + (license (list license:gpl2 license:gpl3)))) + (define-public plasma-integration (package (name "plasma-integration") From 4646bc2f59ba5fcd2918370ddaa8e81c8ecebaf0 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:13:24 +0200 Subject: [PATCH 112/824] gnu: Add plasma-firewall. * gnu/packages/kde-plasma.scm (plasma-firewall): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 8ee5999211..4496eab31c 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -753,6 +753,32 @@ on QtMultimedia and @command{yt-dlp}.") (home-page "https://invent.kde.org/plasma/plasma-disks") (license (list license:gpl2 license:gpl3)))) +(define-public plasma-firewall + (package + (name "plasma-firewall") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0k3pc0dcsjr2hhh4hr8vhsvaddn66s6imm8skrr02icxqvljs6jh")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list iproute + kcoreaddons + kcmutils + ki18n + kdeclarative + python + qtdeclarative-5)) + (synopsis "Control Panel for system firewall") + (description "This package provides interface to system firewall.") + (home-page "https://invent.kde.org/plasma/plasma-firewall") + (license (list license:gpl2 license:gpl3)))) + (define-public plasma-integration (package (name "plasma-integration") From c3358f9bc5c8b1607630915a129fc1ca3deefdb3 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 21:36:25 +0200 Subject: [PATCH 113/824] gnu: Add plasma-active-window-control. * gnu/packages/kde-plasma.scm (plasma-active-window-control): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 4496eab31c..073b4f972e 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -26,6 +26,7 @@ (define-module (gnu packages kde-plasma) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix gexp) #:use-module (guix build-system cmake) @@ -724,6 +725,35 @@ KDE Frameworks components.") on QtMultimedia and @command{yt-dlp}.") (license license:gpl3+))) +(define-public plasma-active-window-control +(let ((commit "0b1c091b5662fb21917064d7809b3be8b4a8be47") + (revision "1")) + (package + (name "plasma-active-window-control") + (version (git-version "1.7.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/plasma/plasma-active-window-control") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lns1n7p6b64z7l3bn27hni100pp3k2whzzzg0adr4hiynycdix6")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs + (list kwindowsystem + libsm + plasma-framework + qtdeclarative-5 + qtx11extras)) + (home-page "https://invent.kde.org/plasma/plasma-active-window-control") + (synopsis "Plasma applet for controlling the currently active window") + (description "This package provides window control applet for the current +active window on Plasma Desktop.") + (license (list license:gpl2 license:gpl3))))) + (define-public plasma-disks (package (name "plasma-disks") From f17f1e1f71fbc8b645f5ffe70600e4a51adb52b0 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 05:54:06 +0200 Subject: [PATCH 114/824] gnu: Add drkonqi. * gnu/packages/kde-plasma.scm (drkonqi): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 41 +++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 073b4f972e..20d2b27755 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -126,6 +126,47 @@ Breeze is the default theme for the KDE Plasma desktop.") (license (list license:bsd-3 ;cmake/FindSass.cmake license:lgpl2.1+)))) ; +(define-public drkonqi + (package + (name "drkonqi") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0vw4bfld2jdiwm4g3008x8s1lq1ydf87ckb0fvyzsp11hq9nnnk7")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "connectiontest"))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kcoreaddons + kconfig + kservice + kdeclarative + kjobwidgets + kio + kcrash + kcompletion + kwidgetsaddons + kwallet + knotifications + kidletime + kwindowsystem + ksyntaxhighlighting + qtdeclarative-5)) + (synopsis "Crash handler for KDE software") + (description "This package provides an automatic handler for crashed apps.") + (home-page "https://invent.kde.org/plasma/drkonqi") + (license license:gpl2+))) + (define-public kactivitymanagerd (package (name "kactivitymanagerd") From b2b88471d6c3ca08115d5e8079cccad2b7f92369 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 18 Sep 2022 10:39:18 +0200 Subject: [PATCH 115/824] gnu: packagekit: Remove input labels and use gexp. * gnu/packages/freedesktop.scm (pacakgekit): Remove input labels and use gexp. Signed-off-by: Marius Bakke --- gnu/packages/freedesktop.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 61d959e03f..6e496dbc99 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -995,16 +995,16 @@ with localed. This package is extracted from the broader systemd package.") "1dr1laic65ld95abp2yxbwvijnngh0dwyb1x49x4wjm5rhq43dl8")))) (build-system gnu-build-system) (arguments - `(#:tests? #f - #:make-flags (list (string-append "BASH_COMPLETIONS_DIR=" - %output "/etc/bash_completion.d")) - #:configure-flags - '("--disable-systemd"))) + (list #:tests? #f + #:make-flags + #~(list (string-append "BASH_COMPLETIONS_DIR=" + #$output "/etc/bash_completion.d")) + #:configure-flags #~'("--disable-systemd"))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("glib:bin" ,glib "bin"))) + (list intltool + pkg-config + python-wrapper + `(,glib "bin"))) (inputs (list glib bash-completion polkit)) (propagated-inputs From c707530c1fa4387ac1c6171ad89df89c080fd0ac Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 18 Sep 2022 10:45:18 +0200 Subject: [PATCH 116/824] gnu: packagekit: Update to 1.2.5. * gnu/packages/freedesktop.scm (packagekit): Update to 1.2.5. [build-system]: Use meson-build-system. [arguments]: Disable systemd. Fix xsl. [native-inputs]: Add docbook-xsl, gobject-introspection, libxml2, libxslt and vala. [inputs]: Add gstreamer, gst-plugins-base and gtk+. Co-authored-by: Marius Bakke --- gnu/packages/freedesktop.scm | 43 ++++++++++++++++++++---------------- 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 6e496dbc99..9a588b21a6 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -983,32 +983,37 @@ with localed. This package is extracted from the broader systemd package.") (define-public packagekit (package (name "packagekit") - (version "1.1.13") + (version "1.2.5") (source (origin - (method url-fetch) - (uri (string-append - "https://www.freedesktop.org/software/" - "PackageKit/releases/" - "PackageKit-" version ".tar.xz")) - (sha256 - (base32 - "1dr1laic65ld95abp2yxbwvijnngh0dwyb1x49x4wjm5rhq43dl8")))) - (build-system gnu-build-system) + (method url-fetch) + (uri (string-append "https://www.freedesktop.org/software/" + "PackageKit/releases/" "PackageKit-" version + ".tar.xz")) + (sha256 + (base32 + "09md23m4fw87x264mls1f5isrswk6iw7y9g4hr1nib008wbbk370")))) + (build-system meson-build-system) (arguments (list #:tests? #f - #:make-flags - #~(list (string-append "BASH_COMPLETIONS_DIR=" - #$output "/etc/bash_completion.d")) - #:configure-flags #~'("--disable-systemd"))) + #:configure-flags #~'("-Dsystemd=false" "-Doffline_update=false"))) (native-inputs - (list intltool + (list bash-completion + docbook-xsl + gettext-minimal + `(,glib "bin") + gobject-introspection + libxml2 ;for XML_CATALOG_FILES + libxslt pkg-config python-wrapper - `(,glib "bin"))) + vala)) (inputs - (list glib bash-completion polkit)) - (propagated-inputs - (list sqlite)) + (list glib + gstreamer + gst-plugins-base + gtk+ + polkit)) + (propagated-inputs (list sqlite)) (home-page "https://www.freedesktop.org/software/PackageKit/") (synopsis "API for package management, through D-Bus") (description From fc85a45aecd64556e1f3ec82e66de54665684933 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 12 Sep 2022 05:25:02 +0200 Subject: [PATCH 117/824] gnu: Add packagekit-qt5. * gnu/packages/qt.scm (packagekit-qt5): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index e6afbf4ac4..f37392f199 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -4374,6 +4374,30 @@ credentials and service-specific settings.") GLib applications.") (license license:lgpl2.1+))) +(define-public packagekit-qt5 + (package + (name "packagekit-qt5") + (version "1.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hughsie/PackageKit-Qt") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1d20r503msw1vix3nb6a8bmdqld7fj8k9jk33bkqsc610a2zsms6")))) + (build-system cmake-build-system) + (arguments '(#:tests? #f)) ;no test suite + (native-inputs (list pkg-config)) + (inputs (list packagekit qtbase-5)) + (home-page "https://www.freedesktop.org/software/PackageKit/pk-intro.html") + (synopsis "Qt5 bindings for PackageKit") + (description "Provides Qt5 bindings to PackageKit which is a DBUS +abstraction layer that allows the session user to manage packages in +a secure way.") + (license license:lgpl2.1+))) + (define-public signond (package (name "signond") From ebd651c32a8bf2f37e95f2ea63f9de715f3d0e83 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 4 Oct 2022 21:06:41 +0200 Subject: [PATCH 118/824] gnu: fwupd: Move some inputs to propagated-inputs. * gnu/packages/firmware.scm (fwupd)[propagated-inputs]: Move curl, gcab, glib, gusb, libarchive, gnutls, json-glib and libjcat here from inputs. Signed-off-by: Marius Bakke --- gnu/packages/firmware.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 696814cc71..d192671eec 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -259,19 +259,11 @@ driver.") help2man gettext-minimal)) (inputs (list bash-completion - glib libgudev libxmlb - gusb sqlite - libarchive - libjcat - json-glib - curl polkit eudev - gcab - gnutls libelf tpm2-tss cairo @@ -281,6 +273,15 @@ driver.") mingw-w64-tools libsmbios gnu-efi)) + ;; In Requires of fwupd*.pc. + (propagated-inputs (list curl + gcab + glib + gnutls + gusb + json-glib + libarchive + libjcat)) (home-page "https://fwupd.org/") (synopsis "Daemon to allow session software to update firmware") (description "This package aims to make updating firmware on GNU/Linux From c939f558552f7284be30ac461dca2497541363ca Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 06:12:31 +0200 Subject: [PATCH 119/824] gnu: Add discover. * gnu/packages/kde-plasma.scm (discover): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 86 +++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 20d2b27755..e67ee58970 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -37,6 +37,10 @@ #:use-module (gnu packages authentication) #:use-module (gnu packages bash) #:use-module (gnu packages compression) + #:use-module (gnu packages elf) ; patchelf + #:use-module (gnu packages display-managers) + #:use-module (gnu packages firmware) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) @@ -48,6 +52,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) + #:use-module (gnu packages package-management) ; flatpak #:use-module (gnu packages video) #:use-module (gnu packages vpn) #:use-module (gnu packages qt) @@ -126,6 +131,87 @@ Breeze is the default theme for the KDE Plasma desktop.") (license (list license:bsd-3 ;cmake/FindSass.cmake license:lgpl2.1+)))) ; +(define-public discover + (package + (name "discover") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version + "/" + name + "-" + version + ".tar.xz")) + (sha256 + (base32 + "01vdi66c7v60db25p0qi0q73wgqw6dy2kirbk34bvhld41gpxhhv")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'install 'fix-so + (lambda* _ + (invoke "patchelf" "--replace-needed" + "libDiscoverCommon.so" + (string-append #$output + "/lib/plasma-discover/libDiscoverCommon.so") + (string-append #$output + "/lib/qt5/plugins/discover/fwupd-backend.so")) + (invoke "patchelf" "--replace-needed" + "libDiscoverCommon.so" + (string-append #$output + "/lib/plasma-discover/libDiscoverCommon.so") + (string-append #$output + "/lib/qt5/plugins/discover/packagekit-backend.so")) + (invoke "patchelf" "--replace-needed" + "libDiscoverCommon.so" + (string-append #$output + "/lib/plasma-discover/libDiscoverCommon.so") + (string-append #$output + "/lib/qt5/plugins/discover/kns-backend.so")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "knsbackendtest"))))))) + (native-inputs (list extra-cmake-modules patchelf pkg-config)) + (inputs (list appstream-qt + attica + fwupd ; optional + flatpak ; optional + kcoreaddons + kconfig + kcrash + kdbusaddons + ki18n + karchive + kxmlgui + kirigami + kuserfeedback + knewstuff + knotifications + kio + kdeclarative + kcmutils + kidletime + packagekit-qt5 + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5)) + ;; -- The following features have been disabled: + ;; * Ostree, Library to manage ostree repository. Required to build the rpm-ostree backend + ;; * RpmOstree, rpm-ostree binary to manage the system. Required to build the rpm-ostree backend + ;; + ;; -- The following OPTIONAL packages have not been found: + ;; * Snapd, Library that exposes Snapd, + ;; Required to build the Snap backend + (synopsis "KDE and Plasma resources management GUI") + (description + "This package provides a way to find and install applications, +games, and tools.") + (home-page "https://invent.kde.org/plasma/discover") + (license (list license:gpl2 license:gpl3)))) + (define-public drkonqi (package (name "drkonqi") From 787fd473bef78d955cb735b1aa565b471bb4bb37 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 21 Nov 2022 15:25:38 +0100 Subject: [PATCH 120/824] gnu: discover: Don't use patchelf. * gnu/packages/kde-plasma.scm (discover)[arguments]: Add phase to set LDFLAGS instead of patching RUNPATH directly. [native-inputs]: Remove PATCHELF. --- gnu/packages/kde-plasma.scm | 38 +++++++++++-------------------------- 1 file changed, 11 insertions(+), 27 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index e67ee58970..6a87a67331 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -37,7 +37,6 @@ #:use-module (gnu packages authentication) #:use-module (gnu packages bash) #:use-module (gnu packages compression) - #:use-module (gnu packages elf) ; patchelf #:use-module (gnu packages display-managers) #:use-module (gnu packages firmware) #:use-module (gnu packages fontutils) @@ -149,32 +148,17 @@ Breeze is the default theme for the KDE Plasma desktop.") "01vdi66c7v60db25p0qi0q73wgqw6dy2kirbk34bvhld41gpxhhv")))) (build-system qt-build-system) (arguments - (list #:phases #~(modify-phases %standard-phases - (add-after 'install 'fix-so - (lambda* _ - (invoke "patchelf" "--replace-needed" - "libDiscoverCommon.so" - (string-append #$output - "/lib/plasma-discover/libDiscoverCommon.so") - (string-append #$output - "/lib/qt5/plugins/discover/fwupd-backend.so")) - (invoke "patchelf" "--replace-needed" - "libDiscoverCommon.so" - (string-append #$output - "/lib/plasma-discover/libDiscoverCommon.so") - (string-append #$output - "/lib/qt5/plugins/discover/packagekit-backend.so")) - (invoke "patchelf" "--replace-needed" - "libDiscoverCommon.so" - (string-append #$output - "/lib/plasma-discover/libDiscoverCommon.so") - (string-append #$output - "/lib/qt5/plugins/discover/kns-backend.so")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "ctest" "-E" "knsbackendtest"))))))) - (native-inputs (list extra-cmake-modules patchelf pkg-config)) + (list #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'set-LDFLAGS + (lambda _ + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" #$output + "/lib/plasma-discover")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "knsbackendtest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) (inputs (list appstream-qt attica fwupd ; optional From 9366402ef2dafd0aed865c86091d11a65d9b0c35 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 07:23:20 +0200 Subject: [PATCH 121/824] gnu: Add ksystemstats. * gnu/packages/kde-plasma.scm (ksystemstats): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 40 +++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 6a87a67331..860c54c98b 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -409,6 +409,46 @@ directly, you need to tell @code{ssh-add} about it. @code{ssh-add} will then call it if it is not associated to a terminal.") (license license:gpl2+))) +(define-public ksystemstats + (package + (name "ksystemstats") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "07xm6gn2k3vsl1pkrd2n9w8w8b7jq26h3cpslqha4ipw0by2mlqa")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "ksystemstatstest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list glib + kcoreaddons + kdbusaddons + solid + networkmanager-qt + kiconthemes + kio + ki18n + libksysguard + libnl + eudev + `(,lm-sensors "lib") + network-manager)) + (synopsis "Plugin based system monitoring daemon") + (description + "This package provides a daemon that collects statistics about +the running system.") + (home-page "https://invent.kde.org/plasma/ksystemstats") + (license (list license:gpl2 license:gpl3)))) + (define-public latte-dock (package (name "latte-dock") From 10dad3a1fd5ff07abfe67fb066b48cf8e0e281d5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 07:30:45 +0200 Subject: [PATCH 122/824] gnu: Add kwallet-pam. * gnu/packages/kde-plasma.scm (kwallet-pam): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 860c54c98b..234045ea85 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -41,6 +41,8 @@ #:use-module (gnu packages firmware) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gnupg) + #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) @@ -48,6 +50,7 @@ #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) + #:use-module (gnu packages networking) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) @@ -713,6 +716,29 @@ manage running processes. It obtains this information by interacting with a ksysguardd daemon, which may also run on a remote system.") (license license:gpl3+))) +(define-public kwallet-pam + (package + (name "kwallet-pam") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "14w803lc3s2c0f4mqzzdhpfy5qnlz7wv00pbrc3v4k3zv381ci8n")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f)) ;no tests + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list linux-pam kwallet libgcrypt socat)) + (synopsis "PAM Integration with KWallet") + (description "Provide PAM Integration with KWallet to unlock KWallet when +you login.") + (home-page "https://invent.kde.org/plasma/kwallet-pam") + (license (list license:lgpl2.1+)))) + (define-public kwayland-server (package (name "kwayland-server") From c106297111b67ad99ee71c2d10d791697355310f Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:01:45 +0200 Subject: [PATCH 123/824] gnu: Add milou. * gnu/packages/kde-plasma.scm (milou): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 234045ea85..853a3cce07 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -854,6 +854,35 @@ KDE Frameworks components.") "This package provides a daemon that listens to system notifications.") (license license:gpl2+))) +(define-public milou + (package + (name "milou") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0ijdbiq169sy47g0x22pj9x6abldpfxcnski4w1jh9hi9qz1rc25")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + ki18n + kdeclarative + kitemmodels + kservice + plasma-framework + kwindowsystem + krunner + qtdeclarative-5)) + (synopsis "Dedicated search application built on top of Baloo") + (description "This package provides a dedicated search application built +on top of Baloo.") + (home-page "https://invent.kde.org/plasma/milou") + (license (list license:gpl2+)))) + (define-public oxygen-sounds (package (name "oxygen-sounds") From 75e34ecc24170d087ea011d2038f7395117aa5b8 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:27:35 +0200 Subject: [PATCH 124/824] gnu: Add plasma-systemmonitor. * gnu/packages/kde-plasma.scm (plasma-systemmonitor): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 853a3cce07..20ebd9f3a9 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1194,3 +1194,38 @@ PulseAudio.") (description "Provides Plasma applet and services for creating encrypted vaults.") (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-systemmonitor + (package + (name "plasma-systemmonitor") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0rs3avhpmfapzha8dkir9ny60ba2m92bbfv4avsd85vz5kggg29h")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kconfig + kdeclarative + kservice + kiconthemes + kglobalaccel + kio + kdbusaddons + kirigami + knewstuff + ksystemstats + kitemmodels + libksysguard + qtdeclarative-5 + qtquickcontrols2-5)) + (synopsis "System sensors, process information and other system resources +monitor") + (description "This package provides an interface for monitoring system +sensors, process information and other system resources.") + (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") + (license (list license:gpl2 license:gpl3)))) From 5a6833113b633267197f8a39c8932aab7954681c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 08:51:18 +0200 Subject: [PATCH 125/824] gnu: Add polkit-kde-agent. * gnu/packages/kde-plasma.scm (polkit-kde-agent): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 20ebd9f3a9..4fc347b967 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -52,6 +52,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages networking) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages polkit) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages package-management) ; flatpak @@ -1229,3 +1230,31 @@ monitor") sensors, process information and other system resources.") (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") (license (list license:gpl2 license:gpl3)))) + +(define-public polkit-kde-agent + (package + (name "polkit-kde-agent") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-1-" version ".tar.xz")) + (sha256 + (base32 + "1qb9nxlkgcv0c30l2vqgf9xs9d220q5pg7ikpb6zjzvj4wsvlvwd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kwindowsystem + kdbusaddons + kwidgetsaddons + kcoreaddons + kcrash + kiconthemes + polkit-qt)) + (synopsis "Polkit authentication UI for Plasma") + (description + "This package contains a daemon providing a Polkit authentication +UI for Plasma") + (home-page "https://invent.kde.org/plasma/polkit-kde-agent-1") + (license license:gpl2+))) From 4cb6ef78dc23a352b965e505afeec2c6626737ee Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 09:58:25 +0200 Subject: [PATCH 126/824] gnu: Add xdg-desktop-portal-kde. * gnu/packages/freedesktop.scm (xdg-desktop-portal-kde): New variable. Signed-off-by: Marius Bakke --- gnu/packages/freedesktop.scm | 38 ++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 9a588b21a6..3a4fee5e20 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -61,6 +61,7 @@ #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix build-system glib-or-gtk) + #:use-module (guix build-system qt) #:use-module (gnu packages) #:use-module (gnu packages acl) #:use-module (gnu packages admin) @@ -73,6 +74,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cryptsetup) + #:use-module (gnu packages cups) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages disk) @@ -2665,6 +2667,42 @@ which uses GTK+ and various pieces of GNOME infrastructure, such as the interfaces.") (license license:lgpl2.1+))) +(define-public xdg-desktop-portal-kde + (package + (name "xdg-desktop-portal-kde") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0l3lmwihxyl65y0mkyg3afk1k6gc0ldjw2vg92g7yydbgmn39q7k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list cups + kcoreaddons + kconfig + ki18n + kdeclarative + kio + kirigami + knotifications + plasma-framework + plasma-wayland-protocols + kwayland + kwidgetsaddons + kwindowsystem + kiconthemes + qtdeclarative-5 + qtwayland-5 + wayland)) + (synopsis "Backend implementation for xdg-desktop-portal using Qt/KF5") + (description "This package provides a backend implementation +for xdg-desktop-portal that is using Qt/KF5.") + (home-page "https://invent.kde.org/plasma/xdg-desktop-portal-kde") + (license license:lgpl2.0+))) + (define-public xdg-desktop-portal-wlr (package (name "xdg-desktop-portal-wlr") From eba5097c07d755db258868586955636a5af57cb5 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 29 Aug 2022 15:05:21 +0200 Subject: [PATCH 127/824] gnu: Add calindori. * gnu/packages/kde-plasma.scm (kde-plasma): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 4fc347b967..596da55942 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -134,6 +134,38 @@ Breeze is the default theme for the KDE Plasma desktop.") (license (list license:bsd-3 ;cmake/FindSass.cmake license:lgpl2.1+)))) ; +(define-public calindori + (package + (name "calindori") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/calindori-" version ".tar.xz")) + (sha256 + (base32 + "1pwgdqznp76mhk0ikzjhy3c67qgk91kgv69ygqwzlh5hwiw5sl4n")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kconfig + kcoreaddons + kdbusaddons + ki18n + kirigami + kcalendarcore + knotifications + kpeople + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5 + qtgraphicaleffects)) + (home-page "https://invent.kde.org/plasma-mobile/calindori") + (synopsis "Calendar for Plasma Mobile") + (description + "This package provides a touch friendly calendar application.") + (license license:gpl3+))) + (define-public discover (package (name "discover") From 83f7a0b114bf2c8a3c160f9997e23773f7b28c8c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 2 Oct 2022 23:57:12 +0200 Subject: [PATCH 128/824] gnu: Add libqaccessibilityclient. * gnu/packages/kde.scm (libqaccessibilityclient): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 422e85a553..5669588b9c 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -678,6 +678,41 @@ the generated @file{massif.out.%pid} in the visualizer. Gzip or Bzip2 compressed massif files can also be opened transparently.") (license license:gpl2+))) +(define-public libqaccessibilityclient + (package + (name "libqaccessibilityclient") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name + "/libqaccessibilityclient-" version + ".tar.xz")) + (sha256 + (base32 + "0a9lv2jb5gyqxvrkl5xl09gjnlp05b5yfzfb0wmaxz0l8d7qnxhw")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;TODO: Failing tests + #:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ; + ;; make Qt render "offscreen", required for tests + (setenv "QT_QPA_PLATFORM" "offscreen") + ;; For missing '/etc/machine-id' + (setenv "DBUS_FATAL_WARNINGS" "0") + (setenv "HOME" + (getcwd)) + (invoke "dbus-launch" "ctest"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list qtbase-5)) + (home-page "https://invent.kde.org/libraries/libqaccessibilityclient") + (synopsis "Helper library to make writing accessibility tools easier") + (description "This package provides library that is used when writing +accessibility clients such as screen readers.") + (license license:lgpl2.1+))) + (define-public libkomparediff2 (package (name "libkomparediff2") From 62bb071355edf6e09455524da850dfac323fcf94 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 05:43:16 +0200 Subject: [PATCH 129/824] gnu: Add bluedevil. * gnu/packages/kde-plasma.scm (bluedevil): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 596da55942..7aa30198f5 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -63,6 +63,37 @@ #:use-module (gnu packages xorg) #:use-module (gnu packages web)) +(define-public bluedevil + (package + (name "bluedevil") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1dsah7rcx2brcd1d5x7bvhrixx5nvwp1fwq9b8k2zc038xzpx6ys")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools-5)) + (inputs (list kcoreaddons + kwidgetsaddons + kdbusaddons + knotifications + kwindowsystem + plasma-framework + ki18n + kio + kdeclarative + bluez-qt + shared-mime-info + qtdeclarative-5)) + (synopsis "Manage the Bluetooth settings from Plasma") + (description + "This package provides Bluetooth manager for Plasma Shell.") + (home-page "https://invent.kde.org/plasma/bluedevil") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public breeze (package (name "breeze") From fa5bf49f822f922537a6ffc9819c060a27984e7a Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Tue, 8 Feb 2022 17:03:20 +1100 Subject: [PATCH 130/824] gnu: Add kwin. * gnu/packages/kde-plasma.scm (kwin): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 146 ++++++++++++++++++++++++++++++++++++ 1 file changed, 146 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 7aa30198f5..17609a1dbc 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages firmware) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages gnupg) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -51,6 +52,7 @@ #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) #:use-module (gnu packages networking) + #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) #:use-module (gnu packages polkit) #:use-module (gnu packages pulseaudio) @@ -897,6 +899,150 @@ KDE Frameworks components.") (home-page "https://invent.kde.org/plasma/kwayland-integration") (license (list license:lgpl2.1 license:lgpl3)))) +(define-public kwin + (package + (name "kwin") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1dh7ydwxbb9r53p353d53gq7w9vmp7idvsr4s5ldxmah35436v2s")))) + (build-system qt-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/plugins/kdecorations/aurorae/src/aurorae.cpp") + (("(^\\s*QDirIterator it.path, QDirIterator::Subdirectories)(\\);)" + _ a b) + (string-append a + " | QDirIterator::FollowSymlinks" b))) + (substitute* + '("autotests/integration/dont_crash_glxgears.cpp" + "autotests/integration/debug_console_test.cpp" + "autotests/integration/x11_window_test.cpp") + (("setProgram\\(QStringLiteral\\(\"glxgears\"\\)") + (string-append + "setProgram(QByteArrayLiteral(\"" (which "glxgears") "\")"))) + (substitute* + '("src/wayland/tests/renderingservertest.cpp" + "src/wayland/tests/waylandservertest.cpp") + (("QByteArrayLiteral\\(\"Xwayland\"\\)") + (string-append + "QByteArrayLiteral(\"" (which "Xwayland") "\")"))) + (substitute* '("src/xwayland/xwaylandlauncher.cpp") + (("(m_xwaylandProcess->setProgram.QStringLiteral..)(Xwayland)(...;)" + _ a Xwayland b) + (string-append a + (which "Xwayland") b))) + (substitute* '("cmake/modules/Findhwdata.cmake") + (("/usr/share") + (string-append #$hwdata:pnp "/share"))))) + (add-after 'install 'add-symlinks + (lambda* (#:key outputs #:allow-other-keys) + (let ((kst5 (string-append #$output + "/share/kservicetypes5/"))) + (symlink (string-append kst5 "kwineffect.desktop") + (string-append kst5 "kwin-effect.desktop")) + (symlink (string-append kst5 "kwinscript.desktop") + (string-append kst5 "kwin-script.desktop"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "HOME" (getcwd)) + (setenv "XDG_DATA_DIRS" + (string-append #$output "/share:" + (getenv "XDG_DATA_DIRS"))) + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH"))) + (setenv "DISPLAY" ":1") + (system "Xvfb :1 &") + (sleep 5) + (invoke "ctest" "-E" + "(kwayland-testXdgDecoration|kwin-testLockScreen|kwin-testPointerInput|kwin-testXdgShellWindow|kwin-testXdgShellWindow-waylandonly|kwin-testSceneOpenGLES|kwin-testSceneOpenGLES-waylandonly|kwin-testInputMethod|kwin-testInputMethod-waylandonly|kwin-testNightColor|kwin-testNightColor-waylandonly|kwin-testPlasmaWindow|kwin-testSceneQPainter|kwin-testLibinputDevice)"))))))) + (native-inputs (list extra-cmake-modules + dbus + kdoctools + mesa-utils + pkg-config + qttools-5 + wayland-protocols-next + xorg-server-for-tests)) + (inputs (list breeze + eudev + fontconfig + freetype + `(,hwdata "pnp") + kactivities + kcmutils + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kdecoration + kglobalaccel + ki18n + kiconthemes + kidletime + kio + kirigami + knewstuff + knotifications + kpackage + krunner + kscreenlocker + ktextwidgets + kwayland + kwayland-server + kwindowsystem + kxmlgui + libqaccessibilityclient + lcms + libcap + libepoxy + libglvnd ; For OpenGLES + libinput + libxkbcommon + pipewire-0.3 + plasma-framework + plasma-wayland-protocols + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtwayland-5 + qtx11extras + wayland + xcb-util ;fails at build time without this + xcb-util-cursor + xcb-util-keysyms + xcb-util-wm + xcmsdb + xinput ;XXX: Says disabled in configure phase + xorg-server-xwayland + zlib)) + ;; Runtime-only dependency needed for mapping monitor hardware vendor IDs to full names + ;; * QtQuick.Controls-QMLModule, QML module 'QtQuick.Controls' is a runtime dependency. + ;; * org.kde.plasma.core-QMLModule, QML module 'org.kde.plasma.core' is a runtime dependency. + ;; * org.kde.plasma.components-QMLModule, QML module 'org.kde.plasma.components' is a runtime dependency. + (home-page "https://userbase.kde.org/KWin") + (synopsis "KDE Plasma Window Manager") + (description + "KWin is an easy to use, but flexible, composited Window Manager for +Xorg windowing systems (Wayland, X11) on Linux. Its primary usage is in +conjunction with the KDE Plasma Desktop.") + (license license:gpl2+))) + (define-public kwrited (package (name "kwrited") From dbe5ede0a6bb579f590ed13ae3f8c4a55265b43f Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 10:39:35 +0200 Subject: [PATCH 131/824] gnu: Add plasma-workspace-wallpapers. * gnu/packages/kde-plasma.scm (plasma-workspace-wallpapers): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 17609a1dbc..fdcbc2af29 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1440,6 +1440,25 @@ sensors, process information and other system resources.") (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") (license (list license:gpl2 license:gpl3)))) +(define-public plasma-workspace-wallpapers + (package + (name "plasma-workspace-wallpapers") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0pdgg8h6zwyxf1pj241mg3hd94wh38bqxj68af5jfp10xrwkzcyr")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Oxygen wallpapers for the KDE desktop") + (description + "This package provides wallpapers for the KDE desktop.") + (license license:lgpl3+))) + (define-public polkit-kde-agent (package (name "polkit-kde-agent") From 8f877c2c4b619c6f4d7ae670d7eb40744dda7229 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 28 Aug 2022 23:11:00 +0200 Subject: [PATCH 132/824] gnu: Add appmenu-gtk-module. * gnu/packages/gtk.scm (appmenu-gtk-menu): New variable. Co-authored-by: Marius Bakke --- gnu/packages/gtk.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 56104b2124..ad34dd51ec 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2022 Zhu Zihao ;;; Copyright © 2022 Benjamin Slade ;;; Copyright © 2022 Denis 'GNUtoo' Carikli +;;; Copyright © 2022 Petr Hodina ;;; ;;; This file is part of GNU Guix. ;;; @@ -117,6 +118,43 @@ #:use-module (srfi srfi-26) #:use-module (ice-9 match)) +(define-public appmenu-gtk-module + (package + (name "appmenu-gtk-module") + (version "0.7.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/vala-panel-project/vala-panel-appmenu") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ywpygjwlbli65203ja2f8wwxh5gbavnfwcxwg25v061pcljaqmm")))) + (build-system meson-build-system) + (arguments + (list + #:glib-or-gtk? #t + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-install-gtk-module + (lambda* _ + (substitute* + "subprojects/appmenu-gtk-module/src/gtk-3.0/meson.build" + (("gtk3.get_pkgconfig_variable\\('libdir'\\)") + #$output))))))) + (native-inputs + (list `(,glib "bin") vala pkg-config)) + (inputs + (list gtk+ libwnck)) + (synopsis "Application Menu applet") + (description + "This package provides a global menu applet for use with desktop panels +such as mate-panel and xfce4-panel.") + (home-page "https://gitlab.com/vala-panel-project/vala-panel-appmenu") + (license (list license:lgpl3)))) + (define-public atk (package (name "atk") From 72b80b9b177ef11054482f3a53d66a8aa67d83c2 Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Mon, 21 Feb 2022 21:47:28 +1100 Subject: [PATCH 133/824] gnu: Add plasma-workspace. * gnu/packages/kde-plasma.scm (plasma-workspace): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 148 ++++++++++++++++++++++++++++++++++++ 1 file changed, 148 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index fdcbc2af29..7bb627a789 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -47,11 +47,14 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages iso-codes) #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) #:use-module (gnu packages networking) + #:use-module (gnu packages maths) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) #:use-module (gnu packages polkit) @@ -1440,6 +1443,151 @@ sensors, process information and other system resources.") (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") (license (list license:gpl2 license:gpl3)))) +(define-public plasma-workspace + (package + (name "plasma-workspace") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0pxwg3i07sipfchn4qkmlr6kcgqbhj2s10xq69wi32x1fc13jx5x")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools pkg-config qtsvg-5 + qttools-5)) + (inputs (list appmenu-gtk-module + appstream-qt + baloo + breeze + breeze-icons + dbus + fontconfig + iso-codes + kactivities + kactivities-stats + karchive + kcmutils + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kded + kdesu + kglobalaccel + kguiaddons + kholidays + ki18n + kiconthemes + kidletime + kinit + kio + kio-extras + kio-fuse + kitemmodels + kirigami + knewstuff + knotifications + knotifyconfig + kquickcharts + kpackage + kpeople + krunner + kscreenlocker + ktexteditor + ktextwidgets + kunitconversion + kuserfeedback + kwallet + kwayland + kwin + layer-shell-qt + libkscreen + libksysguard + libqalculate + gmp + mpfr + libsm + libxft + libxkbcommon + libxrender + libxtst + networkmanager-qt + phonon + pipewire-0.3 + plasma-framework + plasma-workspace-wallpapers + plasma-wayland-protocols + prison + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland-5 + qtgraphicaleffects + qtx11extras + wayland + wayland-protocols-next + xcb-util + xcb-util-image + xcb-util-keysyms + xrdb + xmessage + xsetroot + zlib)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-wallpaper + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "sddm-theme/theme.conf.cmake" + (("background=..KDE_INSTALL_FULL_WALLPAPERDIR.") + (string-append "background=" + #$(this-package-input "breeze") + "/share/wallpapers"))))) + (add-after 'unpack 'patch-workspace-bins + (lambda* (#:key inputs #:allow-other-keys) + (let ((xmessage (search-input-file inputs "/bin/xmessage")) + (xsetroot (search-input-file inputs "/bin/xsetroot")) + (xrdb (search-input-file inputs "/bin/xrdb")) + (kinit #$(this-package-input "kinit"))) + (substitute* "startkde/startplasma.cpp" + (("xmessage") xmessage) + (("xsetroot") xsetroot)) + (substitute* (list "kcms/fonts/fontinit.cpp" + "kcms/fonts/fonts.cpp" + "kcms/krdb/krdb.cpp") + (("xrdb") xrdb)) + (substitute* "startkde/plasma-session/startup.cpp" + (("CMAKE_INSTALL_FULL_LIBEXECDIR_KF5..") + (string-append "\"" kinit + "/lib/libexec/kf5"))) + (substitute* (list + "startkde/startplasma-wayland.cpp" + "startkde/startplasma-x11.cpp") + (("kdeinit5_shutdown") + (string-append kinit "/bin/kdeinit5_shutdown")))))) + (delete 'check) + (add-after 'install 'check-after-install + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH"))) + (invoke "ctest" "-E" + "(appstreamtest|lookandfeel-kcmTest|tst_triangleFilter|systemtraymodeltest|testdesktop| screenpooltest)"))))))) + (home-page "https://invent.kde.org/plasma/plasma-workspace") + (synopsis "Plasma workspace components") + (description + "Workspaces provide support for KDE Plasma Widgets, integrated search, +hardware management, and a high degree of customizability.") + (license (list license:gpl2 license:gpl3)))) + (define-public plasma-workspace-wallpapers (package (name "plasma-workspace-wallpapers") From b6e75ce7337dffdab2f99e7a7d6cc76c108d7f7e Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 09:04:19 +0200 Subject: [PATCH 134/824] gnu: Add system-settings. * gnu/packages/kde-plasma.scm (system-settings): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 41 +++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 7bb627a789..a1e03f240f 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1634,3 +1634,44 @@ hardware management, and a high degree of customizability.") UI for Plasma") (home-page "https://invent.kde.org/plasma/polkit-kde-agent-1") (license license:gpl2+))) + +(define-public system-settings + (package + (name "system-settings") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/systemsettings-" version ".tar.xz")) + (sha256 + (base32 + "0n7mf6ygi8fgn1m6pk2fadnqj1h58mxqni3h19xbi373wfypq5fl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + kcrash + kitemviews + kitemmodels + kcmutils + ki18n + kio + kservice + kiconthemes + kwidgetsaddons + kwindowsystem + kxmlgui + kdbusaddons + kconfig + kpackage + kactivities + kactivities-stats + kguiaddons + kirigami + knotifications + krunner + plasma-workspace + qtdeclarative-5)) + (synopsis "Control center to configure Plasma Desktop") + (description "This package provides configuration UI for Plasma Desktop.") + (home-page "https://invent.kde.org/plasma/systemsettings") + (license license:gpl2+))) From 12ae7cb61aa9010a7d1597c22bca65fdb5bea69c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 30 Sep 2022 21:20:08 +0200 Subject: [PATCH 135/824] gnu: Add wayland-utils. * gnu/packages/freedesktop.scm (wayland-utils): New variable. Signed-off-by: Marius Bakke --- gnu/packages/freedesktop.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 3a4fee5e20..1c510951e9 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1221,6 +1221,29 @@ protocol either in Wayland core, or some other protocol in wayland-protocols.") (base32 "04vgllmpmrv14x3x64ns01vgwx4hriljayjkz9idgbv83i63hly5")))))) +(define-public wayland-utils + (package + (name "wayland-utils") + (version "1.1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.freedesktop.org/wayland/wayland-utils") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04k1yhyh7h4xawbhpz9pf6cpfmmp1l862fdgsvvnyp4hg9n3j9aj")))) + (build-system meson-build-system) + (native-inputs (list pkg-config)) + (inputs (list libdrm wayland wayland-protocols-next)) + (home-page "https://wayland.freedesktop.org/") + (synopsis "Display information about the Wayland protocols") + (description "This package provides @code{wayland-info} tool that can be +used to check which Wayland protocols and versions are advertised by the Wayland +compositor.") + (license license:expat))) + (define-public waylandpp (package (name "waylandpp") From 227a3a1d712bf50289270d32a642ef1c9d3aab03 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 30 Sep 2022 21:21:15 +0200 Subject: [PATCH 136/824] gnu: mesa-utils: Install eglinfo. * gnu/packages/gl.scm (mesa-utils)[inputs]: Remove input labels. [arguments]: Install eglinfo to bin. Signed-off-by: Marius Bakke --- gnu/packages/gl.scm | 35 +++++++++++++++++------------------ 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 68c751ace5..01ab6135a4 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -587,30 +587,29 @@ from software emulation to complete hardware acceleration for modern GPUs.") (source (mesa-demos-source version)) (build-system gnu-build-system) (inputs - `(("mesa" ,mesa) - ("glut" ,freeglut) - ("glew" ,glew))) + (list mesa freeglut glew)) (native-inputs (list pkg-config)) (arguments - '(#:phases - (modify-phases %standard-phases - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/bin")) - (for-each - (lambda (file) - (copy-file file (string-append out "/bin/" (basename file)))) - '("src/xdemos/glxdemo" "src/xdemos/glxgears" - "src/xdemos/glxinfo" "src/xdemos/glxheads")) - #t)))))) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out #$output)) + (mkdir-p (string-append out "/bin")) + (for-each (lambda (file) + (copy-file file + (string-append out "/bin/" + (basename file)))) + '("src/xdemos/glxdemo" "src/xdemos/glxgears" + "src/egl/opengl/eglinfo" + "src/xdemos/glxinfo" "src/xdemos/glxheads")))))))) (home-page "https://mesa3d.org/") (synopsis "Utility tools for Mesa") (description - "The mesa-utils package contains several utility tools for Mesa: glxdemo, -glxgears, glxheads, and glxinfo.") + "The mesa-utils package contains several utility tools for Mesa: eglinfo, +glxdemo, glxgears, glxheads, and glxinfo.") ;; glxdemo is public domain; others expat. (license (list license:expat license:public-domain)))) From 12f8ea204a4914d4b98702cda0495d6e3940cdad Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 30 Sep 2022 21:19:52 +0200 Subject: [PATCH 137/824] gnu: Add kinfocenter. * gnu/packages/kde-plasma.scm (kinfocenter): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 57 +++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index a1e03f240f..d229b6e7ea 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -52,6 +52,7 @@ #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) + #:use-module (gnu packages libusb) #:use-module (gnu packages networking) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) @@ -63,6 +64,8 @@ #:use-module (gnu packages package-management) ; flatpak #:use-module (gnu packages video) #:use-module (gnu packages vpn) + #:use-module (gnu packages vulkan) + #:use-module (gnu packages textutils) #:use-module (gnu packages qt) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) @@ -388,6 +391,60 @@ manager which re-parents a Client window to a window decoration frame.") (home-page "https://invent.kde.org/plasma/kgamma5") (license license:gpl2+))) +(define-public kinfocenter + (package + (name "kinfocenter") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0zvki76yghkn158s7hb5g9drz7xaqxkmp2747404n2n0gmnmsdif")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-systemsettings-symlink + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("\\$\\{KDE_INSTALL_FULL_BINDIR\\}/systemsettings5") + (search-input-file inputs + "/bin/systemsettings5")))))))) + (native-inputs (list aha extra-cmake-modules kdoctools pkg-config)) + ;; * vulkaninfo + ;; Wayland KCM + (inputs (list dmidecode + ;; fwupdmgr ;; Packaged on master branch already + kconfig + kconfigwidgets + kcoreaddons + kirigami + ki18n + kcmutils + kio + kservice + libusb + kwidgetsaddons + kdeclarative + kpackage + kwayland + mesa-utils + pciutils + plasma-framework + qtbase-5 + solid + util-linux + vulkan-tools + wayland-utils + xdpyinfo)) + (propagated-inputs (list system-settings)) + (home-page "https://invent.kde.org/plasma/kinfocenter") + (synopsis "View information about computer's hardware") + (description "This package provides tool to view information about +computer's hardware.") + (license (list license:gpl2 license:gpl3)))) + (define-public kmenuedit (package (name "kmenuedit") From 20d7c6b1a29abfff32e98f2ad12672a15bf8aacf Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 30 Sep 2022 22:09:02 +0200 Subject: [PATCH 138/824] gnu: Add kde-cli-tools. * gnu/packages/kde-plasma.scm (kde-cli-tools): New variable. * gnu/local.mk (dist_patch_DATA): Add patch. * gnu/packages/patches/kde-cli-tools-delay-mime-db.patch: New file. Signed-off-by: Marius Bakke --- gnu/local.mk | 1 + gnu/packages/kde-plasma.scm | 48 +++++++++++++++++++ .../patches/kde-cli-tools-delay-mime-db.patch | 26 ++++++++++ 3 files changed, 75 insertions(+) create mode 100644 gnu/packages/patches/kde-cli-tools-delay-mime-db.patch diff --git a/gnu/local.mk b/gnu/local.mk index 68ea09cb91..a8674cd6bd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1388,6 +1388,7 @@ dist_patch_DATA = \ %D%/packages/patches/lightdm-vnc-color-depth.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ %D%/packages/patches/kcontacts-incorrect-country-name.patch \ + %D%/packages/patches/kde-cli-tools-delay-mime-db.patch \ %D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ %D%/packages/patches/kiki-makefile.patch \ diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index d229b6e7ea..e98c13c2bf 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -31,6 +31,7 @@ #:use-module (guix gexp) #:use-module (guix build-system cmake) #:use-module (guix build-system qt) + #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages bash) #:use-module (gnu packages boost) @@ -365,6 +366,53 @@ These window decorations can be used by for example an X11 based window manager which re-parents a Client window to a window decoration frame.") (license license:lgpl3+))) +(define-public kde-cli-tools + (package + (name "kde-cli-tools") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version ".tar.xz")) + (patches (search-patches "kde-cli-tools-delay-mime-db.patch")) + (sha256 + (base32 + "0i1lnkyb2bdvbhnr2wsgjy2sjichzxxqkvn30ca85rj21cavk2z3")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;TODO: Failing sub-tests 3/7 + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-writable-location + (lambda* _ + (substitute* "keditfiletype/tests/filetypestest.cpp" + (("QStandardPaths::writableLocation.QStandardPaths::\ +GenericDataLocation.") + (string-append "\"" (getcwd) "/\""))))) + (add-before 'check 'setup-env + (lambda* _ + (setenv "HOME" (getcwd))))))) + (native-inputs (list extra-cmake-modules pkg-config shared-mime-info)) + (inputs (list kconfig + kdesu + kdoctools + kiconthemes + ki18n + kcmutils + kio + kservice + kwindowsystem + kactivities + kparts + plasma-workspace + qtx11extras + qtsvg-5)) + (synopsis "CLI tools for interacting with KDE") + (description "This package provides command-line tools based on +KDE Frameworks 5 to better interact with the system.") + (home-page "https://invent.kde.org/plasma/kde-cli-tools") + (license license:lgpl2.0+))) + (define-public kgamma (package (name "kgamma") diff --git a/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch b/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch new file mode 100644 index 0000000000..e29b3b192d --- /dev/null +++ b/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch @@ -0,0 +1,26 @@ +From f8cfb96a1540fc3256af95adf8003b75c305183c Mon Sep 17 00:00:00 2001 +From: Petr Hodina +Date: Fri, 30 Sep 2022 21:55:55 +0200 +Subject: [PATCH] Add delay to update the mime db in testCreateMimeType test + function. + + +diff --git a/keditfiletype/tests/filetypestest.cpp b/keditfiletype/tests/filetypestest.cpp +index e58e6f2..a41d4ad 100644 +--- a/keditfiletype/tests/filetypestest.cpp ++++ b/keditfiletype/tests/filetypestest.cpp +@@ -315,6 +315,9 @@ private Q_SLOTS: + QVERIFY(data.isDirty()); + QVERIFY(data.sync()); + MimeTypeWriter::runUpdateMimeDatabase(); ++ // QMimeDatabase doesn't even try to update the cache if less than ++ // 5000 ms have passed (can't use qmime_secondsBetweenChecks) ++ QTest::qSleep(5000); + QMimeType mime = db.mimeTypeForName(mimeTypeName); + QVERIFY(mime.isValid()); + QCOMPARE(mime.comment(), fakeComment); + +base-commit: b5911cda17521156b22429436e19b508aa442a57 +-- +2.37.2 + From 10dba30fb33ab8aa13d28a82c781d28945089c02 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 06:50:41 +0200 Subject: [PATCH 139/824] gnu: Add kdeplasma-addons. * gnu/packages/kde-plasma.scm (kdeplasma-addons): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 44 +++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index e98c13c2bf..01018f705f 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -413,6 +413,50 @@ KDE Frameworks 5 to better interact with the system.") (home-page "https://invent.kde.org/plasma/kde-cli-tools") (license license:lgpl2.0+))) +(define-public kdeplasma-addons + (package + (name "kdeplasma-addons") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1a5cq0jz69hlcr22wxi2p5mzxv5xcp88220irxmq0dhpk85kywlx")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" + "(converterrunnertest|spellcheckrunnertest)"))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive + kconfig + kcoreaddons + kdeclarative + kholidays + ki18n + kio + kcmutils + knotifications + krunner + kservice + kunitconversion + knewstuff + plasma-framework + purpose + sonnet + qtdeclarative-5)) + ;qtwebengine-5)) ;; Optional for online dictionary + (synopsis "Add-ons to improve your Plasma experience") + (description + "This package provides multiple addons for the Plasma Desktop.") + (home-page "https://invent.kde.org/plasma/kdeplasma-addons") + (license license:lgpl2.0))) + (define-public kgamma (package (name "kgamma") From 60caef04e69fff529cb127bd0c236e7199faf0fd Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 26 Aug 2022 06:57:37 +0200 Subject: [PATCH 140/824] gnu: Add khotkeys. * gnu/packages/kde-plasma.scm (khotkeys): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 01018f705f..eb5f137aca 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -483,6 +483,37 @@ KDE Frameworks 5 to better interact with the system.") (home-page "https://invent.kde.org/plasma/kgamma5") (license license:gpl2+))) +(define-public khotkeys + (package + (name "khotkeys") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0c9i4vxiiv90dpzsd2hjwavks87cvwplkj63751z8mazax6r95as")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kdbusaddons + kdoctools + kglobalaccel + ki18n + kcmutils + kio + ktextwidgets + kxmlgui + kdelibs4support + plasma-workspace + qtx11extras)) + (synopsis "Trigger actions with the keyboard") + (description + "This package provides a way to trigger actions when certain keys +are pressed.") + (home-page "https://invent.kde.org/plasma/khotkeys") + (license license:lgpl2.0))) + (define-public kinfocenter (package (name "kinfocenter") From ee62d19d9e098afc131d1c329f39a5d8e5167c4c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 22 Aug 2022 18:13:36 +0200 Subject: [PATCH 141/824] gnu: Add powerdevil. * gnu/packages/kde-plasma.scm (powerdevil): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 44 +++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index eb5f137aca..d537285834 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1815,6 +1815,50 @@ UI for Plasma") (home-page "https://invent.kde.org/plasma/polkit-kde-agent-1") (license license:gpl2+))) +(define-public powerdevil + (package + (name "powerdevil") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0anisirn7z8aw442npdnk1csb5ghpzj2hx49gpw4l6ijk70b76pr")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules qttools-5 pkg-config)) + (inputs (list bluez-qt + glib + kauth + kactivities + kscreen + kidletime + kconfig + kdbusaddons + solid + ki18n + kcrash + knotifyconfig + networkmanager-qt + kio + kwayland + kglobalaccel + kcrash + knotifications + kirigami + libcap + libkscreen + network-manager + plasma-workspace + eudev + qtx11extras)) + (synopsis "Manage power consumption") + (description "This package provides the power consumption settings +of a Plasma shell.") + (home-page "https://invent.kde.org/plasma/powerdevil") + (license license:gpl2+))) + (define-public system-settings (package (name "system-settings") From 02f3055114c5e88cde552f3fe66bb1f9bad8931a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 21:34:07 +0200 Subject: [PATCH 142/824] gnu: Add plasma-browser-integration. * gnu/packages/kde-plasma.scm (plasma-browser-integration): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index d537285834..a4cb8c7909 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1353,6 +1353,44 @@ on QtMultimedia and @command{yt-dlp}.") active window on Plasma Desktop.") (license (list license:gpl2 license:gpl3))))) +(define-public plasma-browser-integration + (package + (name "plasma-browser-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "18pbn5ic5l3m8i1y99yprpwd4x4746aq3abqn1f2cq5h2683h2ia")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + ;; TODO: Figure out how to integrate this package into web browsers + ;; CHROMIUM_EXTENSIONS_DIR - extension for chromium + ;; MOZILLA_DIR - extension for firefox + (inputs (list kio + ki18n + kcoreaddons + kconfig + kcrash + kdbusaddons + knotifications + kitemmodels + krunner + kactivities + purpose + kfilemetadata + kjobwidgets + qtdeclarative-5)) + (propagated-inputs (list plasma-workspace)) + (home-page "https://invent.kde.org/plasma/plasma-browser-integration") + (synopsis "Integrate browsers into the Plasma Desktop") + (description + "This package aims to provide better integration of web browsers with +the KDE Plasma 5 desktop.") + (license license:gpl3+))) + (define-public plasma-disks (package (name "plasma-disks") From 1ad1517dac14a064d9ea7332a1a2af025174bc6a Mon Sep 17 00:00:00 2001 From: Brendan Tildesley Date: Sat, 5 Mar 2022 11:46:54 +1100 Subject: [PATCH 143/824] gnu: Add plasma-desktop. * gnu/packages/kde-plasma.scm (plasma-desktop): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 155 +++++++++++++++++++++++++++++++++++- 1 file changed, 154 insertions(+), 1 deletion(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index a4cb8c7909..eb151180d5 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -48,9 +48,11 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages ibus) #:use-module (gnu packages iso-codes) #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) + #:use-module (gnu packages kde-pim) #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) #:use-module (gnu packages libusb) @@ -59,7 +61,6 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages polkit) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages package-management) ; flatpak @@ -1391,6 +1392,158 @@ active window on Plasma Desktop.") the KDE Plasma 5 desktop.") (license license:gpl3+))) +(define-public plasma-desktop + (package + (name "plasma-desktop") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "05s1pkwr4xmkghp8jrwcyrvjm83n68ngmk2694055xcfgi0pxicg")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules + dbus + kdoctools + intltool + pkg-config + qtsvg-5 + qttools-5)) + (inputs (list packagekit-qt5 + signon-plugin-oauth2 + signond + attica + appstream-qt + baloo + breeze + breeze-icons + eudev + fontconfig + glib + ibus + kaccounts-integration + kactivities + kactivities-stats + kauth + karchive + kcmutils + kconfig + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kded + kdesu + kdelibs4support + kglobalaccel + kguiaddons + kholidays + ki18n + kiconthemes + kidletime + kinit + kio + kitemmodels + knewstuff + knotifications + knotifyconfig + kpackage + kpeople + krunner + kscreenlocker + ktexteditor + ktextwidgets + kunitconversion + kuserfeedback + kwallet + kwayland + kwin + layer-shell-qt + libaccounts-qt + libcanberra + libkscreen + libksysguard + libqalculate + gmp + mpfr + libsm + libxi + libxft + libxkbcommon + libxrender + libxtst + networkmanager-qt + phonon + pipewire-0.3 + plasma-framework + plasma-wayland-protocols + pulseaudio + prison + qqc2-desktop-style + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland + qtx11extras + wayland + wayland-protocols + xcb-util + xcb-util-image + xcb-util-keysyms + xdg-user-dirs + + ;; These are needed for Xserver + xf86-input-libinput + xf86-input-evdev + xorg-server + xf86-input-synaptics + xkeyboard-config + libxkbfile + libxcursor + libxkbcommon)) + (propagated-inputs (list iso-codes kirigami plasma-workspace)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "kcms/keyboard/iso_codes.h" + (("\"/usr/share/xml/iso-codes\"") + (string-append "\"" (search-input-directory + inputs "/share/xml/iso-codes") + "\""))))) + (add-after 'unpack 'patch-qml-import-path + (lambda _ + (substitute* + '("applets/pager/package/contents/ui/main.qml" + "containments/desktop/package/contents/ui/FolderView.qml" + "containments/desktop/package/contents/ui/main.qml" + "containments/panel/contents/ui/main.qml") + (("^import \"(utils|FolderTools|LayoutManager).js\" as " + line mod) + (string-append "import \"../code/" mod + ".js\" as "))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" "foldermodeltest"))))))) + (home-page "https://kde.org/plasma-desktop/") + (synopsis "Plasma for the Desktop") + (description + "Plasma Desktop offers a beautiful looking desktop that takes +complete advantage of modern computing technology. Through the use of visual +effects and scalable graphics, the desktop experience is not only smooth but +also pleasant to the eye. The looks of Plasma Desktop not only provide +beauty, they are also used to support and improve your computer +activities effectively, without being distracting.") + (license license:gpl2+))) + (define-public plasma-disks (package (name "plasma-disks") From 7aac107bde79abac31de73deb2e36114fc96e1cb Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 30 Sep 2022 22:57:52 +0200 Subject: [PATCH 144/824] gnu: qqc2-desktop-style: Add qtx11extras and sonnet to inputs. * gnu/packages/kde-frameworks.scm (qqc2-desktop-style): Add qtx11extras and sonnet to inputs. Signed-off-by: Marius Bakke --- gnu/packages/kde-frameworks.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index dd6d1b303a..aaa5a82d5f 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -1391,7 +1391,9 @@ libpulse.") kirigami qtbase-5 qtdeclarative-5 - qtquickcontrols2-5)) + qtquickcontrols2-5 + qtx11extras ; optional + sonnet)) ; optional (home-page "https://community.kde.org/Frameworks") (synopsis "QtQuickControls2 style that integrates with the desktop") (description "This is a style for QtQuickControls2 which is using From 67313900e1de76e918b921bb58bbcbeeb8cba006 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 23 Aug 2022 21:35:17 +0200 Subject: [PATCH 145/824] gnu: Add plasma meta-package. * gnu/packages/kde-plasma.scm (plasma): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 66 +++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index eb151180d5..c7de340edc 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -30,6 +30,8 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix gexp) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) + #:use-module (guix build-system trivial) #:use-module (guix build-system qt) #:use-module (gnu packages) #:use-module (gnu packages admin) @@ -53,6 +55,8 @@ #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages kde-pim) + ;; Including this module breaks the build + ;#:use-module ((gnu packages kde-systemtools) #:select (konsole)) #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) #:use-module (gnu packages libusb) @@ -61,6 +65,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages polkit) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages package-management) ; flatpak @@ -1296,6 +1301,67 @@ on top of Baloo.") (description "This package provides Oxygen sounds for the KDE desktop.") (license license:lgpl3+))) +(define-public plasma + (package + (name "plasma") + (version "5.25.5") + (source #f) + (build-system trivial-build-system) + (arguments + (list #:builder #~(begin + (mkdir #$output)))) + (propagated-inputs (list bluedevil + breeze + breeze-gtk + discover + drkonqi + kactivitymanagerd + kde-cli-tools + ;; kde-gtk-config + kdecoration + kdeplasma-addons + kgamma + khotkeys + kinfocenter + kmenuedit + kscreen + kscreenlocker + ksshaskpass + ksystemstats + kwallet-pam + kwayland-integration + kwin + kwrited + kinit + layer-shell-qt + libkscreen + libksysguard + milou + ;; oxygen + oxygen-sounds + plasma-browser-integration + plasma-desktop + plasma-disks + plasma-firewall + plasma-integration + plasma-nm + plasma-pa + plasma-systemmonitor + ;; plasma-thunderbolt ;; waiting for bolt + plasma-vault + plasma-workspace + plasma-workspace-wallpapers + polkit-kde-agent + powerdevil + sddm + system-settings + xdg-desktop-portal-kde)) + (synopsis "The KDE Plasma desktop environment") + (home-page "https://kde.org/plasma-desktop/") + (description + "KDE Plasma is an advanced graphical desktop system.") + (license license:gpl2+))) + (define-public plasmatube (package (name "plasmatube") From b3c7ee7c2e29c4c6dd62d5012c4c14635d1df835 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 29 Aug 2022 00:13:36 +0200 Subject: [PATCH 146/824] gnu: Add plasma-nano. * gnu/packages/kde-plasma.scm (plasma-nano): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index c7de340edc..d9c9b4d2fb 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1715,6 +1715,31 @@ activities effectively, without being distracting.") integration of Qt applications when running on a KDE Plasma workspace.") (license license:lgpl2.0))) +(define-public plasma-nano + (package + (name "plasma-nano") + (version "5.24.3") + (source (origin + (method url-fetch) + (uri (string-append "https://download.kde.org/stable/plasma/" + version "/plasma-nano-" version ".tar.xz")) + (sha256 + (base32 + "13jxhfi3c3dhg7zdyfqnsii661h1am0w9dsv82dalqvwr1mw28l5")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list qtbase-5 + qtdeclarative-5 + plasma-framework + kwindowsystem + kwayland + ki18n)) + (home-page "https://plasma-mobile.org/") + (synopsis "Minimal Plasma Shell package") + (description + "This package provides a minimal implementation of Plasma Shell.") + (license license:lgpl2.0+))) + (define-public plasma-nm (package (name "plasma-nm") From 6fb72a8f0dbfb6f67ee9e7b8399f4a3a06f6a266 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 30 Jan 2022 10:56:07 +0100 Subject: [PATCH 147/824] gnu: Add plasma-phone-components. * gnu/packages/kde-plasma.scm (plasma-phone-components): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 50 +++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index d9c9b4d2fb..1bb961cf76 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -62,6 +62,7 @@ #:use-module (gnu packages libusb) #:use-module (gnu packages networking) #:use-module (gnu packages maths) + #:use-module (gnu packages messaging) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) @@ -1840,6 +1841,55 @@ PulseAudio.") "This package provides a Plasma applet for the Pass password manager.") (license license:lgpl2.1+))) +(define-public plasma-phone-components + (package + (name "plasma-phone-components") + (version "5.23.4") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/plasma-phone-components-" version + ".tar.xz")) + (sha256 + (base32 + "0ml5pyi90nlmx5550sf3x9263f8mypj4jmdskzabzhnz44ck8vy9")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list qtbase-5 + qtdeclarative + kactivities + kauth + kbookmarks + kwin + kcodecs + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + kdeclarative + ki18n + kio + kitemviews + kjobwidgets + knotifications + kpackage + kpeople + kservice + kwayland + kwidgetsaddons + kwindowsystem + kxmlgui + libphonenumber + modemmanager-qt + plasma-framework + solid)) + (home-page "https://plasma-mobile.org/") + (synopsis "Modules providing phone functionality for Plasma") + (description "This package provides user-friendly, privacy-enabling +and customizable platform for mobile devices.") + (license (list license:gpl3+ license:lgpl2.1+)))) + (define-public plasma-vault (package (name "plasma-vault") From 28ce8094e231629ae53c2bedbf133656f415186c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 25 Mar 2022 11:36:00 +0100 Subject: [PATCH 148/824] gnu: Add plasma-mobile. * gnu/packages/kde-plasma.scm (plasma-mobile): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 40 +++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 1bb961cf76..f0cef617a5 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1789,6 +1789,46 @@ integration of Qt applications when running on a KDE Plasma workspace.") connections.") (license (list license:lgpl2.1 license:lgpl3)))) +(define-public plasma-mobile + (package + (name "plasma-mobile") + (version "5.24.3") + (source (origin + (method url-fetch) + (uri (string-append "https://download.kde.org/stable/plasma/" + version "/plasma-mobile-" version ".tar.xz")) + (sha256 + (base32 + "1bwmy7xvd8wmh0snqqjh9jjgawib8ks2g30w48sqxwhplhf3da58")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'install 'wrap-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append #$output + "/bin/kwinwrapper") + `("PATH" ":" prefix + (,(string-append #$plasma-framework + "/bin"))))))))) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list bash-minimal + kdeclarative + ki18n + kio + knotifications + kwayland + kwin + modemmanager-qt + networkmanager-qt + plasma-framework + qtbase-5)) + (home-page "https://plasma-mobile.org/") + (synopsis + "General UI components for Plasma Phone including shell, containment and applets") + (description "This package provides user-friendly, privacy-enabling and +customizable platform for mobile devices.") + (license (list license:gpl3+ license:lgpl2.1+)))) + (define-public plasma-pa (package (name "plasma-pa") From 0d53223c814e33bd5b45bf15907953e36e97066a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 25 Mar 2022 11:37:17 +0100 Subject: [PATCH 149/824] gnu: Add plasma-mobile-settings. * gnu/pacakges/kde-plasma.scm (plasma-mobile-settings): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index f0cef617a5..6799bbba64 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1829,6 +1829,34 @@ connections.") customizable platform for mobile devices.") (license (list license:gpl3+ license:lgpl2.1+)))) +(define-public plasma-mobile-settings + (package + (name "plasma-mobile-settings") + (version "22.02") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/plasma-settings-" version ".tar.xz")) + (sha256 + (base32 + "0b7lj3r9z9cz2vr0h15sqqxdaa7m07hsk8i2p8nf4a3yh02ywsxy")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list qtbase-5 + qtdeclarative-5 + kio + modemmanager-qt + networkmanager-qt + ki18n + plasma-framework + kdeclarative + kdbusaddons)) + (home-page "https://plasma-mobile.org/") + (synopsis "Settings application for Plasma Mobile") + (description + "This package provides Settings application for Plasma Mobile.") + (license license:gpl2+))) + (define-public plasma-pa (package (name "plasma-pa") From f48fa54d7c465d4cdb4fc7b2c517b33bebe82c0a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 25 Mar 2022 12:21:56 +0100 Subject: [PATCH 150/824] gnu: Add plasma-mobile-sounds. * gnu/packages/kde-plasma.scm (plasma-mobile-sounds): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 6799bbba64..b07033bd7b 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1857,6 +1857,25 @@ customizable platform for mobile devices.") "This package provides Settings application for Plasma Mobile.") (license license:gpl2+))) +(define-public plasma-mobile-sounds + (package + (name "plasma-mobile-sounds") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kde/stable/plasma-mobile-sounds/" + version "/plasma-mobile-sounds-" version ".tar.xz")) + (sha256 + (base32 + "1br6kzicrr45vgg0ciqczxlcid21n5lfjm6zc06rw86ys7fx7bpi")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (home-page "https://plasma-mobile.org/") + (synopsis "Sounds for Plasma Mobile devices") + (description "This package provides sound files for Plasma Mobile.") + (license (list license:cc0 license:cc-by4.0)))) + (define-public plasma-pa (package (name "plasma-pa") From d5954101fd0a5123067231382b57d8246e929e34 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 8 Apr 2022 13:24:20 +0200 Subject: [PATCH 151/824] gnu: Add plasma-phonebook. * gnu/packages/kde-plasma.scm (plasma-phonebook): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index b07033bd7b..30cd463451 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1928,6 +1928,35 @@ PulseAudio.") "This package provides a Plasma applet for the Pass password manager.") (license license:lgpl2.1+))) +(define-public plasma-phonebook + (package + (name "plasma-phonebook") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-phonebook/" + version "/plasma-phonebook-" version + ".tar.xz")) + (sha256 + (base32 + "13nnzdzpganlp319sc9dm9w5hsjhw4f3w8rb80q3nd8q6nyrpky8")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kpeople + kirigami + kpeoplevcard + kcoreaddons + kcontacts + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://plasma-mobile.org/") + (synopsis "Phonebook for Plasma Mobile devices") + (description "This package provides contacts application which allows +adding, modifying and removing contacts.") + (license license:lgpl2.0+))) + (define-public plasma-phone-components (package (name "plasma-phone-components") From a5c368116a8e0754a6c7c523bcea8b0d1f70ee5c Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 20 Sep 2022 15:36:21 +0200 Subject: [PATCH 152/824] gnu: Add kalendar. * gnu/packages/kde-pim.scm (kalendar): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 70 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 90d124a053..5952beeffa 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -540,6 +540,76 @@ one of the APIs mentioned above.") management system and its Plasma integration components.") (license license:lgpl2.0+))) +(define-public kalendar + (package + (name "kalendar") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0slk9z7p1z5m2kbb8kq05afslxad8w5pjsajxawckcx0mlsd3apj")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;All 2 tests fail + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'wrap-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append #$output + "/bin/kalendar") + `("PATH" ":" prefix + (,(string-append #$(this-package-input "akonadi") + "/bin")))))) + (delete 'check) + (add-after 'wrap-script 'check-again + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list akonadi + akonadi-contacts + breeze-icons + grantlee + grantleetheme + kio + kirigami + kdbusaddons + ki18n + kcalendarcore + kcalendarsupport + kconfigwidgets + kwindowsystem + kcoreaddons + kcontacts + kitemmodels + kmime + kidentitymanagement + kpimtextedit + ktextwidgets + akonadi-calendar + keventviews + kcalutils + kxmlgui + kiconthemes + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5 + qtquickcontrols-5 + qtgraphicaleffects + qtlocation + qqc2-desktop-style)) + (home-page "https://apps.kde.org/kalendar/") + (synopsis "Calendar application") + (description + "Kalendar is a calendar application using Akonadi to sync with +external services.") + (license license:gpl3+))) + (define-public kcalendarsupport (package (name "kcalendarsupport") From 576d8c5babcd52222f7b5dfe7054e2188f23d4bd Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 20 Sep 2022 15:39:39 +0200 Subject: [PATCH 153/824] gnu: Add kongress. * gnu/packages/kde-plasma.scm (kongress): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 30cd463451..6929232290 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -603,6 +603,44 @@ computer's hardware.") (home-page "https://invent.kde.org/plasma/kmenuedit") (license license:gpl2+))) +(define-public kongress + (package + (name "kongress") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/kongress-" version ".tar.xz")) + (sha256 + (base32 + "0pjp2s774sgw2dklqib8alm1a9fkixy3s92i2v8v00znx08zf2jz")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + ;; NOTE: Reporting bugs is linked to web browser, better not link it and let + ;; it reslove through xdg-open in the run time + (inputs (list kirigami + kdbusaddons + ki18n + kcalendarcore + kconfigwidgets + kwindowsystem + kcoreaddons + kcontacts + kitemmodels + knotifications + kxmlgui + kiconthemes + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtgraphicaleffects + qtsvg-5)) + (home-page "https://apps.kde.org/kongress/") + (synopsis "Companion application for conferences") + (description "This application provides list of upcoming conferences with +the schedule and venue information.") + (license license:gpl3+))) + (define-public kscreen (package (name "kscreen") From 9946e5800f4de17e1186cdc405f0ce4acf74afaf Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 17:16:11 +0200 Subject: [PATCH 154/824] gnu: Add lightly. * gnu/packages/kde-plasma.scm (lightly): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 6929232290..b0d2d36ed9 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1292,6 +1292,36 @@ conjunction with the KDE Plasma Desktop.") "This package provides a daemon that listens to system notifications.") (license license:gpl2+))) +(define-public lightly + (package + (name "lightly") + (version "0.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Luwx/Lightly") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qkjzgjplgwczhk6959iah4ilvazpprv7yb809jy75kkp1jw8mwk")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kdecoration + kcoreaddons + kguiaddons + kconfigwidgets + kwindowsystem + ki18n + kiconthemes + qtx11extras)) + (home-page "https://github.com/Luwx/Lightly") + (synopsis "Modern style for Qt applications") + (description + "Lightly is a fork of the Breeze theme that aims to be visually modern +and minimalistic.") + (license license:gpl2+))) + (define-public milou (package (name "milou") From b9a0363b22e28373b3075ebf61854e1ec57c85cc Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Fri, 23 Sep 2022 19:14:41 +0200 Subject: [PATCH 155/824] gnu: Add kirogi. * gnu/packages/kde-utils.scm (kirogi): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 54 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 2d051c74f6..d8dc755a98 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -24,6 +24,7 @@ #:use-module (guix build-system qt) #:use-module (guix gexp) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) @@ -33,6 +34,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages glib) ; dbus for tests #:use-module (gnu packages gnome) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages imagemagick) #:use-module (gnu packages pkg-config) #:use-module (gnu packages kde) @@ -183,6 +185,58 @@ Kate's features include: (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0)))) +(define-public kirogi + (let ((commit "73b009f1fc5ac159c2faba720b302c704f89a806") ; no releases yet + (revision "1")) + (package + (name "kirogi") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/kirogi") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gncfnwadh11ipynfcrsh1vnk2g02c7scd5wanphi8i95jzak9jd")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-gstreamer + (lambda* _ + (substitute* "CMakeLists.txt" + (("gstreamer-video-1.0") + ""))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kconfigwidgets + kcoreaddons + ki18n + kirigami + kcrash + kdnssd + qtquickcontrols2-5 + qtgraphicaleffects + qtdeclarative-5 + qtgamepad + qtlocation)) + (propagated-inputs (list gstreamer)) + (home-page "https://apps.kde.org/kirogi/") + (synopsis "Ground control application for drones") + (description "Kirogi is a ground control application for drones. +@itemize +@item Direct flight controls +@item Fly by touch on a Navigation Map +@item Trigger vehicle actions (e.g. flips, trim) +@item Gamepad/joypad support +@item Live video +@item Take photo and record video +@item Configure flight parameters (speed, altitude limits) +@item Support for Parrot (Anafi, Bebop 2) and Ryze Tello drones +@end itemize") + (license ;GPL for programs, LGPL for libraries + (list license:gpl2+ license:lgpl2.0))))) + (define-public wacomtablet (package (name "wacomtablet") From 4033249e2e8482ba1d6270ee21306200e4dd3715 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 18:28:08 +0200 Subject: [PATCH 156/824] gnu: Add libatcore. * gnu/packages/kde-utils.scm (libatcore): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index d8dc755a98..2657c8aff5 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -237,6 +237,31 @@ Kate's features include: (license ;GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0))))) +(define-public libatcore + (let ((commit "0de6393ed3e721537dec50b0ad174d83f1207eb6") + (revision "1")) + (package + (name "libatcore") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/libraries/atcore") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1830r6ylpn3l7y2frl8cih5cpjgbkfrib9jq7jklf8aszhlsihf2")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list qtcharts qtdeclarative-5 qtserialport)) + (home-page "https://invent.kde.org/libraries/atcore") + (synopsis "Library for connection and management of 3D printers") + (description + "This package provides a API to manage the serial connection between +the computer and 3D Printers.") + (license (list license:lgpl2.1 license:lgpl3))))) + (define-public wacomtablet (package (name "wacomtablet") From 853480957e9b2c2e2eed1683450cf4a2b7727d6d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 18:59:58 +0200 Subject: [PATCH 157/824] gnu: Add basket. * gnu/packages/kde-utils.scm (basket): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 2657c8aff5..642e9f457c 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -119,6 +119,52 @@ with support for multiple formats, including tar, gzip, bzip2, rar and zip, as well as CD-ROM images.") (license license:gpl2+))) +(define-public basket + (let ((commit "e23a8b3b1198d51f770523c7fb4652750810359a") + (revision "1")) + (package + (name "basket") + (version (git-version "2.49" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/basket") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i7hrrlwyzzh7mm9xc8hjix24rvy1b2cvvbkhxh9mmdbmphwdhhd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list breeze-icons + karchive + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + kdoctools + kfilemetadata + kglobalaccel + kguiaddons + ki18n + kiconthemes + kcmutils + kio + knotifications + kparts + kservice + ktextwidgets + kwidgetsaddons + kwindowsystem + kxmlgui + phonon)) + (home-page "https://invent.kde.org/utilities/basket") + (synopsis "Notes and to-dos organizer") + (description "This package provides simple note taking and to-do app.") + (license license:gpl2+)))) + (define-public kate (package (name "kate") From 0aa70baeb860f041f89ecdeaf47a040bd378f4a2 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 19:18:55 +0200 Subject: [PATCH 158/824] gnu: Add filelight. * gnu/packages/kde-utils.scm (filelight): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 642e9f457c..9e37f66a02 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -165,6 +165,35 @@ well as CD-ROM images.") (description "This package provides simple note taking and to-do app.") (license license:gpl2+)))) +(define-public filelight + (package + (name "filelight") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/filelight-" version ".tar.xz")) + (sha256 + (base32 + "1fqgmpq5dznbn5lalx1j6dyynhylijrcqw3x9hrwxcqwr275h9iw")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kquickcharts + kxmlgui + kio + ki18n + kdeclarative + qqc2-desktop-style + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://apps.kde.org/filelight/") + (synopsis "Visualize the disk usage") + (description "Filelight is an application to visualize the disk usage on +your computer.") + (license license:lgpl2.1+))) + (define-public kate (package (name "kate") From ba35be8374e24cdbd7afe8943bdd96195c962a34 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 19:26:07 +0200 Subject: [PATCH 159/824] gnu: Add francis. * gnu/packages/kde-utils.scm (francis): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 9e37f66a02..25671b6432 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -194,6 +194,38 @@ well as CD-ROM images.") your computer.") (license license:lgpl2.1+))) +(define-public francis + (let ((commit "d2c762ad94170430a667ee57f81ec9dbe498642c") ; no release yet + (revision "1")) + (package + (name "francis") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/francis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15bk5iq127mp34n9fzq4d5r3qss3ihk93lqy86z2q3lgwid26s0h")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kcoreaddons + kconfig + ki18n + kdbusaddons + knotifications + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/francis") + (synopsis "Track your time") + (description "This package provides time tracking.") + (license license:lgpl2.1+)))) + (define-public kate (package (name "kate") From de33239e33fb4afb470eeb26ea57c83d6df32185 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 19:35:10 +0200 Subject: [PATCH 160/824] gnu: Add isoimagewriter. * gnu/packages/kde-utils.scm (isoimagewriter): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 25671b6432..d1cdc3d37a 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -226,6 +226,37 @@ your computer.") (description "This package provides time tracking.") (license license:lgpl2.1+)))) +(define-public isoimagewriter + (let ((commit "bd1ef4f0ce179fa874b102689022ebda3e7b4c16") + (revision "1")) + (package + (name "isoimagewriter") + (version (git-version "0.8" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/isoimagewriter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dha2y4kmyppi6c0g0hclp53fjj963vq27q7azznpl0bz6zb4042")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + karchive + kcoreaddons + ki18n + kiconthemes + kcrash + solid + kwidgetsaddons)) + (home-page "https://invent.kde.org/utilities/isoimagewriter") + (synopsis "Write hybrid ISO files onto USB disks") + (description + "This package provides a tool to write ISO files to USB disks.") + (license license:gpl3+)))) + (define-public kate (package (name "kate") From 76af0706a74b9f826467236156cf9fae0c4ace38 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 20:22:25 +0200 Subject: [PATCH 161/824] gnu: Add kdebugsettings. * gnu/packages/kde-utils.scm (kdebugsettings): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index d1cdc3d37a..777448a0e7 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -323,6 +323,33 @@ Kate's features include: (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0)))) +(define-public kdebugsettings + (package + (name "kdebugsettings") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kdebugsettings-" version + ".tar.xz")) + (sha256 + (base32 + "0l9q7cmzc93zz2zc5ncq3q7q6jil6ai36n2vh70s2wsi8b0gsms8")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + kconfig + kdbusaddons + ki18n + kwidgetsaddons + kitemviews + kcompletion)) + (home-page "https://invent.kde.org/utilities/kdebugsettings") + (synopsis "Choose which QLoggingCategory are displayed") + (description + "This package allows to select which QLoggingCategory are displayed.") + (license license:lgpl2.0+))) + (define-public kirogi (let ((commit "73b009f1fc5ac159c2faba720b302c704f89a806") ; no releases yet (revision "1")) From 298ddc073ff0a3861240c7ab721f97fc74badd7a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 20:37:26 +0200 Subject: [PATCH 162/824] gnu: Add keysmith. * gnu/packages/kde-utils.scm (keysmith): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 777448a0e7..cd4e2eb1d9 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -27,11 +27,13 @@ #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages backup) #:use-module (gnu packages bash) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #:use-module (gnu packages glib) ; dbus for tests #:use-module (gnu packages gnome) #:use-module (gnu packages gstreamer) @@ -350,6 +352,36 @@ Kate's features include: "This package allows to select which QLoggingCategory are displayed.") (license license:lgpl2.0+))) +(define-public keysmith + (package + (name "keysmith") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + (version-major+minor version) "/keysmith-" + version ".tar.xz")) + (sha256 + (base32 + "0w3vvmp9rn6ahly2fm9n6f4glfr7d84bfvj33mrs5pn7n99h7jgy")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kdbusaddons + kirigami + ki18n + kwindowsystem + libsodium + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/keysmith") + (synopsis "OTP client for Plasma Mobile and Desktop") + (description + "This package provides OTP client for Plasma Mobile and Desktop +with support for QR scanning.") + (license license:gpl3+))) + (define-public kirogi (let ((commit "73b009f1fc5ac159c2faba720b302c704f89a806") ; no releases yet (revision "1")) From 9305d8b605979592ecc96de808992a782760d897 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 24 Sep 2022 20:59:50 +0200 Subject: [PATCH 163/824] gnu: Add keurocalc. * gnu/packages/kde-utils.scm (keurocalc): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index cd4e2eb1d9..bd9e4d24a7 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -352,6 +352,36 @@ Kate's features include: "This package allows to select which QLoggingCategory are displayed.") (license license:lgpl2.0+))) +(define-public keurocalc + (let ((commit "a760d8a7e58b36eb72d15e847f96599c93785194") ; just one release + (revision "1")) + (package + (name "keurocalc") + (version (git-version "1.3.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/keurocalc") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gh5vwl38hwf1405c980j1fj06g5c52am140lf4mxhrjvnmry7kd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list kconfig + kconfigwidgets + kcoreaddons + ki18n + kio + kwidgetsaddons + kxmlgui)) + (home-page "https://invent.kde.org/utilities/keurocalc") + (synopsis "Currency conversion tool") + (description "This package provides a utility to handle currency +conversions between European currencies.") + (license license:gpl2+)))) + (define-public keysmith (package (name "keysmith") From 9f7040cf7413ba2cfe9dcf50d6ad61c330a32187 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 10:17:37 +0200 Subject: [PATCH 164/824] gnu: Add qt3d-5. * gnu/packages/qt.scm (qt3d-5): New variable. Signed-off-by: Marius Bakke --- gnu/packages/qt.scm | 63 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index f37392f199..30bf429897 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -821,6 +821,69 @@ developers using C++ or QML, a CSS & JavaScript like language.") (variable "XDG_CONFIG_DIRS") (files '("etc/xdg"))))))) +(define-public qt3d-5 + (package + (inherit qtbase-5) + (name "qt3d") + (version "5.15.5") + (source (origin + (method url-fetch) + (uri (qt-urls name version)) + (sha256 + (base32 + "1m3y7d58crn0qgfwkimxcggssn2pbs8nj5b9diwns6rwqg4aqk20")))) + (propagated-inputs `()) + (native-inputs (list perl)) + (inputs (list mesa qtbase-5 vulkan-headers zlib)) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'configure 'configure-qmake + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((tmpdir (string-append (getenv "TMPDIR"))) + (qmake (string-append tmpdir "/qmake")) + (qt.conf (string-append tmpdir "/qt.conf"))) + (symlink (which "qmake") qmake) + (setenv "PATH" + (string-append tmpdir ":" + (getenv "PATH"))) + (with-output-to-file qt.conf + (lambda () + (format #t "[Paths] +Prefix=~a +ArchData=lib/qt5 +Data=share/qt5 +Documentation=share/doc/qt5 +Headers=include/qt5 +Libraries=lib +LibraryExecutables=lib/qt5/libexec +Binaries=bin +Tests=tests +Plugins=lib/qt5/plugins +Imports=lib/qt5/imports +Qml2Imports=lib/qt5/qml +Translations=share/qt5/translations +Settings=etc/xdg +Examples=share/doc/qt5/examples +HostPrefix=~a +HostData=lib/qt5 +HostBinaries=bin +HostLibraries=lib + +[EffectiveSourcePaths] +HostPrefix=~a +HostData=lib/qt5" + #$output #$output #$(this-package-input + "qtbase"))))))) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "qmake" + "QT_BUILD_PARTS = libs tools tests"))) + (add-before 'check 'set-display + (lambda _ + (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (synopsis "Qt module for 3D") + (description "The Qt3d module provides classes for displaying 3D."))) + (define-public qt5compat (package (name "qt5compat") From 19e70470d50d632a90a99da02d378fca36eb17ef Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 09:32:34 +0200 Subject: [PATCH 165/824] gnu: Add atelier. * gnu/packages/kde-utils.scm (atelier): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 39 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index bd9e4d24a7..c88e86b024 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -121,6 +121,45 @@ with support for multiple formats, including tar, gzip, bzip2, rar and zip, as well as CD-ROM images.") (license license:gpl2+))) +(define-public atelier + (let ((commit "93d7d440c42f1e49a4933cbbce9f68d5e4ca725a") ; no releases + (revision "1")) + (package + (name "atelier") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/atelier") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00jccpwvksyp2vr3fjxajs8d9d30rspg4zj6rnj8dai96alp303k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list ki18n + kxmlgui + kconfigwidgets + ktexteditor + libatcore + qt3d-5 + qtbase-5 + qtcharts + qtdeclarative-5 + qtmultimedia-5 + qtserialport)) + (home-page "https://atelier.kde.org") + (synopsis "Desktop interface to control 3D printers powered by AtCore") + (description "Atelier provides interface to control and manage your printer. +@itemize +@item Load and see your GCode File +@item Real time graphic to monitor your bed and hotend temperatures +@item You can log everything that comes and go from your printer +@item Edit gcode file +@end itemize") + (license license:gpl3+)))) + (define-public basket (let ((commit "e23a8b3b1198d51f770523c7fb4652750810359a") (revision "1")) From 8e7e460e7e012a570915bd5566a0b9cfbf97f982 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 09:33:50 +0200 Subject: [PATCH 166/824] gnu: Add fielding. * gnu/packages/kde-utils.scm (fielding): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index c88e86b024..d8ae365c04 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -206,6 +206,39 @@ well as CD-ROM images.") (description "This package provides simple note taking and to-do app.") (license license:gpl2+)))) +(define-public fielding + (let ((commit "6b3c5d67b308e9e7e2043dc6072bfd265ec9f3e1") + ;; no releases yet + (revision "1")) + (package + (name "fielding") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/fielding") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l16am7il7kprmy8irpzj04rb8wbfr84y49wp4i74hspp9xkfick")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kcoreaddons + kconfig + ki18n + kdbusaddons + ksyntaxhighlighting + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/fielding") + (synopsis "REST API testing tool") + (description + "This package provides a tool for testing REST APIs.") + (license license:lgpl2.1+)))) + (define-public filelight (package (name "filelight") From b6a119794a7af94b03f0b32f8207db7cd1a8cbb3 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 09:34:17 +0200 Subject: [PATCH 167/824] gnu: Add kdialog. * gnu/packages/kde-utils.scm (kdialog): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index d8ae365c04..94e95bed25 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -424,6 +424,32 @@ Kate's features include: "This package allows to select which QLoggingCategory are displayed.") (license license:lgpl2.0+))) +(define-public kdialog + (package + (name "kdialog") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kdialog-" version ".tar.xz")) + (sha256 + (base32 + "1lqzhfn5g16qr6ada9i0i3kshna1zxp1y20ylwmmsa82bgmyblhx")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list ktextwidgets + knotifications + kguiaddons + kiconthemes + kwindowsystem + kio + kdbusaddons)) + (home-page "https://invent.kde.org/utilities/kdialog") + (synopsis "Show dialog boxes from shell scripts") + (description "This package provides tool to show nice dialog boxes from +shell scripts.") + (license license:gpl2+))) + (define-public keurocalc (let ((commit "a760d8a7e58b36eb72d15e847f96599c93785194") ; just one release (revision "1")) From a37c426854c19eee85f22bd64d4878ff275d23f1 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 09:34:42 +0200 Subject: [PATCH 168/824] gnu: Add kfind. * gnu/packages/kde-utils.scm (kfind): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 94e95bed25..5f00e0762a 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -510,6 +510,31 @@ conversions between European currencies.") with support for QR scanning.") (license license:gpl3+))) +(define-public kfind + (package + (name "kfind") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kfind-" version ".tar.xz")) + (sha256 + (base32 + "0py6ygnj7qxbwrldf2a3hqc1cqd5yvyfi1l0nji0hwn8lvidnjhc")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list karchive + kcoreaddons + kfilemetadata + ki18n + kio + kwidgetsaddons)) + (home-page "https://apps.kde.org/kfind/") + (synopsis "File search utility") + (description + "This package provides a file search utility for KDE.") + (license license:gpl2+))) + (define-public kirogi (let ((commit "73b009f1fc5ac159c2faba720b302c704f89a806") ; no releases yet (revision "1")) From 94c6b9068b8e07250528148294e10f9c212aa6f4 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sun, 25 Sep 2022 11:03:10 +0200 Subject: [PATCH 169/824] gnu: kwayland-server: Update to 5.24.6. * gnu/packages/kde-plasma.scm (kwayland-server): Update to 5.24.6. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index b0d2d36ed9..9bebd4cafd 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1036,7 +1036,7 @@ you login.") (define-public kwayland-server (package (name "kwayland-server") - (version "5.24.4") + (version "5.24.6") (source (origin (method url-fetch) (uri (string-append @@ -1044,7 +1044,7 @@ you login.") "/" name "-" version ".tar.xz")) (sha256 (base32 - "1279nqhy1qyz84dkn23rvzak8bg71hbrp09jlhv9mkjdb3bhnyfi")))) + "1wwgb1p177g6vvyf4l5jisigwvy5756ray1x355mlp7bi1pfs664")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) From 1ed89fc485fb6f04c882ab445ddc70106c5478f0 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:38:24 +0200 Subject: [PATCH 170/824] gnu: Add plasma-welcome. * gnu/packages/kde-plasma.scm (plasma-welcome): New package. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 39 +++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 9bebd4cafd..1fa41e5004 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -2139,6 +2139,45 @@ sensors, process information and other system resources.") (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") (license (list license:gpl2 license:gpl3)))) +(define-public plasma-welcome +(let ((commit "dac7569078782a96f122782c15d34e51737d2b89") ; no tags + (revision "1")) + (package + (name "plasma-welcome") + (version (git-version "0.1-pre" revision commit)) + (home-page "https://invent.kde.org/plasma/plasma-welcome") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1x7ra699r5a9kpa3isdnx6af4j6778kw2pmprnx4s8f1rwk2idhh")))) + (build-system qt-build-system) + (native-inputs + (list extra-cmake-modules pkg-config)) + (inputs + (list kcoreaddons + kdbusaddons + kdeclarative + ki18n + kio + kirigami + knotifications + kservice + kwindowsystem + networkmanager-qt + plasma-framework + qtdeclarative-5 + qtgraphicaleffects + qtsvg-5 + qtquickcontrols2-5 + system-settings)) + (synopsis "Plasma welcome screen") + (description + "This package provides a wizard for Plasma to configure settings.") + (license (list license:gpl2 license:gpl3))))) + (define-public plasma-workspace (package (name "plasma-workspace") From 7928ac9370548b407cfae51e8668c2e92e390beb Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Sat, 1 Oct 2022 16:34:13 +0200 Subject: [PATCH 171/824] gnu: Add plasma-redshift-control. * gnu/packages/kde-plasma.scm (plasma-redshift-control): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 1fa41e5004..0771abe67a 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -2074,6 +2074,29 @@ adding, modifying and removing contacts.") and customizable platform for mobile devices.") (license (list license:gpl3+ license:lgpl2.1+)))) +(define-public plasma-redshift-control + (let ((commit "d9f38a5f0bcf030be16db1776166581c16e802cb") + (revision "1")) + (package + (name "plasma-redshift-control") + (version (git-version "0.1-pre" revision commit)) + (home-page "https://invent.kde.org/plasma/plasma-redshift-control") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wadxhy6iljhikfw2rbj9dhwb86f2sgwyf62r7sfq6cszcpgp0xi")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kwindowsystem plasma-framework redshift)) + (synopsis "Adjust color temperature") + (description + "This package provides color temperature control applet for the Plasma +Desktop.") + (license (list license:lgpl2.1 license:lgpl3))))) + (define-public plasma-vault (package (name "plasma-vault") From 092472904b6449dc5ea4f76bed2b767fd373cdac Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:39:02 +0200 Subject: [PATCH 172/824] gnu: Add print-manager. * gnu/packages/kde-utils.scm (print-manager): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 5f00e0762a..e74b4f6e8c 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) + #:use-module (gnu packages cups) #:use-module (gnu packages glib) ; dbus for tests #:use-module (gnu packages gnome) #:use-module (gnu packages gstreamer) @@ -932,6 +933,41 @@ redone.") (license ;; GPL for programs, LGPL for libraries, FDL for documentation (list license:gpl2+ license:lgpl2.0+ license:fdl1.2+)))) +(define-public print-manager + (package + (name "print-manager") + (version "22.08.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/print-manager-" version ".tar.xz")) + (sha256 + (base32 "1abwj1ccm70adzx07ykqjlb4f6y55k2rv1j861dl0822187vl799")))) + (build-system qt-build-system) + (native-inputs + (list extra-cmake-modules)) + (inputs + (list cups + kcmutils + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + kiconthemes + ki18n + kio + knotifications + kwidgetsaddons + kwindowsystem + plasma-framework + qtdeclarative-5)) + (home-page "https://invent.kde.org/utilities/print-manager") + (synopsis "Manage print jobs and printers") + (description + "This package provides printing management for KDE.") + (license license:gpl2+))) + (define-public rsibreak (package (name "rsibreak") From 319c7712f67b5d37e2d588f44aca65b0fffdd061 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:39:26 +0200 Subject: [PATCH 173/824] gnu: Add kontrast. * gnu/packages/kde-utils.scm (kontrast): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index e74b4f6e8c..67ba0b9568 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -588,6 +588,33 @@ with support for QR scanning.") (license ;GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0))))) +(define-public kontrast + (package + (name "kontrast") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kontrast-" version ".tar.xz")) + (sha256 + (base32 + "03y3y5p29zx4nmqi7hp3abxq2n2bgwbz2knhn9vhl3im3ghp7lmp")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + ki18n + kcoreaddons + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://apps.kde.org/kontrast/") + (synopsis "Color contrast checker") + (description + "Kontrast is a color contrast checker and tells you if your color +combinations are distinct enough to be readable and accessible.") + (license license:gpl3+))) + (define-public libatcore (let ((commit "0de6393ed3e721537dec50b0ad174d83f1207eb6") (revision "1")) From e10e5f691d0a334187eab269b8164a753167036a Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:41:20 +0200 Subject: [PATCH 174/824] gnu: Add kbackup. * gnu/packages/kde-utils.scm (kbackup): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 67ba0b9568..abdac5b07c 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -425,6 +425,41 @@ Kate's features include: "This package allows to select which QLoggingCategory are displayed.") (license license:lgpl2.0+))) +(define-public kbackup + (package + (name "kbackup") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kbackup-" version ".tar.xz")) + (sha256 + (base32 + "0c0zdk00j9qssjdb5dg5hwc5mx7h5kvriyszia2xizqjq2m53c3k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kguiaddons + knotifications + ki18n + kio + kxmlgui + kiconthemes + karchive + kwidgetsaddons + shared-mime-info)) + (home-page "https://apps.kde.org/kbackup/") + (synopsis "Backup program with an easy-to-use interface") + (description + "This package provides tool to backup your data. +@itemize +@item profile for directories and files to be included or excluded from the +backup +@item The backup target can be either a locally mounted device like a ZIP +drive, USB stick, etc +@item Running automated backups without using a graphical user interface +@end itemize") + (license license:gpl2+))) + (define-public kdialog (package (name "kdialog") From 5c34774871e38ac1d863d6fe5682fa5bb4c79113 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:41:55 +0200 Subject: [PATCH 175/824] gnu: Add kcalc. * gnu/packages/kde-utils.scm (kcalc): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index abdac5b07c..ec1c622259 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages gstreamer) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) @@ -460,6 +461,35 @@ drive, USB stick, etc @end itemize") (license license:gpl2+))) +(define-public kcalc + (package + (name "kcalc") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kcalc-" version ".tar.xz")) + (sha256 + (base32 + "01rn6qy40q4b90i5mysrygkqh5fzq885dgcd11l6r8s59ijjcjlk")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list gmp + kcoreaddons + kcrash + kconfig + kconfigwidgets + kguiaddons + ki18n + knotifications + kxmlgui + mpfr)) + (home-page "https://apps.kde.org/kcalc/") + (synopsis "Scientific calculator") + (description + "This package provides a scientific calculator.") + (license license:gpl2+))) + (define-public kdialog (package (name "kdialog") From cc1ff122d71e32095cf81e5f2e8e01b3d0d0fc24 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 26 Sep 2022 17:42:28 +0200 Subject: [PATCH 176/824] gnu: Add kcharselect. * gnu/packages/kde-utils.scm (kcharselect): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-utils.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index ec1c622259..2742d6b846 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -490,6 +490,30 @@ drive, USB stick, etc "This package provides a scientific calculator.") (license license:gpl2+))) +(define-public kcharselect + (package + (name "kcharselect") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kcharselect-" version + ".tar.xz")) + (sha256 + (base32 + "1gs9jkq76dkhjgjqpl5dcsx0l2qi6i0pk122y1qmwgyd6f8af35b")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kbookmarks kcoreaddons kcrash ki18n kwidgetsaddons kxmlgui)) + (home-page "https://apps.kde.org/kcharselect/") + (synopsis "Select and copy special characters from installed fonts") + (description + "This package provides a tool to display various information +about the selected character. This includes not only the Unicode character +name, but also aliases, general notes and cross references to similar +characters.") + (license license:gpl2+))) + (define-public kdialog (package (name "kdialog") From beb859d52b0e0ab904bb0344d5d36b50be4eb4b7 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 3 Oct 2022 17:09:31 +0200 Subject: [PATCH 177/824] gnu: Add khealthcertificate. * gnu/packages/kde-pim.scm (khealthcertificate): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 5952beeffa..f98204cc63 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -895,6 +895,40 @@ for applying cryptography to short pieces of text, and can also quickly apply cryptography to the contents of the clipboard.") (license license:gpl2+))) +(define-public khealthcertificate + (package + (name "khealthcertificate") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + (version-major+minor version) + "/khealthcertificate-" version ".tar.xz")) + (sha256 + (base32 + "16vkjpyxwx34pvdpnci0l6mx2bdjialiscjvbdx53xbsq9ff701k")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" + "(icaovdsparsertest|nlcoronacheckparsertest)"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list karchive + kcodecs + ki18n + openssl + qtdeclarative-5 + zlib)) + (home-page "https://api.kde.org/khealthcertificate/html/index.html") + (synopsis "Digital vaccination and recovery certificate library") + (description + "This package provides a library for arsing of digital vaccination, +test and recovery certificates.") + (license license:lgpl2.0))) + (define-public kidentitymanagement (package (name "kidentitymanagement") From ea576461f29f10fad7343e964c583aab3b2d6cea Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 3 Oct 2022 17:33:16 +0200 Subject: [PATCH 178/824] gnu: Add kopeninghours. * gnu/packages/kde.scm (kopeninghours): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 5669588b9c..2558530203 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -768,6 +768,40 @@ including SSL/TLS, X.509 certificates, SASL, OpenPGP, S/MIME CMS, and smart cards.") (license license:lgpl2.1+))) +(define-public kopeninghours + (package + (name "kopeninghours") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "03hslgx4zgg7gsnz2xhx4wnchvqfc5n8c6ihgwz3972fkxsjfdvq")))) + (build-system cmake-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(evaluatetest|iterationtest)"))))))) + (native-inputs (list bison extra-cmake-modules flex)) + (inputs (list boost + kholidays + ki18n + osmctools + qtbase-5 + qtdeclarative-5)) + (home-page "https://invent.kde.org/libraries/kopeninghours") + (synopsis "Get opening hours from OpenStreetMap") + (description + "This package provides a library for parsing and evaluating OpenStreetMap +opening hours expressions.") + (license license:lgpl2.0+))) + (define-public kpmcore (package (name "kpmcore") From 7fa0e39acb1819a2c88158c73a9622288ac5acda Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 3 Oct 2022 17:33:54 +0200 Subject: [PATCH 179/824] gnu: Add kosmindoormap. * gnu/packages/kde.scm (kosmindoormap): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 2558530203..1c1c371fb8 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -802,6 +802,32 @@ cards.") opening hours expressions.") (license license:lgpl2.0+))) +(define-public kosmindoormap + (package + (name "kosmindoormap") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "042axwxa1497snr8f0m6a61gl9ypdkvllnhnlw4h5ffah7yl5n3s")))) + (build-system cmake-build-system) + (native-inputs (list bison extra-cmake-modules flex)) + (inputs (list ki18n + kopeninghours + kpublictransport + qtbase-5 + qtdeclarative-5 + zlib)) + (home-page "https://invent.kde.org/libraries/kosmindoormap") + (synopsis "Indoor map renderer") + (description + "This package provides facilities for rendering OpenStreetMap +multi-floor indoor maps.") + (license license:lgpl2.0+))) + (define-public kpmcore (package (name "kpmcore") From 1b1bbe3eb08a417766b9835d60f0a4207f3c977d Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Mon, 3 Oct 2022 17:47:08 +0200 Subject: [PATCH 180/824] gnu: Add itinerary. * gnu/packages/kde-pim.scm (itinerary): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-pim.scm | 54 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index f98204cc63..6f3cbf2999 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -362,6 +362,60 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0+)))) +(define-public itinerary + (package + (name "itinerary") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1w1gl4lz8gwf8cmxhsfyp4afiaq9anc8glrxay407bqp28andp3a")))) + (build-system qt-build-system) + (arguments + `(#:tests? #f)) ;Fails 20/27 + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive + kdbusaddons + ki18n + kio + kirigami + kitinerary + kitemmodels + kcoreaddons + kcontacts + kholidays + kmime + knotifications + kpublictransport + kcalendarcore + khealthcertificate + kosmindoormap + kopeninghours + kpkpass + kunitconversion + kwindowsystem + prison + qtdeclarative-5 + qtgraphicaleffects + qtlocation + qtmultimedia-5 + qtquickcontrols2-5 + qqc2-desktop-style + shared-mime-info + solid + sonnet + zlib)) + (home-page "https://invent.kde.org/pim/itinerary") + (synopsis "Itinerary and boarding pass management") + (description + "This package provides a tool for managing itinerary and boarding pass +information.") + (license ;GPL for programs, LGPL for libraries + (list license:gpl2+ license:lgpl2.0+)))) + (define-public kincidenceeditor (package (name "kincidenceeditor") From 7d9cd434777bc341ae098e057a209d9ae90677a2 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 4 Oct 2022 15:09:20 +0200 Subject: [PATCH 181/824] gnu: Add plasma-bigscreen. * gnu/packages/kde-plasma.scm (plasma-bigscreen): New variable. Signed-off-by: Marius Bakke --- gnu/packages/kde-plasma.scm | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 0771abe67a..ebed48234d 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1431,6 +1431,52 @@ on top of Baloo.") "KDE Plasma is an advanced graphical desktop system.") (license license:gpl2+))) +(define-public plasma-bigscreen + (package + (name "plasma-bigscreen") + (version "5.25.90") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/unstable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1445j8hzfvh2z91fa8nxrc0z576c67cq5fxcs19pmzpnjjli1ads")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-startplasma + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bin/plasma-bigscreen-wayland.in" + (("^startplasma-wayland") + (search-input-file inputs + "/bin/startplasma-wayland"))) + (substitute* "bin/plasma-bigscreen-x11" + (("startplasma-x11") + (search-input-file inputs + "/bin/startplasma-x11")))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list kactivities + kactivities-stats + plasma-framework + ki18n + kirigami + kdeclarative + kcmutils + knotifications + kio + kwayland + kwindowsystem + plasma-workspace + qtbase-5 + qtmultimedia-5)) + (home-page "https://invent.kde.org/plasma/plasma-bigscreen") + (synopsis "Plasma shell for TVs") + (description + "This package provides a big launcher designed for large screens. It +is controllable via voice or TV remote.") + (license license:gpl2+))) + (define-public plasmatube (package (name "plasmatube") From 82804298ad5587721628bbd1030248d0733a4359 Mon Sep 17 00:00:00 2001 From: Petr Hodina Date: Tue, 4 Oct 2022 20:55:37 +0200 Subject: [PATCH 182/824] gnu: libksysguard: Apply patch. * gnu/packages/kde-plasma.scm (libksysguard)[source]: Apply patch. * gnu/local.mk: Add patch. * gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch: New file. Signed-off-by: Marius Bakke --- gnu/local.mk | 1 + gnu/packages/kde-plasma.scm | 1 + ...ysguard-qdiriterator-follow-symlinks.patch | 24 +++++++++++++++++++ 3 files changed, 26 insertions(+) create mode 100644 gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch diff --git a/gnu/local.mk b/gnu/local.mk index a8674cd6bd..c524666a12 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1442,6 +1442,7 @@ dist_patch_DATA = \ %D%/packages/patches/libofa-ftbfs-2.diff \ %D%/packages/patches/libotr-test-auth-fix.patch \ %D%/packages/patches/libksieve-Fix-missing-link-libraries.patch \ + %D%/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch \ %D%/packages/patches/libmad-armv7-thumb-pt1.patch \ %D%/packages/patches/libmad-armv7-thumb-pt2.patch \ %D%/packages/patches/libmad-length-check.patch \ diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index ebed48234d..5af37e8de0 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -963,6 +963,7 @@ basic needs and easy to configure for those who want special setups.") (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/libksysguard-" version ".tar.xz")) + (patches (search-patches "libksysguard-qdiriterator-follow-symlinks.patch")) (sha256 (base32 "1gqsjsdkp25abqqp4f6cv6ih199q9ad7q1a4lkhjgsh4h8jq1856")))) (native-inputs diff --git a/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch b/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch new file mode 100644 index 0000000000..ec4a34037d --- /dev/null +++ b/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch @@ -0,0 +1,24 @@ +From 46164a50de4102d02ae9d1d480acdd4b12303db8 Mon Sep 17 00:00:00 2001 +From: Thomas Tuegel +Date: Wed, 14 Oct 2015 07:07:22 -0500 +Subject: [PATCH] qdiriterator follow symlinks + +--- + processui/scripting.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/processui/scripting.cpp b/processui/scripting.cpp +index efed8ff..841761a 100644 +--- a/processui/scripting.cpp ++++ b/processui/scripting.cpp +@@ -293,7 +293,7 @@ void Scripting::loadContextMenu() + const QStringList dirs = + QStandardPaths::locateAll(QStandardPaths::GenericDataLocation, QStringLiteral("ksysguard/scripts/"), QStandardPaths::LocateDirectory); + for (const QString &dir : dirs) { +- QDirIterator it(dir, QStringList() << QStringLiteral("*.desktop"), QDir::NoFilter, QDirIterator::Subdirectories); ++ QDirIterator it(dir, QStringList() << QStringLiteral("*.desktop"), QDir::NoFilter, QDirIterator::Subdirectories | QDirIterator::FollowSymlinks); + while (it.hasNext()) { + scripts.append(it.next()); + } +-- +2.5.2 From 945fd54f65118ce35199319d98f2e406df33d3a6 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Nov 2022 22:57:49 +0100 Subject: [PATCH 183/824] gnu: bzflag: Update to 2.4.26. * gnu/packages/games.scm (bzflag): Update to 2.4.26. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 357dee69d0..78327956be 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -880,14 +880,14 @@ Quizzes: arithmetic and quiz.") (define-public bzflag (package (name "bzflag") - (version "2.4.24") + (version "2.4.26") (source (origin (method url-fetch) (uri (string-append "https://download.bzflag.org/bzflag/source/" version "/bzflag-" version ".tar.bz2")) (sha256 - (base32 "1i73ijlnxsz52fhqgkj2qcvibfgav3byq1is68gab2zwnyz330az")))) + (base32 "050h933lmcdf4bw9z3c6g3k8c9sch9f6kq57jp2ivb96zw2h90q1")))) (build-system gnu-build-system) (arguments (list From 3ba966c56c23b4079fd42a1c771a743c59077c06 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Nov 2022 22:59:40 +0100 Subject: [PATCH 184/824] gnu: emacs-corfu: Update to 0.31. * gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.31. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 821240b6b2..1ca507e430 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3467,7 +3467,7 @@ of bibliographic references.") (define-public emacs-corfu (package (name "emacs-corfu") - (version "0.28") + (version "0.31") (source (origin (method git-fetch) @@ -3476,7 +3476,7 @@ of bibliographic references.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0lmjmaijanhhimkd006y5g1pvpllqgm30wj2y3wf3h4sl7h23rcz")))) + (base32 "10gz4x21dm73xf0w2zfxpfa0wykmmrid8yh0mxp1xbqpl86ig1x9")))) (build-system emacs-build-system) (arguments `(#:phases From 0a84c0e8eac7d649ad00339964e2eaf4f4732d52 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Nov 2022 23:02:50 +0100 Subject: [PATCH 185/824] gnu: emacs-crdt: Update to 0.3.5. * gnu/packages/emacs-xyz.scm (emacs-crdt): Update to 0.3.5. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1ca507e430..bcaa313932 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20819,8 +20819,8 @@ never confused by comments or @code{foo-bar} matching @code{foo}.") (define-public emacs-crdt ;; XXX: Upstream does not always tag new releases. The commit below ;; corresponds exactly to latest version bump. - (let ((commit "92a7c93a3b4cb4b40f133acd22c89a5fda5cdd30") - (version "0.3.4")) + (let ((commit "e6d42f42c5dedb73560048f4bf6263c63ffa21bb") + (version "0.3.5")) (package (name "emacs-crdt") (version version) @@ -20832,7 +20832,7 @@ never confused by comments or @code{foo-bar} matching @code{foo}.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1vh4d15g62crm4vimc7lgr11ws68g25ylipnvqlrrkvl6qrz3fhj")))) + (base32 "16dpg0d8p4fqjl2nir290iim9bb7f87rwnxs16lx67dasvbfawph")))) (build-system emacs-build-system) (home-page "https://code.librehq.com/qhong/crdt.el") (synopsis "Real-time collaborative editing environment") From aa9e31809d5127fb917f66644b9ad5d64ea95558 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Nov 2022 23:04:00 +0100 Subject: [PATCH 186/824] gnu: emacs-pg: Update to 0.19. * gnu/packages/emacs-xyz.scm (emacs-pg): Update to 0.19. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index bcaa313932..f5673aa59f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -19364,7 +19364,7 @@ match and total match information in the mode-line in various search modes.") (define-public emacs-pg (package (name "emacs-pg") - (version "0.16") + (version "0.19") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/emarsden/pg-el") @@ -19372,7 +19372,7 @@ match and total match information in the mode-line in various search modes.") (file-name (git-file-name name version)) (sha256 (base32 - "1jdnslpgdm16klaga02p33g7c8bjzg164kxz3jd7gs5v9gqa6ppz")))) + "13fkkpimhxh91hmsp551wzrdcic5ws7wj7vjwnh8l83hsrxmxz0y")))) (build-system emacs-build-system) (home-page "https://github.com/emarsden/pg-el") (synopsis "Emacs Lisp interface for PostgreSQL") From 544fcac62bb84feac4d72baea3cf237fdea495a5 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Nov 2022 23:06:18 +0100 Subject: [PATCH 187/824] gnu: wob: Update to 0.14.2. * gnu/packages/xdisorg.scm (wob): Update to 0.14.2. [inputs]: Add LIBINIH. --- gnu/packages/xdisorg.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 298e6f3e47..1a4d805f19 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1140,19 +1140,19 @@ transparent text on your screen.") (define-public wob (package (name "wob") - (version "0.13") + (version "0.14.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/francma/wob/releases/download/" version "/wob-" version ".tar.gz")) (sha256 - (base32 "0i8y6kq37qcgdq85ll4rapisjl7zw6aa11yx2f2xw2d3j93kdxh8")))) + (base32 "12s9pc0dhqgawq6jiqhamj1zq9753kgpswny1rcsdx1lkpzrgaq1")))) (build-system meson-build-system) (native-inputs (list pkg-config scdoc)) (inputs - (list libseccomp wayland wayland-protocols)) + (list libinih libseccomp wayland wayland-protocols)) (home-page "https://github.com/francma/wob") (synopsis "Lightweight overlay bar for Wayland") (description From 988ff3c8de504fe6ce4a5e6b4af04ab11fec02f0 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Mon, 21 Nov 2022 16:57:26 +0100 Subject: [PATCH 188/824] gnu: emacs-restclient: Update to 0-4.1fb5706. * gnu/packages/emacs-xyz.scm (emacs-restclient): Update to 0-4.1fb5706. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f5673aa59f..82e5bd0a98 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16957,9 +16957,9 @@ formatting, and utility methods for jsonnet files.") (license license:gpl3+))) (define-public emacs-restclient - (let ((commit "ac8aad6c6b9e9d918062fa3c89c22c2f4ec48bc3") + (let ((commit "1fb570643b08ba66eb70831b6f874f52546917f1") (version "0") - (revision "3")) ;Guix package revision, + (revision "4")) ;Guix package revision, ;upstream doesn't have official releases (package (name "emacs-restclient") @@ -16971,7 +16971,7 @@ formatting, and utility methods for jsonnet files.") (commit commit))) (sha256 (base32 - "1a2c7xzy7rsan1zcdskia6m7n6j29xacfkqjlfdhzk6rr1bpzkwk")) + "0npij1p1yw4p1f1yrx6bl8q18nav5p2xvbp7qhzhn7lb2fdn5jqv")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (propagated-inputs From 84100023e23045be2735a6b53f26b2a3c3a1f606 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Mon, 21 Nov 2022 17:05:02 +0100 Subject: [PATCH 189/824] gnu: emacs-ob-restclient: Update to 0.02-3.1b021ce. * gnu/packages/emacs-xyz.scm (emacs-ob-restclient): Update to 0.02-3.1b021ce. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 82e5bd0a98..754d2e3cb8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6133,10 +6133,10 @@ blocks with @code{org-babel} in @code{org-mode}.") (license license:gpl3+)))) (define-public emacs-ob-restclient - (let ((commit "f7449b2068498fe9d8ab9589e0a638148861533f")) + (let ((commit "1b021ce1c67c97fa1aa4d2c0816edb7add129e48")) (package (name "emacs-ob-restclient") - (version (git-version "0.02" "2" commit)) + (version (git-version "0.02" "3" commit)) (source (origin (method git-fetch) @@ -6145,7 +6145,7 @@ blocks with @code{org-babel} in @code{org-mode}.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0s3931w9ab3yfml2pmq71rw21yf6hpg7m3vihxyy3vs6zli1cvmq")))) + (base32 "1bcjj01q5n9w2cch6brbz8pzwnwsmdlgaa4sf5s97b9frmqb2ffg")))) (propagated-inputs (list emacs-restclient)) (build-system emacs-build-system) From 437718442ca758a3857702cecfe5c80aa5df272b Mon Sep 17 00:00:00 2001 From: Yarl Baudig Date: Mon, 21 Nov 2022 15:16:27 +0100 Subject: [PATCH 190/824] gnu: Add texlive-mathdots. * gnu/packages/tex.scm (texlive-mathdots): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/tex.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 81f74f17df..a600bcae58 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3993,6 +3993,47 @@ definitions.") (define-deprecated-package texlive-latex-amsmath texlive-amsmath) +(define-public texlive-mathdots + (let ((template + (simple-texlive-package + "texlive-mathdots" + (list "doc/generic/mathdots/" + "source/generic/mathdots/" + "tex/generic/mathdots/") + (base32"1jaffj343p1chdxs2g7s6lpckvihk0jfw22nw0vmijyjxfiy9yg0")))) + (package + (inherit template) + (outputs '("out" "doc")) + (arguments + (substitute-keyword-arguments (package-arguments template) + ((#:tex-directory _ '()) + "generic/mathdots") + ((#:build-targets _ '()) + '(list "mathdots.ins")) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "source/generic/mathdots"))) + (replace 'copy-files + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((origin (assoc-ref inputs "source")) + (source (string-append (assoc-ref outputs "out") + "/share/texmf-dist/source")) + (doc (string-append (assoc-ref outputs "doc") + "/share/texmf-dist/doc"))) + (copy-recursively (string-append origin "/source") source) + (copy-recursively (string-append origin "/doc") doc)))))))) + (home-page "https://ctan.org/macros/generic/mathdots") + (synopsis "Commands to produce dots in math that respect font size") + (description + "Mathdots redefines @code{\\ddots} and @code{\\vdots}, and defines +@code{\\iddots}. The dots produced by @code{\\iddots} slant in the opposite +direction to @code{\\ddots}. All the commands are designed to change size +appropriately in scripts, as well as in response to LaTeX size changing +commands. The commands may also be used in plain TeX.") + (license license:lppl)))) + (define-public texlive-amscls (let ((template (simple-texlive-package "texlive-amscls" From 628afdc39271852baf2aac07e236568aeee1d611 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 05:53:00 +0100 Subject: [PATCH 191/824] gnu: Remove acme-client. This package does not build and has been unmaintained since 2018: https://github.com/kristapsdz/acme-client-portable/commit/ba153daacb62d8a24fef6d6a5a737d2eff607509 * gnu/packages/tls.scm (acme-client): Remove variable. --- gnu/packages/tls.scm | 41 ----------------------------------------- 1 file changed, 41 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 3aceb349bf..f1e844b608 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -995,47 +995,6 @@ correct OpenSSL include path. It is intended for use in your number generator") (license license:perl-license))) -(define-public acme-client - (package - (name "acme-client") - (version "0.1.16") - (source (origin - (method url-fetch) - (uri (string-append "https://kristaps.bsd.lv/" name "/" - "snapshots/" name "-portable-" - version ".tgz")) - (sha256 - (base32 - "00q05b3b1dfnfp7sr1nbd212n0mqrycl3cr9lbs51m7ncaihbrz9")))) - (build-system gnu-build-system) - (arguments - '(#:tests? #f ; no test suite - #:make-flags - (list "CC=gcc" - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((pem (search-input-file inputs "/etc/ssl/cert.pem"))) - (substitute* "http.c" - (("/etc/ssl/cert.pem") pem)) - #t))) - (delete 'configure)))) ; no './configure' script - (native-inputs - (list pkg-config)) - (inputs - (list libbsd libressl)) - (synopsis "Let's Encrypt client by the OpenBSD project") - (description "acme-client is a Let's Encrypt client implemented in C. It -uses a modular design, and attempts to secure itself by dropping privileges and -operating in a chroot where possible. acme-client is developed on OpenBSD and -then ported to the GNU / Linux environment.") - (home-page "https://kristaps.bsd.lv/acme-client/") - ;; acme-client is distributed under the ISC license, but the files 'jsmn.h' - ;; and 'jsmn.c' are distributed under the Expat license. - (license (list license:isc license:expat)))) - ;; The "-apache" variant is the upstreamed prefered variant. A "-gpl" ;; variant exists in addition to the "-apache" one. (define-public mbedtls-apache From 3d62d7648a87885404f2513e05d7d7e350cf7a23 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 05:59:00 +0100 Subject: [PATCH 192/824] gnu: arpack-ng: Remove 3.3.0. This package fails to build and has no users in Guix. * gnu/packages/maths.scm (arpack-ng-3.3.0): Remove variable. --- gnu/packages/maths.scm | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 972221798e..15c020e6c4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -894,20 +894,6 @@ large scale eigenvalue problems.") (license (license:non-copyleft "file://COPYING" "See COPYING in the distribution.")))) -(define-public arpack-ng-3.3.0 - (package - (inherit arpack-ng) - (version "3.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference (url (package-home-page arpack-ng)) - (commit version))) - (file-name (git-file-name (package-name arpack-ng) version)) - (sha256 - (base32 - "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918")))))) - (define-public arpack-ng-openmpi (package (inherit arpack-ng) (name "arpack-ng-openmpi") From 4bf4e051d1d3a820867e39273213374d2bc6df75 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:00:52 +0100 Subject: [PATCH 193/824] gnu: protobuf@3.5: Inherit from protobuf@3.6. * gnu/packages/protobuf.scm (protobuf-3.5): Change inheritance, so it gets the correct build system and phases. --- gnu/packages/protobuf.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index a052a38853..f7184bd49a 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -189,7 +189,7 @@ internal RPC protocols and file formats.") ;; The 3.5 series are the last versions that do not require C++ 11. (define-public protobuf-3.5 (package - (inherit protobuf) + (inherit protobuf-3.6) (version "3.5.1") (source (origin (method url-fetch) From ae24d4b34af54017d62ec30364219fa3482e9fd9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:07:21 +0100 Subject: [PATCH 194/824] gnu: ashuffle: Update to 3.13.4. * gnu/packages/mpd.scm (ashuffle): Update to 3.13.4. [inputs]: Add ABSEIL-CPP-CXXSTD17, GOOGLETEST, and YAML-CPP. [arguments]: New field. --- gnu/packages/mpd.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 4e9cb0cb37..0c8dc16cf9 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cdrom) #:use-module (gnu packages cmake) ;for MPD + #:use-module (gnu packages cpp) #:use-module (gnu packages freedesktop) ;elogind #:use-module (gnu packages gettext) #:use-module (gnu packages gnome) @@ -72,6 +73,7 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) #:use-module (gnu packages video) @@ -380,7 +382,7 @@ MPD servers, search and multimedia key support.") (define-public ashuffle (package (name "ashuffle") - (version "2.0.2") + (version "3.13.4") (source (origin (method git-fetch) (uri (git-reference @@ -389,10 +391,20 @@ MPD servers, search and multimedia key support.") (file-name (git-file-name name version)) (sha256 (base32 - "11aa95cg0yca2m2d00sar6wr14g3lc7cfm9bin1h7lk7asdm8azp")))) + "09dvar0aglyy2h9y115ymgryd8l6npc2y2ccdzij0b70f47ncqmf")))) (native-inputs (list pkg-config)) - (inputs (list libmpdclient)) + (inputs + (list abseil-cpp-cxxstd17 + googletest + libmpdclient + yaml-cpp)) (build-system meson-build-system) + (arguments + (list #:configure-flags + #~'("-Dtests=enabled" + "-Dunsupported_use_system_absl=true" + "-Dunsupported_use_system_gtest=true" + "-Dunsupported_use_system_yamlcpp=true"))) (home-page "https://github.com/joshkunz/ashuffle") (synopsis "Automatic library-wide shuffle for mpd") (description "ashuffle is an application for automatically shuffling your From 3d2de69c066518a95bb8bc07e306cd2c337ef12c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:38:38 +0100 Subject: [PATCH 195/824] gnu: gpgme: Add 1.18.0. * gnu/packages/gnupg.scm (gpgme-1.18, qgpgme-1.18): New variables. --- gnu/packages/gnupg.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 210b1ab8b3..064b775ab1 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -431,6 +431,19 @@ and every application benefits from this.") (properties '((ftp-server . "ftp.gnupg.org") (ftp-directory . "/gcrypt/gpgme"))))) +;; TODO: Merge with gpgme in the next rebuild cycle. +(define-public gpgme-1.18 + (package + (inherit gpgme) + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnupg/gpgme/gpgme-" + version ".tar.bz2")) + (sha256 + (base32 + "17hfigfnq6xz45b5xrp299f68b5mwx0aysd51sx5v4nf8yp4w79n")))))) + (define-public qgpgme (package (inherit gpgme) @@ -459,6 +472,16 @@ QGpgME was originally developed as part of libkleo and incorporated into gpgpme starting with version 1.7.") (license license:gpl2+))) ;; Note: this differs from gpgme +;; TODO: Merge with qgpgme in the next rebuild cycle. +(define-public qgpgme-1.18 + (package + (inherit qgpgme) + (version (package-version gpgme-1.18)) + (source (package-source gpgme-1.18)) + (inputs + (modify-inputs (package-inputs qgpgme) + (replace "gpgme" gpgme-1.18))))) + (define-public guile-gcrypt (package (name "guile-gcrypt") From 12673ef450262fb6618f97f267cd37afd355276d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:39:05 +0100 Subject: [PATCH 196/824] gnu: kleopatra: Build with gpgme@1.18. * gnu/packages/kde-pim.scm (kleopatra)[inputs]: Change from GPGME and QGPGME to GPGME-1.18 and QGPGME-1.18. --- gnu/packages/kde-pim.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 6f3cbf2999..55ad21f952 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -1139,7 +1139,7 @@ protocol for querying and modifying directory services running over TCP/IP.") kdoctools)) (inputs (list boost - gpgme + gpgme-1.18 kcmutils kcodecs kconfig @@ -1159,7 +1159,7 @@ protocol for querying and modifying directory services running over TCP/IP.") libassuan libkleo breeze-icons ;; default icon set - qgpgme + qgpgme-1.18 qtbase-5)) (arguments `(#:phases From dc7397845dbb85eee83f8d2a890a479690d60a5a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:45:16 +0100 Subject: [PATCH 197/824] gnu: kmail: Build with gpgme@1.18. * gnu/packages/kde-pim.scm (kmail)[inputs]: Change from GPGME and QGPGME to GPGME-1.18 and QGPGME-1.18. --- gnu/packages/kde-pim.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 55ad21f952..19066fd289 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -1196,7 +1196,7 @@ and retrieving certificates from LDAP servers.") akonadi-mime akonadi-search boost - gpgme + gpgme-1.18 grantlee grantleetheme kbookmarks @@ -1243,7 +1243,7 @@ and retrieving certificates from LDAP servers.") libkleo libksieve breeze-icons ; default icon set, required for tests - qgpgme + qgpgme-1.18 qtbase-5 qtdeclarative-5 qtkeychain From 41ca8f9c207a04f266b061ec91cb9031967ed109 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:47:30 +0100 Subject: [PATCH 198/824] gnu: dune-alugrid: Fix build failure. * gnu/packages/maths.scm (dune-alugrid)[arguments]: Provide the INPUTS key in build-tests phase. --- gnu/packages/maths.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 15c020e6c4..98bae9ecb5 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6811,7 +6811,7 @@ assemble global function spaces on finite-element grids.") "doc/dune-grid/grids/gridfactory/testgrids")) #t)) (add-after 'build 'build-tests - (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (lambda* (#:key inputs make-flags parallel-build? #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) (apply invoke "make" "build_tests" From 0fec067efec0e70a9cd3c25d7a3aa40401667b4a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 06:54:02 +0100 Subject: [PATCH 199/824] gnu: ecl: Remove 16.1.3. This package fails to build and has no users in Guix. * gnu/packages/sagemath.scm (ecl-16): Remove variable. * gnu/packages/patches/ecl-16-format-directive-limit.patch, gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch, gnu/packages/patches/ecl-16-libffi.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. --- gnu/local.mk | 3 - .../ecl-16-format-directive-limit.patch | 83 ------------------- .../ecl-16-ignore-stderr-write-error.patch | 17 ---- gnu/packages/patches/ecl-16-libffi.patch | 16 ---- gnu/packages/sagemath.scm | 21 ----- 5 files changed, 140 deletions(-) delete mode 100644 gnu/packages/patches/ecl-16-format-directive-limit.patch delete mode 100644 gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch delete mode 100644 gnu/packages/patches/ecl-16-libffi.patch diff --git a/gnu/local.mk b/gnu/local.mk index c524666a12..3b0e6b0c2c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1044,9 +1044,6 @@ dist_patch_DATA = \ %D%/packages/patches/dstat-skip-devices-without-io.patch \ %D%/packages/patches/dvd+rw-tools-add-include.patch \ %D%/packages/patches/dynaconf-unvendor-deps.patch \ - %D%/packages/patches/ecl-16-format-directive-limit.patch \ - %D%/packages/patches/ecl-16-ignore-stderr-write-error.patch \ - %D%/packages/patches/ecl-16-libffi.patch \ %D%/packages/patches/efibootmgr-remove-extra-decl.patch \ %D%/packages/patches/efivar-211.patch \ %D%/packages/patches/eigen-fix-strict-aliasing-bug.patch \ diff --git a/gnu/packages/patches/ecl-16-format-directive-limit.patch b/gnu/packages/patches/ecl-16-format-directive-limit.patch deleted file mode 100644 index 237db92722..0000000000 --- a/gnu/packages/patches/ecl-16-format-directive-limit.patch +++ /dev/null @@ -1,83 +0,0 @@ -Patch backported by Sage. - -Fix from upstream that happens to work around -https://trac.sagemath.org/ticket/23011 -diff --git a/src/lsp/format.lsp b/src/lsp/format.lsp -index 77ca799..53b887c 100644 ---- a/src/lsp/format.lsp -+++ b/src/lsp/format.lsp -@@ -307,11 +307,13 @@ - :start (format-directive-start struct) - :end (format-directive-end struct)))) - -+(defconstant +format-directive-limit+ (1+ (char-code #\~))) -+ - #+formatter - (defparameter *format-directive-expanders* -- (make-array char-code-limit :initial-element nil)) -+ (make-array +format-directive-limit+ :initial-element nil)) - (defparameter *format-directive-interpreters* -- (make-array char-code-limit :initial-element nil)) -+ (make-array +format-directive-limit+ :initial-element nil)) - - (defparameter *default-format-error-control-string* nil) - (defparameter *default-format-error-offset* nil) -@@ -550,24 +552,24 @@ - (write-string directive stream) - (interpret-directive-list stream (cdr directives) orig-args args)) - (#-ecl format-directive #+ecl vector -+ (multiple-value-bind -+ (new-directives new-args) -+ (let* ((code (char-code (format-directive-character directive))) -+ (function -+ (and (< code +format-directive-limit+) -+ (svref *format-directive-interpreters* code))) -+ (*default-format-error-offset* -+ (1- (format-directive-end directive)))) -+ (unless function -+ (error 'format-error -+ :complaint "Unknown format directive.")) - (multiple-value-bind - (new-directives new-args) -- (let ((function -- (svref *format-directive-interpreters* -- (char-code (format-directive-character -- directive)))) -- (*default-format-error-offset* -- (1- (format-directive-end directive)))) -- (unless function -- (error 'format-error -- :complaint "Unknown format directive.")) -- (multiple-value-bind -- (new-directives new-args) -- (funcall function stream directive -- (cdr directives) orig-args args) -- (values new-directives new-args))) -- (interpret-directive-list stream new-directives -- orig-args new-args))))) -+ (funcall function stream directive -+ (cdr directives) orig-args args) -+ (values new-directives new-args))) -+ (interpret-directive-list stream new-directives -+ orig-args new-args))))) - args)) - - -@@ -639,11 +641,12 @@ - (values `(write-string ,directive stream) - more-directives)) - (format-directive -- (let ((expander -- (aref *format-directive-expanders* -- (char-code (format-directive-character directive)))) -- (*default-format-error-offset* -- (1- (format-directive-end directive)))) -+ (let* ((code (char-code (format-directive-character directive))) -+ (expander -+ (and (< code +format-directive-limit+) -+ (svref *format-directive-expanders* code))) -+ (*default-format-error-offset* -+ (1- (format-directive-end directive)))) - (if expander - (funcall expander directive more-directives) - (error 'format-error diff --git a/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch b/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch deleted file mode 100644 index 42d213c0e9..0000000000 --- a/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch +++ /dev/null @@ -1,17 +0,0 @@ -Patch adapted from Sage. -diff -Naur ecl-16.1.2.orig/src/c/file.d ecl-16.1.2/src/c/file.d ---- ecl-16.1.2.orig/src/c/file.d 2016-05-11 13:10:51.867673867 +1200 -+++ ecl-16.1.2/src/c/file.d 2016-05-11 14:44:48.121907307 +1200 -@@ -3354,8 +3354,10 @@ - ecl_disable_interrupts(); - do { - out = fwrite(c, sizeof(char), n, IO_STREAM_FILE(strm)); -- } while (out < n && restartable_io_error(strm, "fwrite")); -- ecl_enable_interrupts(); -+ /* Ignore write errors to stderr to avoid an infinite loop */ -+ } while (out < n && (IO_STREAM_FILE(strm) != stderr) && restartable_io_error(strm, "fwrite")); -+ -+ ecl_enable_interrupts(); - return out; - } - diff --git a/gnu/packages/patches/ecl-16-libffi.patch b/gnu/packages/patches/ecl-16-libffi.patch deleted file mode 100644 index fc06a07606..0000000000 --- a/gnu/packages/patches/ecl-16-libffi.patch +++ /dev/null @@ -1,16 +0,0 @@ -Patch adapted from Sage. Allows building ECL on libffi 3.3. -diff --git a/src/c/ffi.d b/src/c/ffi.d -index 8861303e..8a959c23 100644 ---- a/src/c/ffi.d -+++ b/src/c/ffi.d -@@ -133,8 +133,8 @@ static struct { - #elif defined(X86_WIN64) - {@':win64', FFI_WIN64}, - #elif defined(X86_ANY) || defined(X86) || defined(X86_64) -- {@':cdecl', FFI_SYSV}, -- {@':sysv', FFI_SYSV}, -+ {@':cdecl', FFI_UNIX64}, -+ {@':sysv', FFI_UNIX64}, - {@':unix64', FFI_UNIX64}, - #endif - }; diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 4542bc1c88..3d8c07b813 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -170,27 +170,6 @@ represented as strings.") (license license:public-domain) (home-page "https://github.com/miguelmarco/libhomfly"))) -;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is -;; released. See https://trac.sagemath.org/ticket/22191 -(define-public ecl-16 - (package - (inherit ecl) - (version "16.1.3") - (source - (origin - (method url-fetch) - (uri (string-append - "https://common-lisp.net/project/ecl/static/files/release/ecl" - "-" version ".tgz")) - (sha256 - (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn")) - (patches (search-patches - "ecl-16-libffi.patch" - "ecl-16-ignore-stderr-write-error.patch" - "ecl-16-format-directive-limit.patch")))) - ;; Current ECL uses LGPL 2.1+ - (license license:lgpl2.0+))) - (define-public pynac (package (name "pynac") From 2f69eeabd667f64c674c19e7c3e91decb8ed0439 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:10:07 +0100 Subject: [PATCH 200/824] gnu: ifstatus: Update to 2.0.0. * gnu/packages/networking.scm (ifstatus): Update to 2.0.0. [source](uri): Adjust. [source](modules, snippet): Remove. --- gnu/packages/networking.scm | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 3f44d082fb..8f05ce7d0c 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1538,22 +1538,14 @@ Ethernet devices.") (define-public ifstatus (package (name "ifstatus") - (version "1.1.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/ifstatus/ifstatus/" - "ifstatus%20v" version "/ifstatus-v" - version ".tar.gz")) + "ifstatus-v" version ".tar.gz")) (sha256 (base32 - "045cbsq9ps32j24v8y5hpyqxnqn9mpaf3mgvirlhgpqyb9jsia0c")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Main.h" - (("#include ") - "#include \n#include ")) - #t)))) + "0n622f2m3x901hcmad4ns52r2x75csy4nqraagzb8h9fn0j62jkv")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no "check" target From db6225d9dcfe617ec4e6f1b1baae0c3b9a6d7ca1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:19:59 +0100 Subject: [PATCH 201/824] gnu: Remove libbson. This package fails to build and has been deprecated since 2018: https://github.com/mongodb/libbson * gnu/packages/serialization.scm (libbson): Remove variable. --- gnu/packages/serialization.scm | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 79c55e2b2f..8ab1efd311 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -578,27 +578,6 @@ object, without whitespace.") RPC system. Think JSON, except binary. Or think Protocol Buffers, except faster.") (license license:expat))) -(define-public libbson - (package - (name "libbson") - (version "1.6.2") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/mongodb/libbson/releases/" - "download/" version "/libbson-" version ".tar.gz")) - (sha256 - (base32 - "1fj4554msq0rrz14snbj908dzqj46gh7jg9w9j0akn2b7q911m5a")))) - (build-system gnu-build-system) - (native-inputs (list perl)) - (home-page "http://mongoc.org/libbson/current/index.html") - (synopsis "C BSON library") - (description "Libbson can create and parse BSON documents. It can also -convert JSON documents to BSON and the opposite. BSON stands for Binary JSON, -it is comparable to protobuf.") - (license license:asl2.0))) - (define-public python-ruamel.yaml (package (name "python-ruamel.yaml") From 26f76355bf00505a6fa271d47c44be87db73e81e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:24:25 +0100 Subject: [PATCH 202/824] gnu: libsbsms: Fix build. * gnu/packages/audio.scm (libsbsms)[arguments]: Adjust path to ar-lib. --- gnu/packages/audio.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 70d9d4421d..b4a0189f8b 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3707,7 +3707,8 @@ analysis plugins or audio feature extraction plugins.") (symlink (search-input-file inputs (string-append "/share/automake-" - ,(package-version automake) + ,(version-major+minor + (package-version automake)) "/ar-lib")) "ar-lib") #t))))) From 256a63ce0b8dae05a44ccdadf682f23a8be5396b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:30:05 +0100 Subject: [PATCH 203/824] gnu: libwindowswm: Add missing input. * gnu/packages/xorg.scm (libwindowswm)[inputs]: Add WINDOWSWMPROTO. --- gnu/packages/xorg.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index a6b7b71d1d..7767a35afe 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1217,7 +1217,7 @@ hit when running single-threaded.") "1p0flwb67xawyv6yhri9w17m1i4lji5qnd0gq8v1vsfb8zw7rw15")))) (build-system gnu-build-system) (inputs - (list xorgproto libxext libx11)) + (list xorgproto libxext libx11 windowswmproto)) (native-inputs (list pkg-config)) (home-page "https://www.x.org/wiki/") From c0a39f12f14f45e84c457de2aa1cc8a856052526 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:38:03 +0100 Subject: [PATCH 204/824] gnu: neatmail: Fix build. * gnu/packages/mail.scm (neatmail)[arguments]: Fix quoting issue. --- gnu/packages/mail.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 414308d9fe..dc9fed90eb 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -4557,7 +4557,7 @@ databases, and other tools to process Outlook email archives.") (build-system gnu-build-system) (arguments `(#:tests? #f ;no tests - #:make-flags `((string-append "CC=" ,(cc-for-target))) + #:make-flags (list (string-append "CC=" ,(cc-for-target))) #:phases (modify-phases %standard-phases (delete 'configure) ;no configure script From a3c87f14608fdf103139d76a602b26db196a6018 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:42:16 +0100 Subject: [PATCH 205/824] gnu: nickle: Update to 2.90. * gnu/packages/nickle.scm (nickle): Update to 2.90. --- gnu/packages/nickle.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/nickle.scm b/gnu/packages/nickle.scm index 95b9915414..6b69d7cb92 100644 --- a/gnu/packages/nickle.scm +++ b/gnu/packages/nickle.scm @@ -28,14 +28,14 @@ (define-public nickle (package (name "nickle") - (version "2.82") + (version "2.90") (source (origin (method url-fetch) (uri (string-append "https://nickle.org/release/nickle-" version ".tar.gz")) (sha256 (base32 - "0jy96z01qbrnmsrywn5mfa14615qdix6b8520qd65c6yjyrk8gs0")))) + "197532b7ghkfnzx9qvxd2qjpnqba7bfl79iff3hk2jxcl0d83czv")))) (build-system gnu-build-system) (native-inputs (list readline)) From b122a40df41b238e8950efaa4e733425c6ca1576 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:44:20 +0100 Subject: [PATCH 206/824] gnu: python-socksipychain: Add missing input. * gnu/packages/python-xyz.scm (python-socksipychain)[propagated-inputs]: Add PYTHON-SIX. --- gnu/packages/python-xyz.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index eaad292a7f..2bbb7697b3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7066,6 +7066,8 @@ as the original project seems to have been abandoned circa 2007.") (build-system python-build-system) (arguments `(#:tests? #f)) ; Tests try to access the network. + (propagated-inputs + (list python-six)) (home-page "http://pagekite.net/wiki/Floss/PySocksipyChain/") (synopsis "Python SOCKS module with chained proxies support") (description From ff8ac616e729ff79202f1439a49389ab0ec0bbbc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:50:36 +0100 Subject: [PATCH 207/824] gnu: python-bigfloat: Update to 0.4.0. * gnu/packages/python-xyz.scm (python-bigfloat): Update to 0.4.0. [propagated-inputs]: Add PYTHON-SIX. --- gnu/packages/python-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2bbb7697b3..718a0eb79c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10291,16 +10291,18 @@ more advanced mathematics.") (define-public python-bigfloat (package (name "python-bigfloat") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (pypi-uri "bigfloat" version)) (sha256 - (base32 "0xd7q4l7v0f463diznjv4k9wlaks80pn9drdqmfifi7zx8qvybi6")))) + (base32 "1f0c1hdr39bbl5rds5r1waa1papjmjiyp0ixs64mkjiahzg6pfaq")))) (build-system python-build-system) (inputs (list mpfr)) + (propagated-inputs + (list python-six)) (home-page "https://github.com/mdickinson/bigfloat") (synopsis "Arbitrary precision floating-point arithmetic for Python") (description From 38f80083599caf8c821b56b20e861c62af2eb5d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:52:11 +0100 Subject: [PATCH 208/824] gnu: python-rnc2rng: Update to 2.6.6. * gnu/packages/python-xyz.scm (python-rnc2rng): Update to 2.6.6. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 718a0eb79c..1a50100f5e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27410,14 +27410,14 @@ and pandoc-citeproc.") (define-public python-rnc2rng (package (name "python-rnc2rng") - (version "2.6.4") + (version "2.6.6") (source (origin (method url-fetch) (uri (pypi-uri "rnc2rng" version)) (sha256 (base32 - "1kmp3iwxxyzjsd47j2sprd47ihhkwhb3yydih3af5bbfq0ibh1w8")))) + "1wbqvz2bhq2f5kqi7q2q3m9y5vs9rj970zhnjh502pvvhmbx20as")))) (build-system python-build-system) (propagated-inputs (list python-rply)) From 868325560eeb622839fcaa0e1ef28ea64b8fe0e2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:53:14 +0100 Subject: [PATCH 209/824] gnu: Remove python-enum34. This compatibility package fails to build and has no users in Guix. * gnu/packages/python-xyz.scm (python-enum34): Remove variable. --- gnu/packages/python-xyz.scm | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1a50100f5e..4f20396a75 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3140,25 +3140,6 @@ system is highly configurable via command line options and embedded commands.") (license license:lgpl2.1+))) -(define-public python-enum34 - (package - (name "python-enum34") - (version "1.1.6") - (source - (origin - (method url-fetch) - (uri (pypi-uri "enum34" version)) - (sha256 - (base32 - "1cgm5ng2gcfrkrm3hc22brl6chdmv67b9zvva9sfs7gn7dwc9n4a")))) - (build-system python-build-system) - (home-page "https://pypi.org/project/enum34/") - (synopsis "Backported Python 3.4 Enum") - (description - "Enum34 is the new Python stdlib enum module available in Python 3.4 -backported for previous versions of Python from 2.4 to 3.3.") - (license license:bsd-3))) - (define-public python-parse-type (package (name "python-parse-type") From 1d7f0a96f47c271f4efd37c23cee827b4cfb9d60 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:55:37 +0100 Subject: [PATCH 210/824] gnu: python-parallel: Add missing input. * gnu/packages/python-xyz.scm (python-parallel)[propagated-inputs]: Add PYTHON-SIX. --- gnu/packages/python-xyz.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4f20396a75..7e667ef7e1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27595,6 +27595,8 @@ module patches @code{asyncio} to allow nested use of @code{asyncio.run} and "1mzk4yabxj6r149fswhis18hd8dnag5sj8i4wb06450zq3pi8dh7")))) (native-inputs (list unzip)) + (propagated-inputs + (list python-six)) (build-system python-build-system) (arguments '(#:tests? #f)) ; No test suite. (home-page "https://www.parallelpython.com") From 4147c43a9c10079bdeacedb5ae259990fc0b2f50 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 07:58:25 +0100 Subject: [PATCH 211/824] gnu: python-py3dns: Fix build failure. * gnu/packages/python-xyz.scm (python-py3dns)[arguments]: Remove sanity check. --- gnu/packages/python-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7e667ef7e1..4ee572096f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17633,8 +17633,10 @@ It supports TSIG authenticated messages and EDNS0.") (lambda _ (substitute* "setup.py" (("import DNS") "") - (("DNS.__version__") (string-append "\"" ,version "\""))) - #t))) + (("DNS.__version__") (string-append "\"" ,version "\""))))) + ;; For the same reason, drop the sanity check because the library + ;; fails to load without /etc/resolv.conf. + (delete 'sanity-check)) #:tests? #f)) ; Also skip the tests. (home-page "https://launchpad.net/py3dns") (synopsis "Python 3 DNS library") From 859a10a47d624167cc2fc603a4bf0c8d618fc9a8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 08:09:10 +0100 Subject: [PATCH 212/824] gnu: remake: Update to 4.3-1.6. * gnu/packages/debug.scm (remake): Update to 4.3-1.6. --- gnu/packages/debug.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 0c7f97b386..e69d1ce83b 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -597,7 +597,7 @@ the position of the variable and allows you to modify its value.") (define-public remake (package (inherit gnu-make) (name "remake") - (version "4.3-1.5") + (version "4.3-1.6") (source (origin (method url-fetch) (uri (let ((upstream-version @@ -609,7 +609,7 @@ the position of the variable and allows you to modify its value.") (file-name (string-append "remake-" version ".tar.gz")) (sha256 (base32 - "0xlx2485y0israv2pfghmv74lxcv9i5y65agy69mif76yc4vfvif")) + "11vvch8bi0yhjfz7gn92b3xmmm0cgi3qfiyhbnnj89frkhbwd87n")) (patches (search-patches "remake-impure-dirs.patch")))) (inputs (modify-inputs (package-inputs gnu-make) From e08ffa2447449dbbdf5708c13cc2ea0e8a1ae281 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 08:20:08 +0100 Subject: [PATCH 213/824] gnu: slurm-monitor: Update to 0.4.4. * gnu/packages/networking.scm (slurm-monitor): Update to 0.4.4. [build-system]: Change to MESON-BUILD-SYSTEM. [native-inputs]: Add PKG-CONFIG. --- gnu/packages/networking.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 8f05ce7d0c..f5276e330e 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -593,7 +593,7 @@ supported, including rtmp://, rtmpt://, rtmpe://, rtmpte://, and rtmps://.") (define-public slurm-monitor (package (name "slurm-monitor") - (version "0.4.3") + (version "0.4.4") (source (origin (method git-fetch) @@ -603,9 +603,10 @@ supported, including rtmp://, rtmpt://, rtmpe://, rtmpte://, and rtmps://.") (commit (string-append "upstream/" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1n6pgrcs8gwrcq5fch1q3yk3jipjwrf21s9a13fbjrl903g5zzv9")))) - (build-system cmake-build-system) + (base32 "07q8895bxsajkwip8dgrrwr1m8a10xnl4p0g6wqcrd2wf4hx5gn3")))) + (build-system meson-build-system) (arguments `(#:tests? #f)) ;no tests + (native-inputs (list pkg-config)) (inputs (list ncurses)) (synopsis "Network load monitor") (description From 372ba7b3dba63dc1689c6eb0144a97f9585c613a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 08:24:44 +0100 Subject: [PATCH 214/824] gnu: perl-conf-libconfig: Update to 0.101. * gnu/packages/perl.scm (perl-conf-libconfig): Update to 0.101. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index b6c33b2a36..0e21176751 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1899,14 +1899,14 @@ as defined by two typical specimens of Perl coders.") (define-public perl-conf-libconfig (package (name "perl-conf-libconfig") - (version "0.100") + (version "0.101") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/C/CN/CNANGEL/" "Conf-Libconfig-" version ".tar.gz")) (sha256 - (base32 "0qdypqd7mx96bwdjlv13fn6p96bs4w0yv94yv94xa7z5lqkdj4rg")))) + (base32 "11dd3kb0k45gqahnnwz50x3b4b25c5jgykkwgf74rcyr0dsy0n5a")))) (build-system perl-build-system) (native-inputs (list perl-extutils-pkgconfig perl-test-deep perl-test-exception From 5e97f912bb623bb84de5b130b0a061056dee48b4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 08:35:04 +0100 Subject: [PATCH 215/824] gnu: zbackup: Build with protobuf@3.6. * gnu/packages/backup.scm (zbackup)[inputs]: Change from PROTOBUF to PROTOBUF-3.6. --- gnu/packages/backup.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index fd17992ab3..67708138a6 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -1036,7 +1036,7 @@ precious backup space. (arguments `(#:tests? #f)) ;no test (inputs - (list lzo libressl protobuf xz zlib)) + (list lzo libressl protobuf-3.6 xz zlib)) (home-page "http://zbackup.org") (synopsis "Versatile deduplicating backup tool") (description From 220669a022f5c064aacd416ca0f16dfb1f3a8976 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 21 Nov 2022 23:21:29 +0100 Subject: [PATCH 216/824] gnu: mate: Remove input labels. * gnu/packages/mate.scm (mate)[inputs]: Remove labels. --- gnu/packages/mate.scm | 84 +++++++++++++++++++++---------------------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm index 03dfabc135..d0e73e5a47 100644 --- a/gnu/packages/mate.scm +++ b/gnu/packages/mate.scm @@ -1490,48 +1490,48 @@ used to bring up authentication dialogs.") (native-inputs (list desktop-file-utils)) (inputs ;; TODO: Add more packages - `(("at-spi2-core" ,at-spi2-core) - ("atril" ,atril) - ("caja" ,caja) - ("dbus" ,dbus) - ("dconf" ,dconf) - ("engrampa" ,engrampa) - ("eom" ,eom) - ("font-abattis-cantarell" ,font-abattis-cantarell) - ("glib-networking" ,glib-networking) - ("gnome-keyring" ,gnome-keyring) - ("gvfs" ,gvfs) - ("hicolor-icon-theme" ,hicolor-icon-theme) - ("libmatekbd" ,libmatekbd) - ("libmateweather" ,libmateweather) - ("libmatemixer" ,libmatemixer) - ("marco" ,marco) - ("mate-session-manager" ,mate-session-manager) - ("mate-settings-daemon" ,mate-settings-daemon) - ("mate-desktop" ,mate-desktop) - ("mate-terminal" ,mate-terminal) - ("mate-themes" ,mate-themes) - ("mate-icon-theme" ,mate-icon-theme) - ("mate-power-manager" ,mate-power-manager) - ("mate-menu" ,mate-menus) - ("mate-panel" ,mate-panel) - ("mate-control-center" ,mate-control-center) - ("mate-media" ,mate-media) - ("mate-applets" ,mate-applets) - ("mate-user-guide" ,mate-user-guide) - ("mate-calc" ,mate-calc) - ("mate-backgrounds" ,mate-backgrounds) - ("mate-netbook" ,mate-netbook) - ("mate-utils" ,mate-utils) - ("mate-polkit" ,mate-polkit) - ("mate-system-monitor" ,mate-system-monitor) - ("mate-utils" ,mate-utils) - ("pluma" ,pluma) - ("pinentry-gnome3" ,pinentry-gnome3) - ("pulseaudio" ,pulseaudio) - ("shared-mime-info" ,shared-mime-info) - ("yelp" ,yelp) - ("zenity" ,zenity))) + (list at-spi2-core + atril + caja + dbus + dconf + engrampa + eom + font-abattis-cantarell + glib-networking + gnome-keyring + gvfs + hicolor-icon-theme + libmatekbd + libmateweather + libmatemixer + marco + mate-session-manager + mate-settings-daemon + mate-desktop + mate-terminal + mate-themes + mate-icon-theme + mate-power-manager + mate-menus + mate-panel + mate-control-center + mate-media + mate-applets + mate-user-guide + mate-calc + mate-backgrounds + mate-netbook + mate-utils + mate-polkit + mate-system-monitor + mate-utils + pluma + pinentry-gnome3 + pulseaudio + shared-mime-info + yelp + zenity)) (propagated-inputs ;; Default font that applications such as IceCat require. (list font-dejavu)) From 3954780bfb99af3034622c24332dcb13b95fb5d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 21 Nov 2022 23:27:06 +0100 Subject: [PATCH 217/824] gnu: gnome-keyring: Mark as 64-bit-only. * gnu/packages/gnome.scm (gnome-keyring)[supported-systems]: New field. --- gnu/packages/gnome.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 78e65d7400..9cebf618e0 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2594,6 +2594,11 @@ GNOME Desktop.") python-wrapper)) ;for tests (propagated-inputs (list gcr)) + + ;; XXX: There are concerning test failures on i686-linux and other 32-bit + ;; platforms: . + (supported-systems %64bit-supported-systems) + (home-page "https://www.gnome.org") (synopsis "Daemon to store passwords and encryption keys") (description From 47ba3f7d25fadb12b78d2728941e4e677fd7ad0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 21 Nov 2022 23:27:38 +0100 Subject: [PATCH 218/824] gnu: mate: Depend on gnome-keyring only on supported systems. This lets us build Mate on i686-linux. * gnu/packages/mate.scm (mate)[inputs]: Add GNOME-KEYRING conditionally. --- gnu/packages/mate.scm | 87 ++++++++++++++++++++++--------------------- 1 file changed, 45 insertions(+), 42 deletions(-) diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm index d0e73e5a47..ce62366985 100644 --- a/gnu/packages/mate.scm +++ b/gnu/packages/mate.scm @@ -1490,48 +1490,51 @@ used to bring up authentication dialogs.") (native-inputs (list desktop-file-utils)) (inputs ;; TODO: Add more packages - (list at-spi2-core - atril - caja - dbus - dconf - engrampa - eom - font-abattis-cantarell - glib-networking - gnome-keyring - gvfs - hicolor-icon-theme - libmatekbd - libmateweather - libmatemixer - marco - mate-session-manager - mate-settings-daemon - mate-desktop - mate-terminal - mate-themes - mate-icon-theme - mate-power-manager - mate-menus - mate-panel - mate-control-center - mate-media - mate-applets - mate-user-guide - mate-calc - mate-backgrounds - mate-netbook - mate-utils - mate-polkit - mate-system-monitor - mate-utils - pluma - pinentry-gnome3 - pulseaudio - shared-mime-info - yelp - zenity)) + (append (if (or (%current-target-system) + (supported-package? gnome-keyring)) + (list gnome-keyring) + '()) + (list at-spi2-core + atril + caja + dbus + dconf + engrampa + eom + font-abattis-cantarell + glib-networking + gvfs + hicolor-icon-theme + libmatekbd + libmateweather + libmatemixer + marco + mate-session-manager + mate-settings-daemon + mate-desktop + mate-terminal + mate-themes + mate-icon-theme + mate-power-manager + mate-menus + mate-panel + mate-control-center + mate-media + mate-applets + mate-user-guide + mate-calc + mate-backgrounds + mate-netbook + mate-utils + mate-polkit + mate-system-monitor + mate-utils + pluma + pinentry-gnome3 + pulseaudio + shared-mime-info + yelp + zenity))) (propagated-inputs ;; Default font that applications such as IceCat require. (list font-dejavu)) From 60bea075938cae10147d1d8fd414dc0140f4118f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 22 Nov 2022 07:16:03 +0100 Subject: [PATCH 219/824] inferior: Raise '&inferior-protocol-error' on invalid response. * guix/inferior.scm (&inferior-protocol-error): New condition type. (read-repl-response): Add default 'match' clause and raise it. --- guix/inferior.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/guix/inferior.scm b/guix/inferior.scm index 2fe34ca0dc..defdcc4e48 100644 --- a/guix/inferior.scm +++ b/guix/inferior.scm @@ -69,6 +69,8 @@ inferior-exception-arguments inferior-exception-inferior inferior-exception-stack + inferior-protocol-error? + inferior-protocol-error-inferior read-repl-response inferior-packages @@ -314,6 +316,10 @@ equivalent. Return #f if the inferior could not be launched." (inferior inferior-exception-inferior) ; | #f (stack inferior-exception-stack)) ;list of (FILE COLUMN LINE) +(define-condition-type &inferior-protocol-error &error + inferior-protocol-error? + (inferior inferior-protocol-error-inferior)) ; + (define* (read-repl-response port #:optional inferior) "Read a (guix repl) response from PORT and return it as a Scheme object. Raise '&inferior-exception' when an exception is read from PORT." @@ -339,7 +345,11 @@ Raise '&inferior-exception' when an exception is read from PORT." (raise (condition (&inferior-exception (arguments (cons key (map sexp->object objects))) (inferior inferior) - (stack '()))))))) + (stack '()))))) + (_ + ;; Protocol error. + (raise (condition (&inferior-protocol-error + (inferior inferior))))))) (define (read-inferior-response inferior) (read-repl-response (inferior-socket inferior) From b2b9571935f9188086b2e7b434840eeda6c42805 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 22 Nov 2022 07:17:17 +0100 Subject: [PATCH 220/824] offload: Gracefully handle 'guix repl' protocol errors. Fixes . Reported by Mathieu Othacehe . Previously, if a machine had a buggy 'guix repl', 'guix offload' would crash with a backtrace instead of just ignoring the machine. * guix/scripts/offload.scm (remote-inferior*): New procedure. (check-machine-availability)[if-true]: New procedure. Use 'remote-inferior*' and 'if-true'. (check-machine-status): Use 'remote-inferior*'. --- guix/scripts/offload.scm | 38 ++++++++++++++++++++++++++------------ 1 file changed, 26 insertions(+), 12 deletions(-) diff --git a/guix/scripts/offload.scm b/guix/scripts/offload.scm index 925325ef5f..8ab393c0ac 100644 --- a/guix/scripts/offload.scm +++ b/guix/scripts/offload.scm @@ -25,7 +25,7 @@ #:autoload (ssh auth) (userauth-public-key!) #:autoload (ssh session) (make-session connect! get-error - disconnect! session-set!) + disconnect! session-set! session-get) #:autoload (ssh version) (zlib-support?) #:use-module (guix config) #:use-module (guix records) @@ -34,7 +34,8 @@ send-files retrieve-files retrieve-files* remote-inferior report-guile-error) #:use-module (guix store) - #:autoload (guix inferior) (inferior-eval close-inferior inferior?) + #:autoload (guix inferior) (inferior-eval close-inferior + inferior? inferior-protocol-error?) #:autoload (guix derivations) (read-derivation-from-file derivation-file-name build-derivations) @@ -473,6 +474,15 @@ logical cores available, to give a rough estimation of CPU usage. Return (vector-set! vec j (vector-ref vec (- i 1))) (loop (cons val result) (- i 1)))))))) +(define (remote-inferior* session) + "Like 'remote-inferior', but upon error return #f." + (or (guard (c ((inferior-protocol-error? c) #f)) + (remote-inferior session)) + (begin + (warning (G_ "failed to run 'guix repl' on machine '~a'~%") + (session-get session 'host)) + #f))) + (define (choose-build-machine machines) "Return two values: the best machine among MACHINES and its build slot (which must later be released with 'release-build-slot'), or #f and #f." @@ -511,7 +521,7 @@ slot (which must later be released with 'release-build-slot'), or #f and #f." ;; too costly to call it once for every machine. (let* ((session (false-if-exception (open-ssh-session best %short-timeout))) - (node (and session (remote-inferior session))) + (node (and session (remote-inferior* session))) (load (and node (node-load node))) (threshold (build-machine-overload-threshold best)) (space (and node (node-free-disk-space node)))) @@ -708,6 +718,11 @@ machine." (and (string=? (build-machine-name m1) (build-machine-name m2)) (= (build-machine-port m1) (build-machine-port m2)))) + (define (if-true proc) + (lambda args + (when (every ->bool args) + (apply proc args)))) + ;; A given build machine may appear several times (e.g., once for ;; "x86_64-linux" and a second time for "i686-linux"); test them only once. (let ((machines (filter pred @@ -718,12 +733,12 @@ machine." (let* ((names (map build-machine-name machines)) (sockets (map build-machine-daemon-socket machines)) (sessions (map (cut open-ssh-session <> %short-timeout) machines)) - (nodes (map remote-inferior sessions))) - (for-each assert-node-has-guix nodes names) - (for-each assert-node-repl nodes names) - (for-each assert-node-can-import sessions nodes names sockets) - (for-each assert-node-can-export sessions nodes names sockets) - (for-each close-inferior nodes) + (nodes (map remote-inferior* sessions))) + (for-each (if-true assert-node-has-guix) nodes names) + (for-each (if-true assert-node-repl) nodes names) + (for-each (if-true assert-node-can-import) sessions nodes names sockets) + (for-each (if-true assert-node-can-export) sessions nodes names sockets) + (for-each (if-true close-inferior) nodes) (for-each disconnect! sessions)))) (define (check-machine-status machine-file pred) @@ -743,10 +758,9 @@ machine." (define session (open-ssh-session machine %short-timeout)) - (match (remote-inferior session) + (match (remote-inferior* session) (#f - (warning (G_ "failed to run 'guix repl' on machine '~a'~%") - (build-machine-name machine))) + #f) ((? inferior? inferior) (let ((now (car (gettimeofday)))) (match (inferior-eval '(list (uname) From d07dd4ccdf499d3151f4d9f9fd8fd81e0015e867 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 22 Nov 2022 08:41:32 +0100 Subject: [PATCH 221/824] reconfigure: Use SRFI-71 instead of SRFI-11. * guix/scripts/system/reconfigure.scm (upgrade-shepherd-services) (channel-relations): Use SRFI-71. --- guix/scripts/system/reconfigure.scm | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/guix/scripts/system/reconfigure.scm b/guix/scripts/system/reconfigure.scm index afd410d4bc..544aacfef4 100644 --- a/guix/scripts/system/reconfigure.scm +++ b/guix/scripts/system/reconfigure.scm @@ -40,9 +40,9 @@ #:use-module (guix diagnostics) #:use-module (ice-9 match) #:use-module (srfi srfi-1) - #:use-module (srfi srfi-11) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) + #:use-module (srfi srfi-71) #:use-module ((guix config) #:select (%guix-package-name)) #:export (switch-system-program switch-to-system @@ -184,8 +184,8 @@ services as defined by OS." #:target-type shepherd-root-service-type)))) (mlet* %store-monad ((live-services (running-services eval))) - (let*-values (((to-unload to-restart) - (shepherd-service-upgrade live-services target-services))) + (let ((to-unload to-restart + (shepherd-service-upgrade live-services target-services))) (let* ((to-unload (map live-service-canonical-name to-unload)) (to-restart (map shepherd-service-canonical-name to-restart)) (running (map live-service-canonical-name @@ -347,14 +347,12 @@ to commits of channels in NEW." (channel-name old))) new))) (and new - (let-values (((checkout commit relation) - (update-cached-checkout - (channel-url new) - #:ref - `(commit . ,(channel-commit new)) - #:starting-commit - (channel-commit old) - #:check-out? #f))) + (let ((checkout commit relation + (update-cached-checkout + (channel-url new) + #:ref `(commit . ,(channel-commit new)) + #:starting-commit (channel-commit old) + #:check-out? #f))) (list new (channel-commit old) (channel-commit new) relation))))) From 78f03567f44f704dfbc03cb64368aa42a01e78ad Mon Sep 17 00:00:00 2001 From: Martin Marshall Date: Fri, 18 Nov 2022 23:49:35 -0500 Subject: [PATCH 222/824] gnu: mpv: Add libxpresent input. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Jorge P. de Morais Neto and Kristian Lein-Mathisen . * gnu/packages/video.scm (mpv)[inputs]: Add libxpresent. Signed-off-by: Ludovic Courtès --- gnu/packages/video.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index c394c65442..16488f8a35 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2242,6 +2242,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") libxext libxkbcommon libxinerama + libxpresent libxrandr libxscrnsaver libxv From 105f17013f260c7cf1d9d70b17031d76e7e2d902 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Tue, 22 Nov 2022 09:44:20 +0100 Subject: [PATCH 223/824] gnu: cl-plump: Update to 2.0.0-3.0c3e0b5. * gnu/packages/lisp-xyz.scm (sbcl-plump): Update to 2.0.0-3.0c3e0b5. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 00ba49bc18..d640cdc15a 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -8972,8 +8972,8 @@ LASS files.") (sbcl-package->ecl-package sbcl-lass)) (define-public sbcl-plump - (let ((commit "3584275f0be9d06c0c51b5c08f89005deafc4ada") - (revision "2")) + (let ((commit "0c3e0b57b43b6e0c5794b6a902f1cf5bee2a2927") + (revision "3")) (package (name "sbcl-plump") (version (git-version "2.0.0" revision commit)) @@ -8984,10 +8984,9 @@ LASS files.") (git-reference (url "https://github.com/Shinmera/plump") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-plump" version)) (sha256 - (base32 - "1w4wz7f6dc2ckdq9wq9r5014bg2nxjifj9yz1zzn41r8h1h5xfcd")))) + (base32 "1fyb66pqvr1iy31ah9638ihs8cax17zkxk0zq14jy7x5l9rq1qlf")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-array-utils sbcl-documentation-utils)) From bb829bb23bc85e8218855e477c564e3b72579069 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Mon, 21 Nov 2022 10:33:45 +0000 Subject: [PATCH 224/824] gnu: cl-array-utils: Update to 1.1.1-1.40cea8f. * gnu/packages/lisp-xyz.scm (sbcl-array-utils): Update to 1.1.1-1.40cea8f. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index d640cdc15a..067c3aecae 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -8903,8 +8903,8 @@ macro. This library provides a set of simple utilities to help with that.") (sbcl-package->ecl-package sbcl-form-fiddle)) (define-public sbcl-array-utils - (let ((commit "f90eb9070d0b2205af51126a35033574725e5c56") - (revision "0")) + (let ((commit "40cea8fc895add87d1dba9232da817750222b528") + (revision "1")) (package (name "sbcl-array-utils") (version (git-version "1.1.1" revision commit)) @@ -8915,10 +8915,9 @@ macro. This library provides a set of simple utilities to help with that.") (git-reference (url "https://github.com/Shinmera/array-utils") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-array-utils" version)) (sha256 - (base32 - "0zhwfbpr53vs1ii4sx75dz2k9yhh1xpwdqqpg8nmfndxkmhpbi3x")))) + (base32 "0d7nddak8h2aa82z11vdbd97srk5bdgq41pzmibsz3ymspnndicd")))) (build-system asdf-build-system/sbcl) (native-inputs (list sbcl-parachute)) From 0435469669ad1f8d02c9580a5eaea6d89bfea66e Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Mon, 21 Nov 2022 12:55:08 +0000 Subject: [PATCH 225/824] gnu: cl-parachute: Update to 1.5.0-0.8bc3e1b. * gnu/packages/lisp-check.scm (sbcl-parachute): Update to 1.5.0-0.8bc3e1b. [inputs]: Add sbcl-trivial-custom-debugger. * gnu/packages/lisp-xyz.scm (sbcl-trivial-custom-debugger) [arguments]: New field. [native-inputs]: Remove field. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-check.scm | 15 ++++++++------- gnu/packages/lisp-xyz.scm | 8 ++++++-- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 7002cd9d92..58b79ba6e5 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -634,11 +634,11 @@ by Chris Riesbeck.") (sbcl-package->cl-source-package sbcl-nst)) (define-public sbcl-parachute - (let ((commit "86563473dc23fb1277d35a3ad2c911a6c8e5b0da") - (revision "1")) + (let ((commit "8bc3e1b5a1808341967aeb89516f9fab23cd1d9e") + (revision "0")) (package (name "sbcl-parachute") - (version (git-version "1.1.1" revision commit)) + (version (git-version "1.5.0" revision commit)) (source (origin (method git-fetch) @@ -646,13 +646,14 @@ by Chris Riesbeck.") (git-reference (url "https://github.com/Shinmera/parachute") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-parachute" version)) (sha256 - (base32 - "026crl465xqh3fnskfd4c1sxa9c33dfy702cf3l5apbjyj1dg20n")))) + (base32 "0cppp1sp9xqkgxgkwidhqzlsj03ywnar7z9mzwcliww8y0kv5555")))) (build-system asdf-build-system/sbcl) (inputs - (list sbcl-documentation-utils sbcl-form-fiddle)) + (list sbcl-documentation-utils + sbcl-form-fiddle + sbcl-trivial-custom-debugger)) (synopsis "Extensible and cross-compatible testing framework for Common Lisp") (description "Parachute is a simple-to-use and extensible testing framework. diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 067c3aecae..7e0e0cb133 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -24610,8 +24610,12 @@ between Lisp objects and some binary (i.e. octet-based) representation.") (sha256 (base32 "1iri5wsp9sc1f5q934cj87zd79r5dc8fda0gl7x1pz95v0wx28yk")))) (build-system asdf-build-system/sbcl) - (native-inputs - (list sbcl-parachute)) + (arguments + '(;; FIXME: Tests disabled because of a circular dependency between + ;; trivial-custom-debugger and parachute. + #:tests? #f)) + ;;(native-inputs + ;; (list sbcl-parachute)) (home-page "https://github.com/phoe/trivial-custom-debugger/") (synopsis "Allow arbitrary functions as the standard Lisp debugger") (description From bb67d7d99decd416b0235593913d23aeaddce734 Mon Sep 17 00:00:00 2001 From: paladhammika Date: Mon, 3 Jan 2022 18:37:55 -0500 Subject: [PATCH 226/824] gnu: Add fff. * gnu/packages/disk.scm (fff): New variable. Signed-off-by: Christopher Baines --- gnu/packages/disk.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 0853eb6d28..8912bb74bc 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -24,6 +24,7 @@ ;;; Copyright © 2021 Justin Veilleux ;;; Copyright © 2014, 2022 Ludovic Courtès ;;; Copyright © 2022 Maxim Cournoyer +;;; Copyright © 2022 Disseminate Dissent ;;; ;;; This file is part of GNU Guix. ;;; @@ -835,6 +836,46 @@ hierarchy. It ships with @code{rifle}, a file launcher that is good at automatically finding out which program to use for what file type.") (license license:gpl3))) +(define-public fff + (package + (name "fff") + (version "2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dylanaraps/fff") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14ymdw6l6phnil0xf1frd5kgznaiwppcic0v4hb61s1zpf4wrshg")))) + (build-system gnu-build-system) + (inputs + (list bash + file)) + (arguments + (list + #:tests? #f ; no tests + #:make-flags + #~(list + (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'refer-to-inputs + (lambda* (#:key inputs #:allow-other-keys) + (let ((file (assoc-ref inputs "file"))) + (substitute* "fff" + (("\\bfile [-\"]" match) + (string-append file "/bin/" match)))))) + (delete 'configure)))) ; no configure script + (home-page "https://github.com/dylanaraps/fff") + (synopsis "Simple file manager written in bash") + (description + "@command{fff} (fast file-manager) is a simple, blazing fast and minimal +file manager for Linux, written in bash. It only requires bash and coreutils, +and its highly optimized now for efficient performance.") + (license license:expat))) + (define-public volume-key (package (name "volume-key") From eda5e9aaafeacc0e21dbf43200d79b91fc1e38ed Mon Sep 17 00:00:00 2001 From: jgart Date: Wed, 16 Nov 2022 19:48:33 -0600 Subject: [PATCH 227/824] gnu: python-pudb: Add python-numpy native-input. This is an optional test dependency. * gnu/packages/python-xyz.scm (python-pudb)[native-inputs]: Add python-numpy. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4ee572096f..a88075cefa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29627,7 +29627,7 @@ development, testing, production]}; (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-vv"))))))) - (native-inputs (list python-pytest python-pytest-mock)) + (native-inputs (list python-pytest python-pytest-mock python-numpy)) (propagated-inputs (list python-jedi python-pygments python-urwid python-urwid-readline)) (home-page "https://documen.tician.de/pudb/") From 15b08918e953b17863229f880db7c81806dcf7ba Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Thu, 17 Nov 2022 20:06:38 +0000 Subject: [PATCH 228/824] gnu: LLVM, Clang, libomp, lld: Update to 15.0.5. * gnu/packages/llvm.scm (llvm-15, clang-15, libomp-15, lld-15): Update to 15.0.5. (lld)[version]: Use version from LLVM-15. (%llvm-monorepo-hashes, %llvm-patches): Adjust accordingly. Signed-off-by: Christopher Baines --- gnu/packages/llvm.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index f854493281..fc5360f288 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -563,11 +563,11 @@ output), and Binutils.") (define %llvm-monorepo-hashes '(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx") - ("15.0.4" . "0j5kx4s970qzcjr83kk6776zzjqfshl61x9fagqz8kjxcjbpg8cj"))) + ("15.0.5" . "1z2szqlanksdmj91590wnxqav5z437mpasg00ghb610xkam2v34m"))) (define %llvm-patches '(("14.0.6" . ("clang-14.0-libc-search-path.patch")) - ("15.0.4" . ("clang-15.0-libc-search-path.patch")))) + ("15.0.5" . ("clang-15.0-libc-search-path.patch")))) (define (llvm-monorepo version) (origin @@ -583,7 +583,7 @@ output), and Binutils.") (define-public llvm-15 (package (name "llvm") - (version "15.0.4") + (version "15.0.5") (source (llvm-monorepo version)) (build-system cmake-build-system) (outputs '("out" "opt-viewer")) @@ -740,7 +740,7 @@ of programming tools as well as libraries with equivalent functionality.") (package-version llvm-15))) (sha256 (base32 - "03adxlh84if9p53m6izjsql500rjza9rng8akab2pdqibgrg73rh"))))) + "0sa6si9v7ddsa9vmg6s3918xx969rvck2v1a0g7hb0fp9jk9j4r1"))))) (define-public clang-14 (clang-from-llvm @@ -1522,7 +1522,7 @@ Library.") (define-public lld-15 (package (name "lld") - (version "15.0.4") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (inputs From 8952a9408620d5d757242f3219223cf4073172ef Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Thu, 17 Nov 2022 20:06:39 +0000 Subject: [PATCH 229/824] gnu: lldb: Update to 15.0.5. * gnu/packages/llvm.scm (lldb): Update to 15.0.5. [version]: Use version from LLVM-15. [inputs]: Change from LLVM-14 and CLANG-14 to LLVM-15 and CLANG-15. Signed-off-by: Christopher Baines --- gnu/packages/llvm.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index fc5360f288..108a190c4b 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -1634,7 +1634,7 @@ misuse of libraries outside of the store."))) (define-public lldb (package (name "lldb") - (version "14.0.6") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (arguments @@ -1648,8 +1648,8 @@ misuse of libraries outside of the store."))) (native-inputs (list pkg-config swig)) (inputs - (list clang-14 - llvm-14 + (list clang-15 + llvm-15 ;; Optional (but recommended) inputs. ncurses libedit From 07746c2b153dfeacf714261f330c04d42e570f3c Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Thu, 17 Nov 2022 20:06:40 +0000 Subject: [PATCH 230/824] gnu: libcxx: Update to 15.0.5. * gnu/packages/llvm.scm (libcxx): Update to 15.0.5. [version]: Use version from LLVM-15. Signed-off-by: Christopher Baines --- gnu/packages/llvm.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 108a190c4b..9ffdf8761b 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -1668,7 +1668,7 @@ which highly leverage existing libraries in the larger LLVM project.") (define-public libcxx (package (name "libcxx") - (version "14.0.6") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (arguments From d54febb86ff71a93a8a62957658512ca4727f89d Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Mon, 21 Nov 2022 14:46:54 +0800 Subject: [PATCH 231/824] gnu: Add emacs-ebuku. * gnu/packages/emacs-xyz.scm (emacs-ebuku): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 754d2e3cb8..85bed7037b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13353,6 +13353,30 @@ Lua programming language}.") news items, openrc and runscripts.") (license license:gpl2+))) +(define-public emacs-ebuku + ;; Upstream has no tagged release. + (let ((revision "0") + (commit "5b8bf34b8ea5d05f0b8dfc12bfea825f9cffbeda")) + (package + (name "emacs-ebuku") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/flexibeast/ebuku") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04733lqa6z3kmdjcgdi58q3wrqan2qib43rvjw51qc739fwmwb5y")))) + (build-system emacs-build-system) + (home-page "https://github.com/flexibeast/ebuku") + (synopsis "Emacs interface to the buku Web bookmark manager") + (description + "Ebuku provides a basic interface to the @code{buku} Web bookmark +manager.") + (license license:gpl3+)))) + (define-public emacs-evil ;; Commit message claims this is 1.15.0, but there's no tag for it, so we ;; use full git-version instead From 1f600136ffd1d1d6a1ebb0130e28d0e0849ba21b Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Mon, 21 Nov 2022 11:28:56 +0100 Subject: [PATCH 232/824] gnu: xfce4-settings: Update to 4.16.5. * gnu/packages/xfce.scm (xfce4-settings): Update to 4.16.5. Signed-off-by: Christopher Baines --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 6840867612..d02e363d6c 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -681,7 +681,7 @@ allows you to shut down the computer from Xfce.") (define-public xfce4-settings (package (name "xfce4-settings") - (version "4.16.4") + (version "4.16.5") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -689,7 +689,7 @@ allows you to shut down the computer from Xfce.") name "-" version ".tar.bz2")) (sha256 (base32 - "1vd3l20myjfbq53x8sywy989zd557adyv3bb2y0nhh2is8ps9aqq")) + "13nj80mshkz3czrp8l1yxj6qmz0kkfhzv94z3ixfgmw64j078kvs")) (patches (search-patches "xfce4-settings-defaults.patch")))) (build-system gnu-build-system) (arguments From a44d6e1ea28ec2ac22ba5699a66817320ddbe915 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Mon, 21 Nov 2022 11:34:53 +0100 Subject: [PATCH 233/824] gnu: xfce4-screenshooter: Update to 1.10.0. * gnu/packages/xfce.scm (xfce4-screenshooter): Update to 1.10.0. Signed-off-by: Christopher Baines --- gnu/packages/xfce.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index d02e363d6c..720a36e3b9 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1335,7 +1335,7 @@ of data to either CD/DVD/BD.") (define-public xfce4-screenshooter (package (name "xfce4-screenshooter") - (version "1.9.11") + (version "1.10.0") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1345,7 +1345,7 @@ of data to either CD/DVD/BD.") version ".tar.bz2")) (sha256 (base32 - "1d7qyc2w4962crmkz5n0mma2qmyp9hhq455karyzacjbb6z0cgg7")))) + "0lvv6iam348n7l3md94lanxyyn87xmrivzdvfi0fa3vgjfk88j56")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool From b8d4c323f5d089dd800b358143d5bae26c965404 Mon Sep 17 00:00:00 2001 From: "pelzflorian (Florian Pelz)" Date: Sat, 19 Nov 2022 13:09:31 +0100 Subject: [PATCH 234/824] doc: Call out potential for security vulnerabilities in old software. * doc/guix.texi (Invoking guix time-machine): Add a note. Co-authored by: Simon Tournier --- doc/guix.texi | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 9155b605f2..c0cb24d709 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -60,7 +60,7 @@ Copyright @copyright{} 2018, 2021 Oleg Pykhalov@* Copyright @copyright{} 2018 Mike Gerwitz@* Copyright @copyright{} 2018 Pierre-Antoine Rouby@* Copyright @copyright{} 2018, 2019 Gábor Boskovits@* -Copyright @copyright{} 2018, 2019, 2020 Florian Pelz@* +Copyright @copyright{} 2018, 2019, 2020, 2022 Florian Pelz@* Copyright @copyright{} 2018 Laura Lazzati@* Copyright @copyright{} 2018 Alex Vong@* Copyright @copyright{} 2019 Josh Holland@* @@ -4834,6 +4834,15 @@ invocation can be expensive: it may have to download or even build a large number of packages; the result is cached though and subsequent commands targeting the same commit are almost instantaneous. +@quotation Note +The history of Guix is immutable and @command{guix time-machine} +provides the exact same software as they are in a specific Guix +revision. Naturally, no security fixes are provided for old versions +of Guix or its channels. A careless use of @command{guix time-machine} +opens the door to security vulnerabilities. @xref{Invoking guix pull, +@option{--allow-downgrades}}. +@end quotation + The general syntax is: @example From d0c8816f3710010f941cc29d9b31cef3a8836e3d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Nov 2022 17:34:21 +0100 Subject: [PATCH 235/824] gnu: emacs-corfu: Update to 0.33. * gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.33. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 85bed7037b..8d6980e750 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3467,7 +3467,7 @@ of bibliographic references.") (define-public emacs-corfu (package (name "emacs-corfu") - (version "0.31") + (version "0.33") (source (origin (method git-fetch) @@ -3476,7 +3476,7 @@ of bibliographic references.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "10gz4x21dm73xf0w2zfxpfa0wykmmrid8yh0mxp1xbqpl86ig1x9")))) + (base32 "0c353k6f4i96gajfw1zvidhlwr2brnhhdr39503hpa5wnp69wak7")))) (build-system emacs-build-system) (arguments `(#:phases From 452386617a5867ccc8b973c839033314ba074151 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Nov 2022 17:36:07 +0100 Subject: [PATCH 236/824] gnu: emacs-cape: Update to 0.11. * gnu/packages/emacs-xyz.scm (emacs-cape): Update to 0.11. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 8d6980e750..13088885f2 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3524,7 +3524,7 @@ be regarded as @code{emacs-company-quickhelp} for @code{emacs-corfu}.") (define-public emacs-cape (package (name "emacs-cape") - (version "0.10") + (version "0.11") (source (origin (method git-fetch) @@ -3533,7 +3533,7 @@ be regarded as @code{emacs-company-quickhelp} for @code{emacs-corfu}.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0kcnyzksj8yglk67g1130wxzscgipm7cz2hs8mvdqpcbz4i38jny")))) + (base32 "0z6ixw7gsx1g7x2xpj5ilslrjrlp6x2ynzh731hs3yf3n281715b")))) (build-system emacs-build-system) (home-page "https://github.com/minad/cape") (synopsis "Completion at point extensions for Emacs") From eb5e650e09dd096c066278918456f3e989f7b9d9 Mon Sep 17 00:00:00 2001 From: Martin Marshall Date: Mon, 21 Nov 2022 22:57:04 -0500 Subject: [PATCH 237/824] gnu: emacs-flymake-proselint: Remove references to Flycheck. * gnu/packages/emacs-xyz.scm (emacs-flymake-proselint): Remove references to flycheck. [source]: Correct URL path-name. [propagated-inputs]: Remove EMACS-FLYCHECK. [home-page]: Correct URL path-name. Package was installing EMACS-FLYCHECK but has no dependency on it. It uses Emacs built-in, Flymake, instead. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 13088885f2..eae2777e19 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -6958,7 +6958,7 @@ files which are intended to be packages.") (source (origin (method git-fetch) (uri (git-reference - (url "https://git.sr.ht/~manuel-uberti/flycheck-proselint") + (url "https://git.sr.ht/~manuel-uberti/flymake-proselint") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -6975,11 +6975,9 @@ files which are intended to be packages.") (("\"proselint\"") (string-append "\"" (search-input-file inputs "/bin/proselint") "\"")))))))) - (propagated-inputs - (list emacs-flycheck)) (inputs (list python-proselint)) - (home-page "https://git.sr.ht/~manuel-uberti/flycheck-proselint") + (home-page "https://git.sr.ht/~manuel-uberti/flymake-proselint") (synopsis "Flymake backend for @code{proselint}") (description "This package adds support for @code{proselint} in Flymake.") (license license:gpl3+)))) From 7534d8067fc1cb1b4f8fad7c6f9b63390fbbb33c Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Fri, 9 Sep 2022 14:31:45 +0000 Subject: [PATCH 238/824] gnu: suitesparse: Update to 5.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (suitesparse): Update to 5.13.0. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 98bae9ecb5..d4c1e4922e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4860,7 +4860,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "5.12.0") + (version "5.13.0") (source (origin (method git-fetch) @@ -4870,7 +4870,7 @@ Fresnel integrals, and similar related functions as well.") (file-name (git-file-name name version)) (sha256 (base32 - "0zpl51pfpv7ap7z97jlryba2la1qdmzm11bhzkn55wlb03xzi6k6")) + "1zwri246yr39p9ymjp18dzv36ch0dn107sf0jghj7capigasfxq2")) (patches (search-patches "suitesparse-mongoose-cmake.patch")) (modules '((guix build utils))) (snippet From ca428f944fa61c63de252af6cc88dd815c074a0f Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Fri, 9 Sep 2022 14:31:46 +0000 Subject: [PATCH 239/824] gnu: octave: Update to 7.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (octave): Update to 7.2.0. Signed-off-by: Ludovic Courtès --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d4c1e4922e..cfe2dcbcf2 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2747,7 +2747,7 @@ can solve two kinds of problems: (define-public octave-cli (package (name "octave-cli") - (version "7.1.0") + (version "7.2.0") (source (origin (method url-fetch) @@ -2755,7 +2755,7 @@ can solve two kinds of problems: version ".tar.xz")) (sha256 (base32 - "0wv26nsfi6cq80np6p4av4wfrvbaflca6szajf6c60mbpdg63m1z")))) + "0w81ncl9d4x1ay3ylsag87k20c0byiyjcmfd9kb7b7ylr71pivsa")))) (build-system gnu-build-system) (inputs `(("alsa-lib" ,alsa-lib) From bddb43b422cb71679be6176dda91e45b6e6f3971 Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Fri, 9 Sep 2022 14:31:47 +0000 Subject: [PATCH 240/824] gnu: python-hmmlearn: Update to 0.2.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/machine-learning.scm (python-hmmlearn): Update to 0.2.7. [source]<#:origin>: Remove deletion snippet for file removed upstream. [propagated-inputs]: Add pybind11. Signed-off-by: Ludovic Courtès --- gnu/packages/machine-learning.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 61b0400715..fbc06f96b6 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -3224,18 +3224,14 @@ Python.") (define-public python-hmmlearn (package (name "python-hmmlearn") - (version "0.2.6") + (version "0.2.7") (source (origin (method url-fetch) (uri (pypi-uri "hmmlearn" version)) (sha256 (base32 - "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a")) - (snippet - #~(begin - (use-modules ((guix build utils))) - (delete-file "lib/hmmlearn/_hmmc.c"))))) + "1qgnf1kdxicygy8nvpv866iqvwq0rc6xkd3s6slmvxvsy8h2fjvb")))) (build-system python-build-system) (arguments `(#:phases @@ -3247,7 +3243,11 @@ Python.") (with-directory-excursion (string-append (assoc-ref outputs "out") "/lib") (invoke "python" "-m" "pytest")))))))) (propagated-inputs - (list python-cython python-numpy python-scikit-learn python-scipy + (list pybind11 + python-cython + python-numpy + python-scikit-learn + python-scipy python-setuptools-scm)) (native-inputs (list python-pytest)) From 80305088b53aebfcdd86a1b0ba44d0e981c428ce Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Nov 2022 11:09:45 +0100 Subject: [PATCH 241/824] gnu: drbd-utils: Fix corrupted man page. * gnu/packages/cluster.scm (drbd-utils)[native-inputs]: Change from DOCBOOK-XSL to DOCBOOK-XSL-NEXT. --- gnu/packages/cluster.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 6e4055736a..4db64d5d19 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -132,7 +132,7 @@ ;; For the documentation. docbook-xml docbook-xml-4.4 ;used by documentation/ra2refentry.xsl - docbook-xsl + docbook-xsl-next libxml2 ;for XML_CATALOG_FILES libxslt ;for xsltproc ruby-asciidoctor)) From 9e44a6f77615fa95990412a7b1dc2ba8086a5124 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 23 Nov 2022 08:21:17 +0100 Subject: [PATCH 242/824] gnu: knot-resolver: Update to 5.5.3. * gnu/packages/dns.scm (knot-resolver): Update to 5.5.3. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index ce184aa8dd..21b711d147 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -1013,14 +1013,14 @@ synthesis, and on-the-fly re-configuration.") (define-public knot-resolver (package (name "knot-resolver") - (version "5.4.4") + (version "5.5.3") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-resolver/" "knot-resolver-" version ".tar.xz")) (sha256 (base32 - "1sic5ccbbqml4c01dbikkg6qx1gg81nqi76cj79pjdllkqqn92aq")))) + "0bgdbx66dsfik3sdqi4g2imddalqc1p41n444xk7s8vxig35g3x3")))) (build-system meson-build-system) (outputs '("out" "doc")) (arguments From 2c8329de516f8f512735e09e5669b65228860b4c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 23 Nov 2022 08:32:52 +0100 Subject: [PATCH 243/824] gnu: emacs-ediprolog: Update source URI. This is a follow-up to commit 575790f5f5bea3a935c83b2d764cfd7205e09e81. * gnu/packages/emacs-xyz.scm (emacs-ediprolog)[source](uri): Download tarball instead of .el. --- gnu/packages/emacs-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index eae2777e19..ce8adc75fb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -28680,8 +28680,7 @@ between \"frame-width\" and \"frame-height\", between \"public\", (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/ediprolog-" - version - ".el")) + version ".tar")) (sha256 (base32 "021jm5zdxrjg7xcja18vgc2v52rk17xi1k7xxw8q802nmixhy0js")))) (build-system emacs-build-system) From 3879c1f6cd648b72849e3631d34b3ae43f052eb3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 23 Nov 2022 08:43:29 +0100 Subject: [PATCH 244/824] gnu: heads-dev-cpio: Add missing module import. * gnu/packages/heads.scm (heads-dev-cpio)[arguments]<#:modules>: Add (guix build syscalls). --- gnu/packages/heads.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/heads.scm b/gnu/packages/heads.scm index d5e36b9b3c..212849f2a9 100644 --- a/gnu/packages/heads.scm +++ b/gnu/packages/heads.scm @@ -172,6 +172,7 @@ done (build-system trivial-build-system) (arguments `(#:modules ((guix build utils) + (guix build syscalls) (guix cpio)) #:builder (begin (use-modules (guix build utils) From 5ba10abc49239d047ece2d573497a6379984b410 Mon Sep 17 00:00:00 2001 From: Andrew Tropin Date: Wed, 23 Nov 2022 13:09:06 +0400 Subject: [PATCH 245/824] gnu: Add emacs-jarchive. * gnu/packages/emacs-xyz.scm (emacs-jarchive): New variable. --- gnu/packages/emacs-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ce8adc75fb..25af69dbd3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -16673,6 +16673,26 @@ for the current file, using the major mode as a hint. It prompts you to enter one if it fails.") (license license:gpl3+))) +(define-public emacs-jarchive + (package + (name "emacs-jarchive") + (version "0.8.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~dannyfreeman/jarchive") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fi3y5kmy7ginyqg12q797bma638xmam7lrk74x6yhx84xgzb4fq")))) + (build-system emacs-build-system) + (home-page "https://sr.ht/~dannyfreeman/jarchive") + (synopsis "Jarchive teaches Emacs how to navigate to files inside JARs") + (description "Jarchive makes Emacs handle Java and LSP URIs pointing to + source inside JARs.") + (license license:gpl3+))) + (define-public emacs-eldoc (package (name "emacs-eldoc") From b8985be94c5186529f2d93df2cf2f9b6e51ac8c4 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Tue, 22 Nov 2022 18:33:57 +0800 Subject: [PATCH 246/824] gnu: font-sarasa-gothic: Update to 0.37.4. * gnu/packages/fonts.scm (font-sarasa-gothic): Update to 0.37.4. Signed-off-by: Christopher Baines --- gnu/packages/fonts.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 343f736ed2..a2578e1bf7 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -1666,7 +1666,7 @@ programming. Iosevka is completely generated from its source code.") (define-public font-sarasa-gothic (package (name "font-sarasa-gothic") - (version "0.36.8") + (version "0.37.4") (source (origin (method url-fetch) @@ -1674,7 +1674,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/sarasa-gothic-ttc-" version ".7z")) (sha256 - (base32 "01fn5mzr1rcz0c8nbhabwbv1pq1c3ylf2msxldc9adks1pi45fmh")))) + (base32 "12i8lccl4ysinhz40s2fz6249r9n35in4rqmk3a0fgcjfaby3kfm")))) (build-system font-build-system) (arguments `(#:phases (modify-phases %standard-phases From e329c5e05d34a854bf1ab21606d924ef4e7cbb27 Mon Sep 17 00:00:00 2001 From: jgart Date: Tue, 22 Nov 2022 15:35:04 -0600 Subject: [PATCH 247/824] gnu: Add emacs-treeview. * gnu/packages/emacs-xyz.scm (emacs-treeview): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 25af69dbd3..5ca8940cfe 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -576,6 +576,28 @@ Emacs, whose initial working directories are determined in relation to the current buffer.") (license license:gpl3+))) +(define-public emacs-treeview + (let ((commit "d9c10feddf3b959e7b33ce83103e1f0a61162723") + (revision "0")) + (package + (name "emacs-treeview") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (uri (git-reference + (url "https://github.com/tilmanrassy/emacs-treeview") + (commit commit))) + (method git-fetch) + (sha256 + (base32 "14s0b6zbapsvgyxki59lglwb3s8wjsjwkgj5r66af9nj2bgz5ms9")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (home-page "https://github.com/tilmanrassy/emacs-treeview/") + (synopsis "Emacs Lisp framework for tree navigation") + (description + "Abstract Emacs Lisp framework for tree navigation.") + (license license:gpl3+)))) + (define-public emacs-hgignore-mode ;; From 2021-03-14. ;; No releases available. From 36562c74dc2783b57298d1486ab8f3395755061f Mon Sep 17 00:00:00 2001 From: jgart Date: Tue, 22 Nov 2022 15:35:05 -0600 Subject: [PATCH 248/824] gnu: Add emacs-inspector. * gnu/packages/emacs-xyz.scm (emacs-inspector): New variable. Signed-off-by: Christopher Baines --- gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5ca8940cfe..7436322ae8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -554,6 +554,30 @@ optional baked-in Evil support, antialiased separators, and an easy configuration language which makes it trivial to write your own themes.") (license license:gpl3+)))) +(define-public emacs-inspector + (let ((commit "0e89d28558f57db4519f154bb72ce617a8c6265d") + (revision "0")) + (package + (name "emacs-inspector") + (version (git-version "0.3" revision commit)) + (source + (origin + (uri (git-reference + (url "https://github.com/mmontone/emacs-inspector") + (commit commit))) + (method git-fetch) + (sha256 + (base32 "0n72sqn29b5sya686cicgp40mkk5x5821b7bw4zs6dcl82cyij5n")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-treeview)) + (home-page "https://github.com/mmontone/emacs-inspector") + (synopsis "Inspection tool for Emacs Lisp objects") + (description + "This package provides an introspection tool similar to those found in +Common Lisp or Smalltalk, but for Emacs Lisp.") + (license license:gpl3+)))) + (define-public emacs-terminal-here (package (name "emacs-terminal-here") From 029234bdad83195c7facad5af05d65cda7772c25 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 22:30:56 +0000 Subject: [PATCH 249/824] gnu: Add cl-simplet. * gnu/packages/lisp-check.scm (cl-simplet, ecl-simplet, sbcl-simplet): New variables. Signed-off-by: Christopher Baines --- gnu/packages/lisp-check.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 58b79ba6e5..59033fdbc5 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -841,6 +841,32 @@ take.") (define-public ecl-should-test (sbcl-package->ecl-package sbcl-should-test)) +(define-public sbcl-simplet + (package + (name "sbcl-simplet") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/simplet") + (commit (string-append "v" version)))) + (file-name (git-file-name "simplet" version)) + (sha256 + (base32 "1iwp3a43mns885k2arr7gbmyv5rsrjfvgarxickj7r2bfgwp1cnn")))) + (build-system asdf-build-system/sbcl) + (home-page "https://github.com/noloop/simplet") + (synopsis "Simple test runner in Common Lisp") + (description "This package provides a Common Lisp test runner system +SIMPLET.") + (license license:gpl3))) + +(define-public ecl-simplet + (sbcl-package->ecl-package sbcl-simplet)) + +(define-public cl-simplet + (sbcl-package->cl-source-package sbcl-simplet)) + (define-public sbcl-stefil (let ((commit "0398548ec95dceb50fc2c2c03e5fb0ce49b86c7a") (revision "0")) From dc95215dc0178b85d1c218494aa8ac7248ab8f0b Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 22:30:57 +0000 Subject: [PATCH 250/824] gnu: Add cl-assertion-error. * gnu/packages/lisp-check.scm (cl-assertion-error, ecl-assertion-error, sbcl-assertion-error): New variables. Signed-off-by: Christopher Baines --- gnu/packages/lisp-check.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 59033fdbc5..2d447533d9 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -94,6 +94,35 @@ consists of: @code{test}, @code{is}, @code{signals}, @code{finishes}, (define-public ecl-2am (sbcl-package->ecl-package sbcl-2am)) +(define-public sbcl-assertion-error + (let ((commit "8eab692a990d4caa193a46bae99af3e13e717b86") + (revision "1")) + (package + (name "sbcl-assertion-error") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/assertion-error") + (commit commit))) + (file-name (git-file-name "assertion-error" version)) + (sha256 + (base32 "0ix23kkakmf4nwx852zsssb831jvajr3qyppqfyks7y1ls617svn")))) + (build-system asdf-build-system/sbcl) + (inputs (list sbcl-dissect)) + (home-page "https://github.com/noloop/assertion-error") + (synopsis "Error pattern for assertion libraries in Common Lisp") + (description "This package provides a Common Lisp assertion system with +minimal dependencies on DISSECT.") + (license license:gpl3)))) + +(define-public ecl-assertion-error + (sbcl-package->ecl-package sbcl-assertion-error)) + +(define-public cl-assertion-error + (sbcl-package->cl-source-package sbcl-assertion-error)) + (define-public sbcl-check-it (let ((commit "b79c9103665be3976915b56b570038f03486e62f")) (package From f39a18e7d43fc7bdf18b135d44bae2159e1526ac Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 22:30:58 +0000 Subject: [PATCH 251/824] gnu: Add cl-assert-p. * gnu/packages/lisp-check.scm (cl-assert-p, ecl-assert-p, sbcl-assert-p): New variables. Signed-off-by: Christopher Baines --- gnu/packages/lisp-check.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 2d447533d9..9b22b195b5 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -123,6 +123,32 @@ minimal dependencies on DISSECT.") (define-public cl-assertion-error (sbcl-package->cl-source-package sbcl-assertion-error)) +(define-public sbcl-assert-p + (package + (name "sbcl-assert-p") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/assert-p") + (commit (string-append "v" version)))) + (file-name (git-file-name "assert-p" version)) + (sha256 + (base32 "1x24rkqkqiw8zd26swi9rmhfplkmr5scz3bhjwccah9d2s36b1xs")))) + (build-system asdf-build-system/sbcl) + (inputs (list sbcl-assertion-error sbcl-simplet)) + (home-page "https://github.com/noloop/assert-p") + (synopsis "Common Lisp assertion library") + (description "This package provides a Common Lisp collection of assertions.") + (license license:gpl3))) + +(define-public ecl-assert-p + (sbcl-package->ecl-package sbcl-assert-p)) + +(define-public cl-assert-p + (sbcl-package->cl-source-package sbcl-assert-p)) + (define-public sbcl-check-it (let ((commit "b79c9103665be3976915b56b570038f03486e62f")) (package From cd9df33e4144ff9d85fef55cdc6caec4ccc007b4 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 22:30:59 +0000 Subject: [PATCH 252/824] gnu: Add cl-eventbus. * gnu/packages/lisp-xyz.scm (cl-eventbus, ecl-eventbus, sbcl-eventbus): New variables. Signed-off-by: Christopher Baines --- gnu/packages/lisp-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 7e0e0cb133..cab953884f 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -14353,6 +14353,34 @@ with a complex event filtering system.") (define-public ecl-deeds (sbcl-package->ecl-package sbcl-deeds)) +(define-public sbcl-eventbus + (let ((commit "92c1fa3846ba0e3cc9e6d7605d765379c8658d84") + (revision "1")) + (package + (name "sbcl-eventbus") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/eventbus") + (commit commit))) + (file-name (git-file-name "eventbus" version)) + (sha256 + (base32 "0slqx3zq6sbz3rg4g79j8y25sx4405y6ff3x6l5v8v4v42m1s0p2")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-simplet)) + (home-page "https://github.com/noloop/eventbus") + (synopsis "Event bus implementation in Common Lisp") + (description "This package provides a Common Lisp system implementing event bus.") + (license license:gpl3)))) + +(define-public ecl-eventbus + (sbcl-package->ecl-package sbcl-eventbus)) + +(define-public cl-eventbus + (sbcl-package->cl-source-package sbcl-eventbus)) + (define-public sbcl-make-hash ;; no tagged branch (let ((revision "1") From 6ffe15bda7ea0f9dd3858e8e36883a22e726f106 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 22:31:00 +0000 Subject: [PATCH 253/824] gnu: Add cl-cacau. * gnu/packages/lisp-check.scm (cl-cacau, ecl-cacau, sbcl-cacau): New variables. Signed-off-by: Christopher Baines --- gnu/packages/lisp-check.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 9b22b195b5..038ca1f18b 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -149,6 +149,35 @@ minimal dependencies on DISSECT.") (define-public cl-assert-p (sbcl-package->cl-source-package sbcl-assert-p)) +(define-public sbcl-cacau + (package + (name "sbcl-cacau") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/cacau") + (commit (string-append "v" version)))) + (file-name (git-file-name "cacau" version)) + (sha256 + (base32 "0m8v1xw68cr5ldv045rxgvnhigr4iahh7v6v32z6xlq2sj6r55x0")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-assert-p)) + (inputs (list sbcl-assertion-error sbcl-eventbus)) + (home-page "https://github.com/noloop/cacau") + (synopsis "Comon Lisp test runner") + (description + "This package provides a Common Lisp testing framework system CACAU which was +built to be independent of assertions systems.") + (license license:gpl3))) + +(define-public ecl-cacau + (sbcl-package->ecl-package sbcl-cacau)) + +(define-public cl-cacau + (sbcl-package->cl-source-package sbcl-cacau)) + (define-public sbcl-check-it (let ((commit "b79c9103665be3976915b56b570038f03486e62f")) (package From 7fa8c0575303908f921a2032eeeaa9c34e37fbdb Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 22 Nov 2022 23:23:12 +0000 Subject: [PATCH 254/824] gnu: python-cdflib: Update to 0.4.9. * gnu/packages/astronomy.scm (python-cdflib): Update to 0.4.9. [build-system]: Use pyproject-build-system to simplify package. [description]: Expand acronym for CDF. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index b37aeacc70..d450d1dd94 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1101,7 +1101,7 @@ to access online Astronomical data. Each web service has its own sub-package.") (define-public python-cdflib (package (name "python-cdflib") - (version "0.4.4") + (version "0.4.9") (source (origin (method git-fetch) ; no tests in pypi archive @@ -1110,16 +1110,14 @@ to access online Astronomical data. Each web service has its own sub-package.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1h7750xvr6qbhnl2w3bhccs3pwp3hci3624pvvxym0yjinmskjlz")))) - (build-system python-build-system) + (base32 "1k557najk7ln293zwyghnhw48ays3nqf9s94kibsc7r70c2q7p08")))) + (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" (getcwd)) - (invoke "pytest" "-vv" "tests"))))))) + (add-before 'check 'set-home-env + (lambda _ + (setenv "HOME" (getcwd))))))) (propagated-inputs (list python-attrs python-numpy)) (native-inputs @@ -1131,7 +1129,8 @@ to access online Astronomical data. Each web service has its own sub-package.") python-xarray)) (home-page "https://github.com/MAVENSDC/cdflib") (synopsis "Python library to deal with NASA's CDF astronmical data format") - (description "This package provides a Python CDF reader toolkit + (description "This package provides a Python @acronym{CDF, Computable +Document Format} reader toolkit. It provides the following functionality: @itemize @item Ability to read variables and attributes from CDF files @@ -1140,7 +1139,7 @@ It provides the following functionality: time formats @item Can convert CDF files into XArray Dataset objects and vice versa, attempting to maintain ISTP compliance -@end itemize\n") +@end itemize") (license license:expat))) (define-public python-ephem From 093bf20cdc54add190b1184f548cb5d3a97c6ad1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 16 Jun 2022 19:00:48 +0200 Subject: [PATCH 255/824] gnu: Add r-alpine. * gnu/packages/bioconductor.scm (r-alpine): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3b67fd2bf..45a511cf13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2276,6 +2276,47 @@ paired or unpaired study designs.") ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript +abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million +mapped reads). It is currently designed for un-stranded paired-end RNA-seq +data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") From 3ab9adba57c529f524e63ffbc663f5ddf8770752 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 00:22:52 +0100 Subject: [PATCH 256/824] gnu: python-munkres: Conditionally disable failing test. * gnu/packages/python-xyz.scm (python-munkres)[arguments]: Add phase "disable-test" to patch test suite. --- gnu/packages/python-xyz.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a88075cefa..7fefbc5bff 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16045,6 +16045,20 @@ way.") (sha256 (base32 "00yvj8bxmhhhhd74v7j0x673is7vizmxwgb3dd5xmnkr74ybyi7w")))) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-test + (lambda _ + ;; See https://github.com/bmc/munkres/issues/40 + (substitute* "test/test_munkres.py" + (("^def test_profit_float" m) + (string-append "\ +import platform +@pytest.mark.skipif(platform.architecture()[0] == \"32bit\", + reason=\"Fails on 32 bit architectures\") +" m)))))))) (build-system python-build-system) (native-inputs (list python-pytest-6)) (home-page "https://software.clapper.org/munkres/") From 48a5dc0ffb9f1c5ed6c0d67afdd442b3b340cb25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 00:29:04 +0100 Subject: [PATCH 257/824] gnu: python-ppmd-cffi: Update to 0.5.0. * gnu/packages/python-compression.scm (python-ppmd-cffi): Update to 0.5.0. [native-inputs]: Remove python-setuptools and python-pep517; add python-hypothesis. --- gnu/packages/python-compression.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 1426ad9f09..7dd01d611e 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -127,21 +127,20 @@ and decompression by implementing Python bindings for the ISA-L library.") (define-public python-ppmd-cffi (package (name "python-ppmd-cffi") - (version "0.3.3") + (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "ppmd-cffi" version)) (sha256 (base32 - "01wcd9l6pp6hivdmd275qh9dhcwficjqfl67hxix5n07vvq7jzz0")))) + "0vprpl29fkflqx0m6anfpx7q7i4cw0d0qxcdm91k4pl82dcad81g")))) (build-system python-build-system) (propagated-inputs (list python-cffi)) (native-inputs - (list python-setuptools + (list python-hypothesis python-setuptools-scm - python-pep517 python-coverage python-pytest python-pytest-cov)) From 32fa8486112ad8fa658a0614bcc70df1f2610fca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:01:27 +0100 Subject: [PATCH 258/824] gnu: python-pyzstd: Update to 0.15.3. * gnu/packages/python-compression.scm (python-pyzstd): Update to 0.15.3. --- gnu/packages/python-compression.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 7dd01d611e..9937299839 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -448,17 +448,18 @@ provided.") (define-public python-pyzstd (package (name "python-pyzstd") - (version "0.14.3") + (version "0.15.3") (source (origin (method url-fetch) (uri (pypi-uri "pyzstd" version)) (sha256 (base32 - "1d3mngs45w2p490vrq5ymd2wz4lp15phmks1ilcx4k7amgibml3d")))) + "0wkli2i4my79l43b996bdga0fac8s8nfd1zjyzl46lwmsfsxlkmc")))) (build-system python-build-system) (home-page "https://github.com/animalize/pyzstd") (synopsis "Zstandard bindings for Python") - (description "This package provides Python bindings to the Zstandard (zstd) + (description "This package provides Python bindings to the +Zstandard (zstd) compression library. The API is similar to Python's bz2/lzma/zlib module.") (license license:bsd-3))) From 0d9b69795dc1c7ccb80ed99079028519f73b1fa3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:02:31 +0100 Subject: [PATCH 259/824] gnu: python-zstandard: Update to 0.19.0. * gnu/packages/python-compression.scm (python-zstandard): Update to 0.19.0. [propagated-inputs]: Add python-cffi. --- gnu/packages/python-compression.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 9937299839..d6578cd932 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -428,14 +428,16 @@ wrapper. It provides a backport of the @code{Path} object.") (define-public python-zstandard (package (name "python-zstandard") - (version "0.15.2") + (version "0.19.0") (source (origin (method url-fetch) (uri (pypi-uri "zstandard" version)) (sha256 - (base32 "0by9z7nxnkzhmza075q6q91rs8lnpf91129k8ppv7kymbwshipjj")))) + (base32 "0qvqhs121spk7yc1l20samflxx47waxv3xm55ksxpn1djk6jzl9i")))) (build-system python-build-system) + (propagated-inputs + (list python-cffi)) (native-inputs (list python-hypothesis)) (home-page "https://github.com/indygreg/python-zstandard") From d2a7bd50a9c29bc48aa6aea8c61927fe4c3d1149 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:05:29 +0100 Subject: [PATCH 260/824] gnu: Add python-pyppmd. * gnu/packages/python-compression.scm (python-pyppmd): New variable. --- gnu/packages/python-compression.scm | 30 ++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index d6578cd932..4e26158b6d 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice -;;; Copyright © 2017, 2019, 2021 Ricardo Wurmus +;;; Copyright © 2017, 2019, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2017 Nikita ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2018, 2019, 2020 Efraim Flashner @@ -31,6 +31,7 @@ #:use-module (guix gexp) #:use-module (guix build-system gnu) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (gnu packages) #:use-module (gnu packages libffi) #:use-module (gnu packages compression) @@ -124,6 +125,33 @@ Jump conversion filter by CFFI for Python.") and decompression by implementing Python bindings for the ISA-L library.") (license license:expat))) +(define-public python-pyppmd + (package + (name "python-pyppmd") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyppmd" version)) + (sha256 + (base32 + "03w4x26mar0ha73c3v39psn1i0k6xrzwmaxfsxysic73jz99np07")))) + (build-system pyproject-build-system) + (native-inputs + (list python-coverage + python-hypothesis + python-pytest + python-pytest-benchmark + python-pytest-cov + python-pytest-timeout + python-setuptools-scm)) + (home-page "https://github.com/miurahr/pyppmd") + (synopsis "PPMd compression/decompression library") + (description "Pyppmd provides classes and functions for compressing and +decompressing text data, using the @dfn{Prediction by partial matching} (PPM) +compression algorithm variation H and I.2. It provides an API similar to +Python's zlib/bz2/lzma modules.") + (license license:lgpl2.1+))) + (define-public python-ppmd-cffi (package (name "python-ppmd-cffi") From fb2d4aa088bad38260095a582987b05c630b5a0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:06:51 +0100 Subject: [PATCH 261/824] gnu: Add python-brotlicffi. * gnu/packages/python-compression.scm (python-brotlicffi): New variable. --- gnu/packages/python-compression.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 4e26158b6d..d7c7d6e9b2 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -96,6 +96,24 @@ were a single file.") Jump conversion filter by CFFI for Python.") (license license:lgpl2.1+))) +(define-public python-brotlicffi + (package + (name "python-brotlicffi") + (version "1.0.9.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "brotlicffi" version)) + (sha256 + (base32 + "15kxgdiqcg0cm6h5xq3vkbhw7674673hcx3n2yicd3wx29l8l90c")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-cffi)) + (home-page "https://github.com/python-hyper/brotlicffi") + (synopsis "Python CFFI bindings to the Brotli library") + (description "This package provides Python CFFI bindings to the Brotli +library.") + (license license:expat))) + (define-public python-isal (package (name "python-isal") From 136760c3a9a5ef05057f199958c1b54f573b51c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:09:39 +0100 Subject: [PATCH 262/824] gnu: python-multivolumefile: Update to 0.2.3. * gnu/packages/python-compression.scm (python-multivolumefile): Update to 0.2.3. [build-system]: Use pyproject-build-system. [native-inputs]: Remove python-pep517 and python-setuptools; add python-hypothesis. --- gnu/packages/python-compression.scm | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index d7c7d6e9b2..a22a093edf 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -48,21 +48,20 @@ (define-public python-multivolumefile (package (name "python-multivolumefile") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (pypi-uri "multivolumefile" version)) (sha256 (base32 - "0j46wab4b09s3favjzp3zs1cn2sn8pr7qyngs5wn31hpqqxbbz76")))) - (build-system python-build-system) + "1mh9sz50s1p8ik83a455pqd57syprad7xhfmk28yb5mwmw58sr50")))) + (build-system pyproject-build-system) (native-inputs - (list python-pep517 - python-setuptools - python-setuptools-scm + (list python-setuptools-scm python-coverage python-coveralls + python-hypothesis python-pyannotate python-pytest python-pytest-cov)) From 6ea2229f89bac7adfbf27f00a8387df3a4ad9310 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:14:37 +0100 Subject: [PATCH 263/824] gnu: Add python-inflate64. * gnu/packages/python-compression.scm (python-inflate64): New variable. --- gnu/packages/python-compression.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index a22a093edf..8aa666cc25 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -113,6 +113,29 @@ Jump conversion filter by CFFI for Python.") library.") (license license:expat))) +(define-public python-inflate64 + (package + (name "python-inflate64") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "inflate64" version)) + (sha256 + (base32 + "0767j35gkwaykl1iq9qn8rc25j1ggv56x3d1vzjpk89bzpzdhbdm")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata)) + (native-inputs + (list python-pyannotate + python-pytest + python-setuptools-scm)) + (home-page "https://pypi.org/project/inflate64/") + (synopsis "deflate64 compression/decompression library") + (description "The @code{inflate64} package provides @code{Deflater} and +@code{Inflater} classes to compress and decompress with the Enhanced Deflate +compression algorithm.") + (license license:lgpl2.1+))) + (define-public python-isal (package (name "python-isal") From 101a4e2718db6b9b96333d75cacb761640074405 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:17:31 +0100 Subject: [PATCH 264/824] gnu: Add python-pybcj. * gnu/packages/python-compression.scm (python-pybcj): New variable. --- gnu/packages/python-compression.scm | 30 +++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 8aa666cc25..999f989102 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -72,6 +72,36 @@ file-object abstraction, making it possible to use multiple files as if they were a single file.") (license license:lgpl2.1+))) +(define-public python-pybcj + (package + (name "python-pybcj") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pybcj" version)) + (sha256 + (base32 + "1hvm3c3mb20z25kmbzyyn6pr5inx50z0ignl8b0bggxaik82ws4b")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata)) + (native-inputs + (list python-coverage + python-hypothesis + python-pytest + python-pytest-cov + python-setuptools-scm)) + (home-page "https://codeberg.org/miurahr/pybcj") + (synopsis "BCJ filter library") + (description "In data compression, BCJ, short for Branch-Call-Jump, refers +to a technique that improves the compression of machine code of executable +binaries by replacing relative branch addresses with absolute ones. This +allows a LZMA compressor to identify duplicate targets and archive higher +compression rate. BCJ is used in the 7-zip compression utility as the default +filter for executable binaries. + +pybcj provides Python bindings to a BCJ implementation in C.") + (license license:lgpl2.1+))) + (define-public python-bcj-cffi (package (name "python-bcj-cffi") From 4b23e2d86881bf7be204a6c3ec85fa86b197a02c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 23 Nov 2022 13:17:39 +0100 Subject: [PATCH 265/824] gnu: python-py7zr: Update to 0.20.2. * gnu/packages/python-compression.scm (python-py7zr): Update to 0.20.2. [build-system]: Use pyproject-build-system. [propagated-inputs]: Add python-brotli, python-brotlicffi, python-importlib-metadata, python-inflate64, python-psutil, python-pybcj, python-pycryptodomex, and python-pyppmd; remove python-bcj-cffi, python-ppmd-cffi, python-pycryptodome, and python-zstandard. --- gnu/packages/python-compression.scm | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 999f989102..9eef74c71b 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -252,23 +252,27 @@ several possible methods.") (define-public python-py7zr (package (name "python-py7zr") - (version "0.14.1") + (version "0.20.2") (source (origin (method url-fetch) (uri (pypi-uri "py7zr" version)) (sha256 (base32 - "1zmgp7yax328fj8yj8pj4l7yh78hp727j6wk12vfi6nmi82wl32i")))) - (build-system python-build-system) + "0lwniinfr3rb10n0c203a09vz06vxnnj637yqn8ipdlml89gj7kr")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-bcj-cffi + (list python-brotli + python-brotlicffi + python-importlib-metadata + python-inflate64 python-multivolumefile - python-ppmd-cffi - python-pycryptodome + python-psutil + python-pybcj + python-pycryptodomex + python-pyppmd python-pyzstd - python-texttable - python-zstandard)) + python-texttable)) (native-inputs (list python-setuptools python-setuptools-scm From 22a788d085ada0dcf8e5d701ce192c87d08e3734 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 23 Nov 2022 13:58:41 +0100 Subject: [PATCH 266/824] gnu: sbcl-cl-prevalence: Update to 20221122. * gnu/packages/lisp-xyz.scm (sbcl-cl-prevalence): Update to 20221122. This update contains a critical bugfix, hence the conssecutive version bump. --- gnu/packages/lisp-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index cab953884f..944e8959ff 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -7724,8 +7724,8 @@ number of other projects. (sbcl-package->ecl-package sbcl-s-sysdeps)) (define-public sbcl-cl-prevalence - (let ((commit "f22105d9728949a8e0c733801cad589f06447e25") - (revision "5")) + (let ((commit "e6b27640ce89ae5f8af38beb740e319bb6cd2368") + (revision "6")) (package (name "sbcl-cl-prevalence") (build-system asdf-build-system/sbcl) @@ -7740,7 +7740,7 @@ number of other projects. (file-name (git-file-name name version)) (sha256 (base32 - "11iqrgpzzyn2xsqyryh5jc5x93s23djsvrzsqyjhcy3zkzrxfkha")))) + "1lb957ivshgp56phqhvhsmnc4r55x5shvi3mpsan2xsm4hvqspp0")))) (inputs (list sbcl-moptilities sbcl-s-sysdeps sbcl-s-xml)) (native-inputs From f7cb2b22a275cc1fa0fdae9023aa3b4788cd1952 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Nov 2022 01:00:00 +0100 Subject: [PATCH 267/824] gnu: guile-torrent: Fix build. * gnu/packages/guile-xyz.scm (guile-torrent)[propagated-inputs]: Replace (3.0) guile-gcrypt with guile2.2-gcrypt. Reported by mirai on #guix. --- gnu/packages/guile-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 62bcfb6a56..b1620618eb 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -4189,7 +4189,7 @@ models and also supports a rich set of boolean query operators.") perl pkg-config)) (propagated-inputs - (list guile-gcrypt)) + (list guile2.2-gcrypt)) (home-page "https://github.com/o-nly/torrent") (synopsis "Torrent library for GNU Guile") (description "This package provides facilities for working with From 7a2082023ad9c7479bfedf39537606a088222d48 Mon Sep 17 00:00:00 2001 From: Jonathan Brielmaier Date: Wed, 23 Nov 2022 17:22:11 +0100 Subject: [PATCH 268/824] NEWS: Update it. * NEWS: Shepherd is already at 0.9.3 now. --- NEWS | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/NEWS b/NEWS index b1eaf896db..27ac11c13a 100644 --- a/NEWS +++ b/NEWS @@ -74,10 +74,11 @@ Please send Guix bug reports to bug-guix@gnu.org. *** The installer now has a crash dump upload mechanism *** Emacs now supports native compilation *** GRUB bootloader now supports chain-loading -*** The GNU Shepherd was upgraded to 0.9.2 +*** The GNU Shepherd was upgraded to 0.9.3 *** The init RAM disk honors more arguments—e.g. ‘root’ and ‘rootflags’ *** ‘guix system image’ can now generate WSL images *** The mcron task scheduler logs now contain the jobs exit statuses + ** Programming interfaces *** Package input fields can now plain package lists *** G-expressions can now be used in build phases From 2b151eb2868f28c098328019e24cb1d05cd19d2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 23 Nov 2022 16:19:39 +0100 Subject: [PATCH 269/824] gnu: gettext: Skip Gnulib tests that fail on GNU/Hurd. * gnu/packages/gettext.scm (gettext-minimal)[arguments]: In 'patch-tests' phase, arrange to not run 'test-tls'. Adjust 'XFAIL_TESTS' flag passed to #:make-flags. --- gnu/packages/gettext.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm index d606acf798..5df30c4be3 100644 --- a/gnu/packages/gettext.scm +++ b/gnu/packages/gettext.scm @@ -120,13 +120,19 @@ "coreutils-gnulib-tests.patch"))))) '()) + #$@(if (hurd-target?) + #~((substitute* + "gettext-tools/gnulib-tests/Makefile.in" + ;; See 'coreutils' for the rationale. + ((" test-tls\\$\\(EXEEXT\\) ") " "))) + '()) + #t))))) ;; When tests fail, we want to know the details. #:make-flags #~'("VERBOSE=yes" #$@(if (hurd-target?) - ;; Linking to libgettextlib.so makes test-raise fail - '("XFAIL_TESTS=test-raise") + '("XFAIL_TESTS=test-perror2") '())))) (home-page "https://www.gnu.org/software/gettext/") (synopsis From 02a4e54250e81664a797466edba46b017ae1a7b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 23 Nov 2022 19:31:12 +0100 Subject: [PATCH 270/824] gnu: grep: Skip 'triple-backref' test. * gnu/packages/base.scm (grep)[arguments]: Add 'skip-triple-backref-test' phase for GNU/Hurd. --- gnu/packages/base.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index bf6435585e..36b27a4e25 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -130,7 +130,19 @@ command-line arguments, multiple languages, and so on.") (substitute* (list (string-append bin "/egrep") (string-append bin "/fgrep")) (("^exec grep") - (string-append "exec " bin "/grep"))))))) + (string-append "exec " bin "/grep")))))) + ,@(if (hurd-target?) + '((add-before 'check 'skip-triple-backref-test + (lambda _ + ;; This test is marked as malfunctioning on glibc systems + ;; due to + ;; + ;; and it triggers a segfault with glibc 2.33 on GNU/Hurd. + ;; Skip it. + (substitute* "tests/triple-backref" + (("^warn_" all) + (string-append "exit 77\n" all)))))) + '())) #:make-flags ,(if (hurd-target?) ''("XFAIL_TESTS=test-perror2 equiv-classes") ;XXX ''()))) From d33ed58169edc027cfb6c256ecabde87e59918ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 23 Nov 2022 19:32:04 +0100 Subject: [PATCH 271/824] offload: Increase default 'overload-threshold' value. When offloading to a single machine, the previous default value would lead 'guix offload' to wait possibly for several minutes between subsequent builds until normalized load would finally go below 0.6. Increasing it mitigates that. * guix/scripts/offload.scm ()[overload-threshold]: Bump to 0.8. * doc/guix.texi (Daemon Offload Setup): Likewise. --- doc/guix.texi | 2 +- guix/scripts/offload.scm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index c0cb24d709..f39a0aa700 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -1409,7 +1409,7 @@ when transferring files to and from build machines. File name of the Unix-domain socket @command{guix-daemon} is listening to on that machine. -@item @code{overload-threshold} (default: @code{0.6}) +@item @code{overload-threshold} (default: @code{0.8}) The load threshold above which a potential offload machine is disregarded by the offload scheduler. The value roughly translates to the total processor usage of the build machine, ranging from 0.0 (0%) to diff --git a/guix/scripts/offload.scm b/guix/scripts/offload.scm index 8ab393c0ac..578b3b9888 100644 --- a/guix/scripts/offload.scm +++ b/guix/scripts/offload.scm @@ -112,7 +112,7 @@ ;; A #f value tells the offload scheduler to disregard the load of the build ;; machine when selecting the best offload machine. (overload-threshold build-machine-overload-threshold ; inexact real between - (default 0.6)) ; 0.0 and 1.0 | #f + (default 0.8)) ; 0.0 and 1.0 | #f (parallel-builds build-machine-parallel-builds ; number (default 1)) (speed build-machine-speed ; inexact real From 22d44f87763f86a05e9679d9ad2c99e17f4c79be Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Nov 2022 01:00:00 +0100 Subject: [PATCH 272/824] =?UTF-8?q?doc:=20Note=20that=20=E2=80=98guix=20pa?= =?UTF-8?q?ckage=E2=80=99=20accepts=20file=20names.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Package Management)[Invoking guix package]: Mention support for operating on store file names. Co-authored-by: Tobias Geerinckx-Rice --- doc/guix.texi | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index f39a0aa700..e547d469f4 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -3423,19 +3423,25 @@ The @var{options} can be among the following: @itemx -i @var{package} @dots{} Install the specified @var{package}s. -Each @var{package} may specify either a simple package name, such as -@code{guile}, or a package name followed by an at-sign and version number, -such as @code{guile@@1.8.8} or simply @code{guile@@1.8} (in the latter -case, the newest version prefixed by @code{1.8} is selected). +Each @var{package} may specify a simple package name, such as +@code{guile}, optionally followed by an at-sign and version number, +such as @code{guile@@3.0.7} or simply @code{guile@@3.0}. In the latter +case, the newest version prefixed by @code{3.0} is selected. -If no version number is specified, the -newest available version will be selected. In addition, @var{package} +If no version number is specified, the newest available version will be +selected. In addition, such a @var{package} specification may contain a colon, followed by the name of one of the outputs of the package, as in @code{gcc:doc} or @code{binutils@@2.22:lib} -(@pxref{Packages with Multiple Outputs}). Packages with a corresponding +(@pxref{Packages with Multiple Outputs}). + +Packages with a corresponding name (and optionally version) are searched for among the GNU distribution modules (@pxref{Package Modules}). +Alternatively, a @var{package} can directly specify a store file name +such as @file{/gnu/store/...-guile-3.0.7}, as produced by, e.g., +@code{guix build}. + @cindex propagated inputs Sometimes packages have @dfn{propagated inputs}: these are dependencies that automatically get installed along with the required package From c4bbdaf2db4204eef2b174f8f565606b529d4abc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Simen=20Endsj=C3=B8?= Date: Wed, 23 Nov 2022 09:21:25 +0100 Subject: [PATCH 273/824] gnu: font-iosevka: Update to 16.4.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fonts.scm (font-iosevka): Update to 16.4.0. Signed-off-by: 宋文武 --- gnu/packages/fonts.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index a2578e1bf7..95e99d5a73 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -35,7 +35,7 @@ ;;; Copyright © 2020 Raghav Gururajan ;;; Copyright © 2020, 2021 Julien Lepiller ;;; Copyright © 2020 Zhu Zihao -;;; Copyright © 2020, 2021 Simen Endsjø +;;; Copyright © 2020, 2021, 2022 Simen Endsjø ;;; Copyright © 2020 Tim Van den Langenbergh ;;; Copyright © 2020 Nicolò Balzarotti ;;; Copyright © 2021 Antoine Côté @@ -1498,7 +1498,7 @@ guix repl < Date: Tue, 22 Nov 2022 20:49:06 -0600 Subject: [PATCH 274/824] gnu: clasp: Update to 3.3.9. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/maths.scm (clasp): Update to 3.3.9. Signed-off-by: 宋文武 --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cfe2dcbcf2..ebb3a8fbd1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2542,7 +2542,7 @@ between aspif and smodels format or to a human-readable text format.") (define-public clasp (package (name "clasp") - (version "3.3.6") + (version "3.3.9") (source (origin (method git-fetch) (uri (git-reference @@ -2551,7 +2551,7 @@ between aspif and smodels format or to a human-readable text format.") (file-name (git-file-name name version)) (sha256 (base32 - "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj")))) + "163ps9zq7xppqy9hj5qnw6z5lcjnm4xf5fwjsavpia5ynm3hngcw")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DCLASP_BUILD_TESTS=on" From 6e142c69bd83cd9a6c846b2fe8f7e885a1225fab Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Mon, 21 Nov 2022 00:46:22 -0500 Subject: [PATCH 275/824] gnu: xfsprogs: Update to 6.0.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (xfsprogs): Update to 6.0.0. Signed-off-by: 宋文武 --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 601162b465..eab734683f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8456,7 +8456,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC (define-public xfsprogs (package (name "xfsprogs") - (version "5.14.2") + (version "6.0.0") (source (origin (method url-fetch) (uri (string-append @@ -8464,7 +8464,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC "xfsprogs-" version ".tar.gz")) (sha256 (base32 - "0368dacdjq55ip38yizs9spdyl7b0b1c0vz3gr1gvcb9rw3a6dnp")))) + "14hc61nfc73nqwhyasc4haj5g7046im1dwz61bx338f86mjj5n5y")))) (build-system gnu-build-system) (outputs (list "out" "python")) (arguments From 4a97591d0a13e88037b3073bd891bcdf35352f87 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Mon, 21 Nov 2022 00:45:07 -0500 Subject: [PATCH 276/824] gnu: btrfs-progs: Update to 6.0.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (btrfs-progs): Update to 6.0.1. Signed-off-by: 宋文武 --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index eab734683f..a984b45fbc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5555,7 +5555,7 @@ and copy/paste text in the console and in xterm.") (define-public btrfs-progs (package (name "btrfs-progs") - (version "5.18.1") + (version "6.0.1") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/" @@ -5563,7 +5563,7 @@ and copy/paste text in the console and in xterm.") "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "0mbj3j2fpjds9i9gm8kk8a20yjacc562ibd1v9a96bpmrxfag63f")))) + "0j0w400fg0lbzljmcwq553cv0awixc4k35v7l39jl7l13pznycdm")))) (build-system gnu-build-system) (outputs '("out" "static")) ; static versions of the binaries in "out" From 8a620036d7490766be1822213ed8ab88cbe4f491 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Wed, 23 Nov 2022 03:26:59 +0000 Subject: [PATCH 277/824] gnu: Add cl-40ants-doc. * gnu/packages/lisp-xyz.scm (sbcl-40ants-doc, cl-40ants-doc, ecl-40ants-doc): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 83 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 944e8959ff..baf7e86d3b 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -3054,6 +3054,89 @@ pretty, documentation is code.") (define-public ecl-mgl-pax (sbcl-package->ecl-package sbcl-mgl-pax)) +(define-public sbcl-40ants-doc + (let ((commit "7725ff67a380e9ebfc6155e14d91e650f256711b") + (revision "0")) + (package + (name "sbcl-40ants-doc") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/40ants/doc") + (commit commit))) + (sha256 + (base32 "1v6gnhrk02vsixmprzk4wvvj7vh11vp5waxyih0qz2ih8d38r5pg")) + (file-name (git-file-name "cl-40ants-doc" version)))) + (build-system asdf-build-system/sbcl) + (arguments + ;; TODO: Add remaining dependencies of 40ants-doc-full and + ;; 40ants-doc-test missing from Guix. + '(#:asd-systems '("40ants-doc" + ;;"40ants-doc-full" + ) + #:tests? #f)) + ;;(native-inputs + ;; (list sbcl-rove)) + (inputs + (list sbcl-named-readtables + sbcl-pythonic-string-reader + ;; For 40ants-doc-full: + ;;sbcl-3bmd + ;;sbcl-alexandria + ;;sbcl-babel + ;;sbcl-cl-cookie + ;;sbcl-cl-fad + ;;sbcl-cl-ppcre + ;;sbcl-common-doc ; Missing from Guix + ;;sbcl-common-html ; Missing from Guix + ;;sbcl-commondoc-markdown ; Missing from Guix + ;;sbcl-dexador + ;;sbcl-docs-builder ; Missing from Guix + ;;sbcl-fare-utils + ;;sbcl-jonathan + ;;sbcl-lass + ;;sbcl-local-time + ;;sbcl-log4cl + ;;sbcl-slime-swank + ;;sbcl-slynk + ;;sbcl-spinneret + ;;sbcl-stem ; Missing from Guix; also, license is unconfirmed + ;;sbcl-str + ;;sbcl-tmpdir ; Missing from Guix + ;;sbcl-trivial-extract ; Missing from Guix + ;;sbcl-xml-emitter + )) + (home-page "https://40ants.com/doc/") + (synopsis "Exploratory programming environment and documentation generator") + (description + "@code{40ants-doc} provides a rudimentary explorable programming +environment. The narrative primarily lives in so-called sections that mix +Markdown docstrings with references to functions, variables, etc., all of +which should probably have their own docstrings. + +The primary focus is on making code easily explorable by using SLIME's +@kbd{M-.} (@code{slime-edit-definition}). Generating documentation in +Markdown or HTML format from sections and all the referenced items is also +implemented. + +With the simplistic tools provided, one may obtain results similar to literate +programming, but documentation is generated from code, not the other way +around, and there is no support for chunking. Code comes first, code must +look pretty, documentation is code. + +@code{40ants-doc} is a fork of MGL-PAX with fewer dependencies (only +@code{named-readtables} and @code{pythonic-string-reader}) for the core +system, and additional features in the full system.") + (license license:expat)))) + +(define-public cl-40ants-doc + (sbcl-package->cl-source-package sbcl-40ants-doc)) + +(define-public ecl-40ants-doc + (sbcl-package->ecl-package sbcl-40ants-doc)) + (define-public sbcl-mssql (let ((commit "045602a19a32254108f2b75871049293f49731eb") (revision "1")) From b0c392ffcf8148aebc5f5c75e92272d58b821278 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Wed, 23 Nov 2022 03:27:04 +0000 Subject: [PATCH 278/824] gnu: Add cl-tar-file. * gnu/packages/lisp-xyz.scm (sbcl-tar-file, cl-tar-file, ecl-tar-file): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 49 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index baf7e86d3b..b548732320 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -9526,6 +9526,55 @@ archives such as those generated by the tar and cpio programs on Unix.") (define-public ecl-archive (sbcl-package->ecl-package sbcl-archive)) +(define-public sbcl-tar-file + (let ((commit "0c10bc82f14702c97a26dc25ce075b5d3a2347d1") + (revision "0")) + (package + (name "sbcl-tar-file") + (version (git-version "0.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.common-lisp.net/cl-tar/cl-tar-file") + (commit commit))) + (file-name (git-file-name "cl-tar-file" version)) + (sha256 + (base32 "0i8j05fkgdqy4c4pqj0c68sh4s3klpx9kc5wp73qwzrl3xqd2svy")))) + (build-system asdf-build-system/sbcl) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-40ants-doc + sbcl-alexandria + sbcl-babel + sbcl-chipz + sbcl-flexi-streams + sbcl-salza2 + sbcl-trivial-gray-streams)) + (home-page "https://gitlab.common-lisp.net/cl-tar/cl-tar-file") + (synopsis "Read and write physical entries to and from tar files") + (description + "@code{cl-tar-file} is a Common Lisp library that allows reading from +and writing to various tar archive formats. Currently supported are the POSIX +ustar, PAX (ustar with a few new entry types), GNU, and v7 (very old) formats. + +This library is rather low level and is focused exclusively on reading and +writing physical tar file entries using streams. Therefore, it contains no +functionality for automatically building archives from a set of files on the +filesystem or writing the contents of a file to the filesystem. Additionally, +there are no smarts that read multiple physical entries and combine them into +a single logical entry (e.g., with PAX extended headers or GNU long link/path +name support). For a higher-level library that reads and writes logical +entries, and also includes filesystem integration, see @code{cl-tar}.") + (license license:bsd-3)))) + +(define-public cl-tar-file + (sbcl-package->cl-source-package sbcl-tar-file)) + +(define-public ecl-tar-file + (sbcl-package->ecl-package sbcl-tar-file)) + (define-public sbcl-misc-extensions (let ((commit "101c05112bf2f1e1bbf527396822d2f50ca6327a") (revision "1")) From 8bde62d17439d62d01d13ad222c9e3fcd8c79c12 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Wed, 23 Nov 2022 03:27:11 +0000 Subject: [PATCH 279/824] gnu: Add cl-tar. * gnu/packages/lisp-xyz.scm (sbcl-tar, cl-tar, ecl-tar): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 48 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index b548732320..270d55af67 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -9575,6 +9575,54 @@ entries, and also includes filesystem integration, see @code{cl-tar}.") (define-public ecl-tar-file (sbcl-package->ecl-package sbcl-tar-file)) +(define-public sbcl-tar + (let ((commit "7c6e07a10c93d9e311f087b5f6328cddd481669a") + (revision "0")) + (package + (name "sbcl-tar") + (version (git-version "0.2.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.common-lisp.net/cl-tar/cl-tar") + (commit commit))) + (file-name (git-file-name "cl-tar" version)) + (sha256 + (base32 "0wp23cs3i6a89dibifiz6559la5nk58d1n17xvbxq4nrl8cqsllf")))) + (build-system asdf-build-system/sbcl) + ;; TODO: Build the tar program with 'build-program' when the + ;; 'asdf-release-ops' library is added to Guix. + (arguments + '(#:asd-systems '("tar" + "tar/common-extract" + "tar/create" + "tar/docs" + "tar/extract" + "tar/simple-extract"))) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-40ants-doc + sbcl-alexandria + sbcl-babel + sbcl-local-time + sbcl-osicat + sbcl-split-sequence + sbcl-tar-file)) + (home-page "https://gitlab.common-lisp.net/cl-tar/cl-tar") + (synopsis "High-level interface for tar files") + (description + "@code{cl-tar} is a Common Lisp library providing a high-level interface +for interacting with tar archives.") + (license license:expat)))) + +(define-public cl-tar + (sbcl-package->cl-source-package sbcl-tar)) + +(define-public ecl-tar + (sbcl-package->ecl-package sbcl-tar)) + (define-public sbcl-misc-extensions (let ((commit "101c05112bf2f1e1bbf527396822d2f50ca6327a") (revision "1")) From 58eef1a258f41e263007aa3a6ab387601e7fe0ae Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 20 Nov 2022 09:23:59 -0800 Subject: [PATCH 280/824] gnu: Add go-github-com-nathan-osman-go-sunrise. * gnu/packages/golang.scm (go-github-com-nathan-osman-go-sunrise): New variable. Signed-off-by: Christopher Baines --- gnu/packages/golang.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 2ed4c7a73c..bea58e9e31 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2485,6 +2485,32 @@ web framework @end itemize") (license license:expat))) +(define-public go-github-com-nathan-osman-go-sunrise + (let ((commit "c8f9f1eb869135f07378e7e3c5ec7a005f806c73") + (revision "0")) + (package + (name "go-github-com-nathan-osman-go-sunrise") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nathan-osman/go-sunrise") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "017zwzx05r5spxcs07dp6bnh7waknzsd819k7aqd8kr819v3x9in")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/nathan-osman/go-sunrise")) + (home-page "https://github.com/nathan-osman/go-sunrise") + (synopsis "Calculate sunrise and sunset times in Go") + (description + "This package provides a Go library for calculating sunrise and +sunset times from geographical coordinates and a date.") + (license license:expat)))) + (define-public go-github-com-aws-sdk (package (name "go-github-com-aws-sdk") From b0307b7c123f741fa14c8a7b87d6427ccb3316ac Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 20 Nov 2022 09:24:00 -0800 Subject: [PATCH 281/824] gnu: Add go-github-com-hebcal-gematriya. * gnu/packages/golang.scm (go-github-com-hebcal-gematriya): New variable. Signed-off-by: Christopher Baines --- gnu/packages/golang.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index bea58e9e31..57ed50157a 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2511,6 +2511,32 @@ web framework sunset times from geographical coordinates and a date.") (license license:expat)))) +(define-public go-github-com-hebcal-gematriya + (let ((commit "fe3043f73e415eb82727701d10f2fb40f87675e9") + (revision "0")) + (package + (name "go-github-com-hebcal-gematriya") + (version (git-version "1.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/gematriya") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xmnb2i80dy380yv8c4pd04bbyqgbc7c40p8hz1vqj2lhbm6jabf")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/gematriya")) + (home-page "https://github.com/hebcal/gematriya") + (synopsis "Print numbers as Hebrew letters in Go") + (description + "This package provides a Go library for printing numbers as +Hebrew letters.") + (license license:bsd-2)))) + (define-public go-github-com-aws-sdk (package (name "go-github-com-aws-sdk") From 4ca2159bab67e9bd2f64e0db244f4eb3e03fd53e Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 20 Nov 2022 09:24:01 -0800 Subject: [PATCH 282/824] gnu: Add go-github-com-hebcal-hebcal-go. * gnu/packages/golang.scm (go-github-com-hebcal-hebcal-go): New variable. Signed-off-by: Christopher Baines --- gnu/packages/golang.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 57ed50157a..e848074cb4 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2537,6 +2537,49 @@ sunset times from geographical coordinates and a date.") Hebrew letters.") (license license:bsd-2)))) +(define-public go-github-com-hebcal-hebcal-go + (let ((commit "d42e881860cfc9e8249fc79f268091c3c4d36b0d") + (revision "0")) + (package + (name "go-github-com-hebcal-hebcal-go") + (version (git-version "0.9.11" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/hebcal-go") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1m9akb8pwxchpaci05gambshrzw626gsrfhl25f36vjl7mq5292n")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/hebcal-go" + ;; Source-only package + #:tests? #f + #:phases + #~(modify-phases %standard-phases + ;; Source-only package + (delete 'build)))) + (native-inputs + (list go-github-com-stretchr-testify)) + (propagated-inputs + (list go-github-com-hebcal-gematriya + go-github-com-nathan-osman-go-sunrise)) + (home-page "https://github.com/hebcal/hebcal-go") + (synopsis "Go library for the Hebcal perpetual Jewish calendar") + (description + "This package provides a library for conversion between Hebrew +and Gregorian dates, and generation of lists of Jewish holidays for +a given year. Shabbat and holiday candle lighting and havdalah times +are approximated based on location. + +Torah readings, Daf Yomi, and counting of the Omer can also be +specified. Algorithms are included to calculate yahrzeits, birthdays, +and anniversaries.") + (license license:gpl2+)))) + (define-public go-github-com-aws-sdk (package (name "go-github-com-aws-sdk") From 963e86af87216e8c1f4967e8047e8de415bb1000 Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Sun, 20 Nov 2022 09:24:02 -0800 Subject: [PATCH 283/824] gnu: Add hebcal. * gnu/packages/calendar.scm (hebcal): New variable. Signed-off-by: Christopher Baines --- gnu/packages/calendar.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 6583810277..32a8f23f19 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -34,6 +34,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) + #:use-module (guix build-system go) #:use-module (guix build-system cmake) #:use-module (guix build-system python) #:use-module (gnu packages admin) @@ -45,6 +46,7 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages perl) @@ -426,3 +428,38 @@ written in C++ using GTK. Launched once, it pops up a small calendar applet, launched again it closes the running instance. It can additionally be configured to show the current time in different timezones.") (license license:bsd-3)))) + +(define-public hebcal + (let ((commit "2384bb88dc1a41a4a5ae57a29fb58b2dd49a475d") + (revision "0")) + (package + (name "hebcal") + (version (git-version "5.3.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/hebcal") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12rv3b51jb7wcjwmmizz9jkw7gh37yklys4xncvpzgxdkkfgmmjx")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/hebcal")) + (inputs + (list go-github-com-hebcal-hebcal-go + go-github-com-pborman-getopt)) + (synopsis "Perpetual Jewish Calendar program") + (description + "Hebcal is a program for converting between Hebrew and Gregorian +dates, and generating lists of Jewish holidays for a given year. +Shabbat, holiday candle lighting, and havdalah times are approximated +using your location. + +It can also show daily prayer times, the weekly Torah reading, and +the daily leaf of Talmud. The program can help with counting of the +Omer or with calculation of Hebrew yahrzeits, birthdays, or +anniversaries.") + (home-page "https://github.com/hebcal/hebcal") + (license license:gpl2+)))) From 42898ae8ca25347a4b889bd44203ee7675f0c407 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 22 Nov 2022 16:11:36 +0000 Subject: [PATCH 284/824] gnu: Add mympd. * gnu/packages/mpd.scm (mympd): New variable. Signed-off-by: Christopher Baines --- gnu/packages/mpd.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 0c8dc16cf9..cd37d4682c 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -56,6 +56,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages libusb) + #:use-module (gnu packages lua) #:use-module (gnu packages readline) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -67,6 +68,7 @@ #:use-module (gnu packages music) #:use-module (gnu packages ncurses) #:use-module (gnu packages pcre) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) @@ -76,7 +78,9 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) + #:use-module (gnu packages tls) #:use-module (gnu packages video) + #:use-module (gnu packages web) #:use-module (gnu packages xiph)) (define-public libmpdclient @@ -573,3 +577,27 @@ which is focused on playing local music without the need of managing playlists. Instead of maintaining a client side database of your music library, mpdevil loads all tags and covers on demand.") (license license:gpl3+))) + +(define-public mympd + (package + (name "mympd") + (version "10.1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jcorporation/myMPD") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cqq09j7mi7dz5y6l7i0sa6vi2n5zrndnrxnqsi4vcg99fc2vwv8")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; no test target + (native-inputs (list jq perl)) + (inputs (list flac libid3tag lua openssl pcre2)) + (home-page "https://jcorporation.github.io/") + (synopsis "Web-based MPD client") + (description "MyMPD is a mobile-friendly web client for the MPD music +player daemon.") + (license license:gpl3+))) From 68113dc2498e507879eeecc583a66a5bc046c91b Mon Sep 17 00:00:00 2001 From: conses Date: Thu, 24 Nov 2022 00:00:58 +0100 Subject: [PATCH 285/824] gnu: Add whoogle-search. * gnu/packages/python-web.scm (whoogle-search): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-web.scm | 59 +++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 905d79886f..4f3a587c6a 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4743,6 +4743,65 @@ Google search engine. Its module is called @code{googlesearch}.") (description "Python client library for Google's discovery based APIs") (license license:asl2.0))) +(define-public whoogle-search + (package + (name "whoogle-search") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "whoogle-search" version)) + (sha256 + (base32 + "0h8cl9bkd3vx17kbvcnmc8cy6pc29lxr0drxm84kj37ka788cj2g")))) + (build-system python-build-system) + (arguments + (list + ;; The tests need network access + #:tests? #f)) + (propagated-inputs + (list python-attrs + python-beautifulsoup4 + python-cachelib + python-certifi + python-cffi + python-brotli + python-chardet + python-click + python-cryptography + python-cssutils + python-defusedxml + python-flask + python-flask-session + python-idna + python-itsdangerous + python-jinja2 + python-markupsafe + python-more-itertools + python-packaging + python-pluggy + python-py + python-pycodestyle + python-pycparser + python-pyopenssl + python-pyparsing + python-pysocks + python-dateutil + python-requests + python-soupsieve + python-stem + python-urllib3 + python-waitress + python-wcwidth + python-werkzeug + python-dotenv)) + (home-page "https://github.com/benbusby/whoogle-search") + (synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine") + (description + "Get Google results, but without any ads, javascript, AMP links, +cookies, or IP address tracking. Quick and simple to implement as a primary +search engine replacement on both desktop and mobile.") + (license license:expat))) + (define-public python-hawkauthlib (package (name "python-hawkauthlib") From f4a7ccc976a8974803ed4b0bfe72af0bd44a9773 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 4 Nov 2022 13:05:12 +0100 Subject: [PATCH 286/824] guix: Upgrade to Bioconductor 3.16. * guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to 3.16. * guix/import/cran.scm (%bioconductor-version): Same. --- guix/build-system/r.scm | 2 +- guix/import/cran.scm | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 620822b870..9b360ae581 100644 --- a/guix/build-system/r.scm +++ b/guix/build-system/r.scm @@ -61,7 +61,7 @@ release corresponding to NAME and VERSION." "/src/contrib/" name "_" version ".tar.gz") ;; TODO: use %bioconductor-version from (guix import cran) - (string-append "https://bioconductor.org/packages/3.15" + (string-append "https://bioconductor.org/packages/3.16" type-url-part "/src/contrib/" name "_" version ".tar.gz")))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 278743d496..286a4c21b9 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -188,9 +188,9 @@ package definition." (define %cran-canonical-url "https://cran.r-project.org/package=") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.15. Bioconductor packages should be +;; The latest Bioconductor release is 3.16. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.15") +(define %bioconductor-version "3.16") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" From 8105b3c09fac897ff2c2464479b1d3e8169d8700 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 16 Nov 2022 23:21:40 +0100 Subject: [PATCH 287/824] gnu: Add r-hdo-db. * gnu/packages/bioconductor.scm (r-hdo-db): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45a511cf13..e55d9e357e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -506,6 +506,31 @@ ID and species. It is used by functions in the GenomeInfoDb package.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) +(define-public r-hdo-db + (package + (name "r-hdo-db") + (version "0.99.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDO.db" version 'annotation)) + (sha256 + (base32 + "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61")))) + (properties `((upstream-name . "HDO.db"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi)) + (native-inputs + (list r-knitr)) + (home-page "https://bioconductor.org/packages/HDO.db") + (synopsis "Annotation maps describing the entire Human Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Human Disease Ontology. The annotation data comes from +@url{Humam Disease Ontology repository, +https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") From c70207ae3be8eb99ae03400c61e9b862b55b2ae1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 16 Nov 2022 23:28:19 +0100 Subject: [PATCH 288/824] gnu: r-ggplot2: Update to 3.4.0. * gnu/packages/statistics.scm (r-ggplot2): Update to 3.4.0. [propagated-inputs]: Add r-cli, r-lifecycle, and r-vctrs. --- gnu/packages/statistics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2d4dbe4a31..ba937e8c4b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1236,25 +1236,28 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.6") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz")))) + (base32 "0gj7n2y8msnmhk3x4r481biknvn2dqhahwazfqwr8f3lz599wbx8")))) (build-system r-build-system) (propagated-inputs - (list r-digest + (list r-cli + r-digest r-glue r-gtable r-isoband + r-lifecycle r-mass r-mgcv r-tibble r-rlang r-scales r-svglite ; Needed for 'ggsave' + r-vctrs r-withr)) (native-inputs (list r-knitr)) From e273f52358e95fbe8a6f545370df34467acd2b3b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 04:23:32 +0100 Subject: [PATCH 289/824] gnu: r-ggprism: Update to 1.0.4. * gnu/packages/cran.scm (r-ggprism): Update to 1.0.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3e5d654c5a..ed84855c90 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1273,13 +1273,13 @@ variables.") (define-public r-ggprism (package (name "r-ggprism") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggprism" version)) (sha256 (base32 - "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp")))) + "0ycklp7764cw65hqh9r61im8vqfd7sjayyw1gvprxzg7k217gnl3")))) (properties `((upstream-name . "ggprism"))) (build-system r-build-system) (propagated-inputs From 3d073b86d3e6bccf1f25d12174a0b88b5db65f23 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 00:38:24 +0100 Subject: [PATCH 290/824] gnu: Add r-biocbaseutils. * gnu/packages/bioconductor.scm (r-biocbaseutils): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e55d9e357e..0b11b5b5e9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14848,6 +14848,28 @@ enrichment analysis and several functions for visualization.") microarray data.") (license license:gpl2+))) +(define-public r-biocbaseutils + (package + (name "r-biocbaseutils") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocBaseUtils" version)) + (sha256 + (base32 + "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69")))) + (properties `((upstream-name . "BiocBaseUtils"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BiocBaseUtils") + (synopsis "General utility functions for developing Bioconductor packages") + (description + "The package provides utility functions related to package development. +These include functions that replace slots, and selectors for show methods. +It aims to coalesce the various helper functions often re-used throughout the +Bioconductor ecosystem.") + (license license:artistic2.0))) + (define-public r-bioccasestudies (package (name "r-bioccasestudies") From 176fd3b052eb70f780dc797539063cd191b49a53 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 00:45:06 +0100 Subject: [PATCH 291/824] gnu: Add r-rorcid. * gnu/packages/cran.scm (r-rorcid): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ed84855c90..06b3c5daac 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -709,6 +709,33 @@ allows transformation of geographic coordinates from one projection and/or datum to another.") (license license:gpl2))) +(define-public r-rorcid + (package + (name "r-rorcid") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rorcid" version)) + (sha256 + (base32 + "1d0s5w48ksyj152nc4xq5w0nsimab8jc5fgspdwnbas2g8a52igr")))) + (properties `((upstream-name . "rorcid"))) + (build-system r-build-system) + (propagated-inputs (list r-crul + r-data-table + r-fauxpas + r-httr + r-jsonlite + r-tibble + r-xml2)) + (home-page "https://github.com/ropensci/rorcid") + (synopsis "Interface to the @url{Orcid.org, https://orcid.org} API") + (description + "This package provides an API for @url{Orcid.org, https://orcid.org}. +Functions include searching for people, searching by DOI, or searching by +Orcid ID.") + (license license:expat))) + (define-public r-waldo (package (name "r-waldo") From 8f67799a1b98dffedd63c9fea2f365aedce80cdb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 02:46:41 +0100 Subject: [PATCH 292/824] gnu: Add r-gson. * gnu/packages/cran.scm (r-gson): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 06b3c5daac..d67b72892d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -599,6 +599,27 @@ Google. @code{googleVis} makes use of the internal R HTTP server to display the output locally.") (license license:gpl2+))) +(define-public r-gson + (package + (name "r-gson") + (version "0.0.9") + (source (origin + (method url-fetch) + (uri (cran-uri "gson" version)) + (sha256 + (base32 + "065ify3i7zqwi7h5jzr7kdgr358kwgw6xrkvvmrznbl7s9f7d57n")))) + (properties `((upstream-name . "gson"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite r-rlang r-tidyr)) + (home-page "https://cran.r-project.org/package=gson") + (synopsis "Base Class and Methods for 'gson' Format") + (description + "This packages proposes a new file format named @code{gson} for storing +gene set and related information, and provides read, write and other utilities +to process this file format.") + (license license:artistic2.0))) + (define-public r-guix-install (package (name "r-guix-install") From 349804b6028b471835cbdd87f4277002ca0930fc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: [PATCH 293/824] gnu: r-abarray: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-abarray): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b11b5b5e9..ae8dda2c05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1684,13 +1684,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) + "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) From f24085bfb389e48dbed7437888a2597e65571aba Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: [PATCH 294/824] gnu: r-absseq: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-absseq): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae8dda2c05..7d1e8beb3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1710,13 +1710,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) + "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) From 38fc0acf4d6752a8a3dcdab41eff1b0b5ed5e2d8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: [PATCH 295/824] gnu: r-adam: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adam): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d1e8beb3f..acd48456f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1739,13 +1739,13 @@ ranking by fold-change and visualization.") (define-public r-adam (package (name "r-adam") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) + "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr From a62284ad13b139436b2072e53e725e144782d74e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:02 +0100 Subject: [PATCH 296/824] gnu: r-adamgui: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adamgui): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index acd48456f4..a8ec425b7a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1774,13 +1774,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) + "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs From daf0729533c791d06cd0d3f001fb5df03eacb433 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 297/824] gnu: r-adimpute: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-adimpute): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8ec425b7a..526ca047c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1822,13 +1822,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) + "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs From b772bc7f757d6f2c18e4e69f0f2327e5fdb36676 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 298/824] gnu: r-adsplit: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-adsplit): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 526ca047c1..3fd7c1aa81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1871,13 +1871,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) + "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs From 69ecae7801cf12fb42300eb54e5aec655c0f85e7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 299/824] gnu: r-affixcan: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-affixcan): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3fd7c1aa81..f23a7775e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1899,13 +1899,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) + "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs From 014fc145f8adc1d3b30be38beb88b632bc41d1fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 300/824] gnu: r-affyrnadegradation: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f23a7775e5..7d22e5949a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1927,13 +1927,13 @@ expression values are known.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) + "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) From f74c670c7f21d77d1811b7f56d6b79851028f520 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 301/824] gnu: r-agdex: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-agdex): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d22e5949a..80b71f3c3e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1952,13 +1952,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) + "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) From fc60b9dfe7cd2638893fcd221009c3e991c2af42 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 302/824] gnu: r-aggregatebiovar: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80b71f3c3e..c753b76142 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1979,13 +1979,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) + "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs From e153f4904d4572ab739c7b8d88e3e12c421cc542 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 303/824] gnu: r-agilp: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-agilp): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c753b76142..f020c608cc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2013,13 +2013,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) + "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") From 5d09a99174227f4025484644ff1c89734a255d28 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 304/824] gnu: r-adductomicsr: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f020c608cc..665f70dc48 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2035,13 +2035,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) + "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs From fb7a1b340b3d51881241d7a3d808a7db5d509de1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 305/824] gnu: r-agimicrorna: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 665f70dc48..8cfcaa4074 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2080,13 +2080,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) + "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs From f217ff646354eae1f2573baec0b244350950932c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 306/824] gnu: r-airpart: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-airpart): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8cfcaa4074..b6769d9cac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2110,13 +2110,13 @@ objects are used so that other packages could be used as well.") (define-public r-airpart (package (name "r-airpart") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06")))) + "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs From c9c4d6b5017dedd33daca72e6d196b6c1dfda796 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 307/824] gnu: r-amountain: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-amountain): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6769d9cac..5dc75591a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2157,13 +2157,13 @@ datasets.") (define-public r-amountain (package (name "r-amountain") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) + "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) From ecb91b340469f1ad043446f5a7e94e1aebd83879 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 308/824] gnu: r-amaretto: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-amaretto): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5dc75591a2..15baba0931 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2181,13 +2181,13 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs From 190ed5f1374e0508924e2c0cfa23a4b5bbcd2eec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 309/824] gnu: r-anaquin: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-anaquin): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15baba0931..64eaf2e5a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2233,13 +2233,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) + "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs From eddbd27be5968eea6a4db20f80af4aae6e234397 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:03 +0100 Subject: [PATCH 310/824] gnu: r-aldex2: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-aldex2): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64eaf2e5a6..316a14b919 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2263,13 +2263,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-aldex2 (package (name "r-aldex2") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs From cbeefda563248df151e4d50370ff4e0d6a8a9e00 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 311/824] gnu: r-aneufinder: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 316a14b919..0b3b25aa55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2345,13 +2345,13 @@ data.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) + "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00")))) (build-system r-build-system) (native-inputs (list r-knitr)) From d18f8e367e0142130a95e1f5c6f25a3ff1a15dd3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 312/824] gnu: r-anf: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-anf): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b3b25aa55..6a08187d34 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2387,13 +2387,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj")))) + "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs From bc62494bc8168516030cad21ae25f686e9c0744a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 313/824] gnu: r-annmap: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-annmap): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a08187d34..658234ce17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2415,13 +2415,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs From 1114e837a9dd10b500ba81a6270c4ee47ea39dcc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 314/824] gnu: r-antiprofiles: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 658234ce17..bbe49a34c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2449,13 +2449,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs From 110f0f8483b5e770cdb4010d6393f6bfa0a9e7a2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 315/824] gnu: r-aseb: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-aseb): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bbe49a34c1..9d3ff84bda 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2475,13 +2475,13 @@ tumor samples from healthy controls.") (define-public r-aseb (package (name "r-aseb") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") From b89305c18dece7c1e4134c9af219041d7c301ef2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 316/824] gnu: r-asgsca: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-asgsca): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9d3ff84bda..03d364da0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2502,13 +2502,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "0mxrrkm2lg7gxjh8ynn6qmryn8wqda7b83sr51dpgblay83jcbaq")))) + "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) From dfb78fd76e4b6086506d96166b786b50923527fc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 317/824] gnu: r-aspli: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-aspli): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03d364da0f..29d44e05c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2525,13 +2525,13 @@ model as latent variables.") (define-public r-aspli (package (name "r-aspli") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz")))) + "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs From 930fab74f2a3ec3beec9574f2803babc62ac1c56 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 318/824] gnu: r-assessorf: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-assessorf): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29d44e05c1..d32af21ea3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2573,13 +2573,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7")))) + "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs From a1dbd6b2da3d77190974bcad1636df022e32a28b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 319/824] gnu: r-asset: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-asset): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d32af21ea3..736ac2c2bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2602,13 +2602,13 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg")))) + "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) From 110ac40dea8267060de1394c3d812316326d708c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 320/824] gnu: r-atena: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-atena): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 736ac2c2bc..f5f0a9dddf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2629,13 +2629,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp")))) + "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs From f185d3f68069ce2641087f17fe853fcfaf1d9ad8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 321/824] gnu: r-atsnp: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-atsnp): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5f0a9dddf..11f13383f8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2670,13 +2670,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz")))) + "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs From 381907d25d3d4595c163ee9dc6f4274c869e9285 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 322/824] gnu: r-attract: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-attract): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11f13383f8..ec22a75d44 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2703,13 +2703,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82")))) + "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs From faddfa8aed1c4441e58b28230a22338383325cb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:04 +0100 Subject: [PATCH 323/824] gnu: r-awfisher: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-awfisher): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec22a75d44..c1ea60490a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2734,13 +2734,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1")))) + "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs From 7bb05be10ac5d154bb552c6f18f3f8c1139a970c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 324/824] gnu: r-awst: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-awst): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1ea60490a..b2a0baafc1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2758,13 +2758,13 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav")))) + "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) From e9a7c42deb2f4564eb75ff85998db46c111ef6f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 325/824] gnu: r-baalchip: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-baalchip): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2a0baafc1..d67d57bafd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2785,13 +2785,13 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl From 91d928706ab51d1bb43300c6ffee4c77dd713db9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 326/824] gnu: r-basespacer: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-basespacer): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d67d57bafd..81494b4c47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2825,13 +2825,13 @@ alleles, a known phenotypical feature of cancer samples.") (define-public r-basespacer (package (name "r-basespacer") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj")))) + "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) From 5fd038bd49ba23e093e8177cf78ce16f5e43ddff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 327/824] gnu: r-bac: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bac): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 81494b4c47..a46e5ee721 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2848,13 +2848,13 @@ rich environment of statistical and data analysis tools.") (define-public r-bac (package (name "r-bac") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BAC" version)) (sha256 (base32 - "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2")))) + "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6")))) (properties `((upstream-name . "BAC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BAC") From 25104e7a6b27537ceb249eff3229b7fed7df43f3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 328/824] gnu: r-bader: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-bader): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a46e5ee721..f6e402a742 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2872,13 +2872,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm")))) + "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") From 5b4f7d11ae809b3d741d13d8f139624dfe49d416 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 329/824] gnu: r-badregionfinder: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6e402a742..831b508f04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2896,13 +2896,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9")))) + "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs From f07c0d00cde6ea625a752d9cdafc4adee9cf8053 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 330/824] gnu: r-bambu: Update to 3.0.1. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 831b508f04..d79af55592 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2923,13 +2923,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "2.2.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w")))) + "08vh0vbmjn1kzp10yrinn0p0ab2cjhgiagx1vhci5sf4s6p20vy4")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs From f3038efb80302ab424f3d06c0e29582a384f0880 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 331/824] gnu: r-bandits: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79af55592..4914a1c6ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2966,13 +2966,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9")))) + "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs From c0324417728ff5d9df5e5f4e79db1bd5a331b9f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 332/824] gnu: r-banocc: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-banocc): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4914a1c6ca..30db1afe62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3004,13 +3004,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx")))) + "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs From 6af37707879ce323871120de6ced9c3767498ba2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 333/824] gnu: r-barcodetrackr: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-barcodetrackr): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30db1afe62..0f56190874 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3032,13 +3032,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3")))) + "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs From 9e0e4bf347254a8de565db327e2fa3aeaa52f7f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 334/824] gnu: r-biocversion: Update to 3.16.0. * gnu/packages/bioconductor.scm (r-biocversion): Update to 3.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f56190874..669af69ec8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3074,14 +3074,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.15.2") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) + "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") From 176e20a1f1d5c5f96da64efb337d100279b4ecb3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 335/824] gnu: r-biocgenerics: Update to 0.44.0. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 669af69ec8..dd3ee3b02b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3094,13 +3094,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) + "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) From 2bfc463a42d6c1fb12945a1669b9d851f7114410 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 336/824] gnu: r-coverageview: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-coverageview): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd3ee3b02b..a3fb0da6af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3114,13 +3114,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) + "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors From f0ed6c519c45978f378c9ce887302ddc773866cb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:05 +0100 Subject: [PATCH 337/824] gnu: r-cummerbund: Update to 2.40.0. * gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3fb0da6af..358eb57622 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3141,13 +3141,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) + "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9")))) (build-system r-build-system) (propagated-inputs (list r-biobase From f5118505f7213fee8d6daee1fbfc3de803dde603 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 338/824] gnu: r-dama: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-dama): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 358eb57622..5a0c11fa10 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3171,13 +3171,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m")))) + "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) From 3a9089522827cf0f3138a3e6c4ce2cf82459ce0e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 339/824] gnu: r-damefinder: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-damefinder): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a0c11fa10..aef30bed3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3193,13 +3193,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf")))) + "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs From 00400127ef258c5c7eca6e07d14ff3027d883867 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 340/824] gnu: r-dearseq: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-dearseq): Update to 1.10.0. [propagated-inputs]: Add r-scattermore. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aef30bed3a..e23df56360 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3234,14 +3234,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.4") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl")))) + "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -3254,6 +3254,7 @@ offers nice visualization of methyl-circle plots.") r-pbapply r-reshape2 r-rlang + r-scattermore r-statmod r-survey r-tibble From e3262cc2e1c8add758c6510ee37d3fa3231c694e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 341/824] gnu: r-debcam: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-debcam): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e23df56360..f156b010c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3273,13 +3273,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) (properties `((upstream-name . "debCAM"))) (build-system r-build-system) (inputs (list openjdk)) From bd622e1464dcee788decbc05e4c1c6a1b70a19c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 342/824] gnu: r-decipher: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-decipher): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f156b010c5..ec7ba3136d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3312,13 +3312,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) + "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1")))) (build-system r-build-system) (propagated-inputs (list r-biostrings From 483084b7f9b6568b42e166e543ac85c1c22b9258 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 343/824] gnu: r-deco: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-deco): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec7ba3136d..24f7023365 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3336,13 +3336,13 @@ biological sequences.") (define-public r-deco (package (name "r-deco") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deco" version)) (sha256 (base32 - "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m")))) + "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw")))) (properties `((upstream-name . "deco"))) (build-system r-build-system) (propagated-inputs From 8fd5bbc31e11d482a56b52e78ace271c62f8b7bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 344/824] gnu: r-decomplexdisease: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-decomplexdisease): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24f7023365..e9aaadee4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3378,13 +3378,13 @@ higher deregulation levels.") (define-public r-decomplexdisease (package (name "r-decomplexdisease") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEComplexDisease" version)) (sha256 (base32 - "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d")))) + "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh")))) (properties `((upstream-name . "DEComplexDisease"))) (build-system r-build-system) (propagated-inputs From 9b717bcad9278bd9b6a89ced348192590ed90382 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 345/824] gnu: r-decomptumor2sig: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-decomptumor2sig): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e9aaadee4e..fd2846a755 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3411,13 +3411,13 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl From 36c940a4d7bf190a8e9423fcfbcfdcdc2f9aade5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 346/824] gnu: r-deconrnaseq: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-deconrnaseq): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd2846a755..081c860572 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3454,13 +3454,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6")))) + "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs From f7dd1e4552a6131d82e91d57ece662fa08f2834f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 347/824] gnu: r-decontam: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-decontam): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 081c860572..52bea2703d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3481,13 +3481,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9")))) + "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs From d3f0d2abe487e3e4bb62c4e7b12f1cf5f4a545c5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 348/824] gnu: r-deconvr: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52bea2703d..bdd1578c94 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3507,13 +3507,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + "14cxrcv5q6w20bq2pbxj75c0lzz96dxwqh1hqh2cl8nvvfi70jsv")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs From ef81f5f55e8c408c162665afc68951991f44afa0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 349/824] gnu: r-decoupler: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-decoupler): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdd1578c94..538fce5bde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3551,13 +3551,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs From b8f0bf3e4d4cb9cf67da214af70d6719c1a901e9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:06 +0100 Subject: [PATCH 350/824] gnu: r-deepsnv: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 538fce5bde..43ce067006 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3592,13 +3592,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn")))) + "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs From 2e48b8b0289844d08621b14af11cff297bb08cea Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 351/824] gnu: r-delayedarray: Update to 0.24.0. * gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43ce067006..44d37db1da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3628,13 +3628,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) + "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) From c7bf9a1a58a4edc2c428f2395d45f537ba78a65b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 352/824] gnu: r-derfinderhelper: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44d37db1da..02c59dd88d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3658,13 +3658,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) + (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs From de72bdab94c7a02b200693c30a1e12a3d2639086 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 353/824] gnu: r-drimseq: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-drimseq): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02c59dd88d..b3cc3823df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3683,13 +3683,13 @@ calculation in parallel.") (define-public r-drimseq (package (name "r-drimseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) + (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs From 81ba7cc7324a2043523b4d6cad76d34e8dc2a7ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 354/824] gnu: r-bluster: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-bluster): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b3cc3823df..74db2fc534 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3718,13 +3718,13 @@ results.") (define-public r-bluster (package (name "r-bluster") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) + "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs From 2564b7bcff739d5c395fe6b03d4a15c672c61e3e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 355/824] gnu: r-ideoviz: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74db2fc534..3e1a22cca4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3748,13 +3748,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) + "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf")))) (build-system r-build-system) (propagated-inputs (list r-biobase From e73a833dd25223de684ed6bbd6454e12e2724308 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 356/824] gnu: r-infercnv: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-infercnv): Update to 1.14.0. [propagated-inputs]: Remove r-leiden and r-reshape. Add r-igraph, r-reshape2, and r-seurat. --- gnu/packages/bioconductor.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e1a22cca4..04dbd0f8e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3772,14 +3772,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -3803,15 +3803,16 @@ arbitrary genomic intervals along chromosomal ideogram.") r-gplots r-gridextra r-hiddenmarkov - r-leiden + r-igraph r-matrix r-paralleldist r-phyclust r-rann r-rcolorbrewer - r-reshape + r-reshape2 r-rjags r-singlecellexperiment + r-seurat r-summarizedexperiment r-tidyr)) (native-inputs (list r-knitr)) From cc0464f5308941c50924e22749ab51099f2e7c2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 357/824] gnu: r-iranges: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-iranges): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 04dbd0f8e7..c2a4b67e60 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3832,13 +3832,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3")))) + "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) From 4daec4dc4d583882dd4105599c92671bc899a6a5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 358/824] gnu: r-isoformswitchanalyzer: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2a4b67e60..11052c38d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3860,13 +3860,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) + (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs From b7359c3b172981e5e195ce920125c878ac023a6a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 359/824] gnu: r-affy: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-affy): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11052c38d2..bb7488b58b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4062,14 +4062,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) + "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj")))) (build-system r-build-system) (propagated-inputs (list r-affyio From 7034dcc2d60a8a916f37873d3e2992b8da5682f4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 360/824] gnu: r-affycomp: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-affycomp): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb7488b58b..197d9287eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4090,14 +4090,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) + "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) From ceb39bfb391df230336e7f81cfc4e1b57cdfa3c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 361/824] gnu: r-affycompatible: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 197d9287eb..6f1b79e188 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4111,14 +4111,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) + "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) From 6e2871262c7923cda93dcec363af39ed9465111b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 362/824] gnu: r-affycontam: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-affycontam): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f1b79e188..e306671e73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4156,14 +4156,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) + "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs From 9947e412aca538d1690375d7a75b99622515a1e2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 363/824] gnu: r-affycoretools: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e306671e73..847890c6a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4179,14 +4179,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) + "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs From 45c83ffbe587be9a84c6f48c68a2bcff1e910111 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:07 +0100 Subject: [PATCH 364/824] gnu: r-affyio: Update to 1.68.0. * gnu/packages/bioconductor.scm (r-affyio): Update to 1.68.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 847890c6a1..f60e3569cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4221,14 +4221,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) + "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) From 261e3c12c2546e6987251af136ef3e6207c7bbf6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 365/824] gnu: r-affxparser: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f60e3569cb..1561c6be05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4245,14 +4245,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) + "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") From dc8c3024c0e66e40ff66dbafc06d48811b2c4ce6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 366/824] gnu: r-annotate: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-annotate): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1561c6be05..e5e3085226 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4273,14 +4273,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) + "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 89f6d1d425e4fef70d181fb5b1cba13db8da2ed3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 367/824] gnu: r-annotationdbi: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5e3085226..8fca3ab9e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4300,13 +4300,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) + "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) From 748599dc6bdce786608c02266218daed46697ea1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 368/824] gnu: r-annotationfilter: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fca3ab9e3..b000df4b84 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4330,13 +4330,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) + "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) From 065fdc2bb1d64b33b09817e63cbee67f760759f5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 369/824] gnu: r-annotationforge: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b000df4b84..d3553c6f2c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4355,14 +4355,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v")))) + "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) From c5bcfef62832e7cd0900041fd1b317f585954e85 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 370/824] gnu: r-annotationhub: Update to 3.6.0. * gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3553c6f2c..37d9473063 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4387,14 +4387,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) + "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs From 203ddafa090e80c048852af8b9ca15ee9d0112bc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 371/824] gnu: r-aroma-light: Update to 3.28.0. * gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37d9473063..f6adcaa72a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4428,14 +4428,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) + "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs From 822ad274c96e52a6da5122e2e26fc48b2f8017a7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 372/824] gnu: r-bamsignals: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6adcaa72a..b847ea5c0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4452,14 +4452,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) + "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From a0d2db2e08c32cb5ce1563d09cda8f36287567a8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 373/824] gnu: r-biobase: Update to 2.58.0. * gnu/packages/bioconductor.scm (r-biobase): Update to 2.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b847ea5c0f..320b611639 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4482,13 +4482,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) + "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) From 1ef39d3d28420979fa566bafb7bde45156252b4a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 374/824] gnu: r-biomart: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 320b611639..9aa18d8d76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4504,13 +4504,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) + "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) From 9048d502dab1a18091ee652671a7c88e9eaffe0a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 375/824] gnu: r-biocparallel: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.1. [arguments]: Update 'make-reproducible' to released files. [propagated-inputs]: Add r-cpp11. --- gnu/packages/bioconductor.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9aa18d8d76..ad26fbe153 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4589,13 +4589,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.30.3") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92")))) + "1fkfbs0n0sdssli7ibrswkfag080kgv8n1zf6ssxx729g1fz3m3h")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -4607,18 +4607,16 @@ only one command.") ;; Remove generated documentation. (for-each delete-file '("inst/doc/BiocParallel_BatchtoolsParam.pdf" - "inst/doc/Introduction_To_BiocParallel.pdf" "inst/doc/Errors_Logs_And_Debugging.pdf" "inst/doc/BiocParallel_BatchtoolsParam.R" "inst/doc/Introduction_To_BiocParallel.R" - "inst/doc/Errors_Logs_And_Debugging.R")) + "inst/doc/Errors_Logs_And_Debugging.R" + "inst/doc/Random_Numbers.R")) ;; Remove time-dependent macro (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" - "inst/doc/Introduction_To_BiocParallel.Rnw" "inst/doc/Errors_Logs_And_Debugging.Rnw" "vignettes/BiocParallel_BatchtoolsParam.Rnw" - "vignettes/Introduction_To_BiocParallel.Rnw" "vignettes/Errors_Logs_And_Debugging.Rnw") (("\\today") "later")) @@ -4628,7 +4626,7 @@ only one command.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-bh r-codetools r-futile-logger r-snow)) + (list r-bh r-cpp11 r-codetools r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") From 30f2fc13c659424681763a9bb3b49cc8c123f641 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:08 +0100 Subject: [PATCH 376/824] gnu: r-biostrings: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad26fbe153..a1679fa59d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4640,13 +4640,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.1") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33")))) + "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) From 3e945a87e0446da41a99cf9db6986bcfc6e699fa Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 377/824] gnu: r-biovizbase: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1679fa59d..519134a52c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4668,14 +4668,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) + "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs From bebf55cbd6c7a12390fd8bcfc2def36311a2522b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 378/824] gnu: r-bsgenome: Update to 1.66.1. * gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.66.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 519134a52c..2c706775f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4710,13 +4710,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.64.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) + "1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) From 9d8107b4d79fb876a15c5923b30a9e14d9a424dc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 379/824] gnu: r-category: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-category): Update to 2.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c706775f2..e38685b6a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4741,14 +4741,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) + "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs From 32629c01ef4f91e2ad3d774960626f396ea94e30 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 380/824] gnu: r-chipseeker: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e38685b6a4..74427343ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4772,13 +4772,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf")))) + "1s90q73lldnmh2nxyb36hv44s3pj2l7pr0qka0z27b3cmnhqh50z")))) (build-system r-build-system) (native-inputs (list r-knitr)) From bfed8f183db3b643ce1d625cff28a3860bc2aa8d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 381/824] gnu: r-chipseq: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-chipseq): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74427343ef..41abb0b9de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4819,14 +4819,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) + "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From ba197ae9883a213a832591a739e02cf5f404f7b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 382/824] gnu: r-complexheatmap: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41abb0b9de..4465776733 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4845,14 +4845,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8")))) + "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) From 539a39c4ef171d9dca2ef1a15ee164ee236b0870 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 383/824] gnu: r-copywriter: Update to 2.29.0. * gnu/packages/bioconductor.scm (r-copywriter): Update to 2.29.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4465776733..4b269d5877 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4885,14 +4885,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.28.0") + (version "2.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) + "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs From ecd3d1ca6310a3e468fa845c747ec2ed2b817b08 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 384/824] gnu: r-deseq2: Update to 1.38.1. * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4b269d5877..07d4c742fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4956,14 +4956,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.36.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) + "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs From 16973c9796225aeeb6f055c36b00fd1381269b13 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 385/824] gnu: r-dexseq: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-dexseq): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07d4c742fe..8704f9be56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4994,14 +4994,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) + "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs From 1e5a6a9fb2a8912435fd79b07847a06c55c8ab4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 386/824] gnu: r-diffcyt: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-diffcyt): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8704f9be56..4e4f040a36 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5039,13 +5039,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) + (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs From 0d9a766fa783a32b74b20d6fc3d867ecddd5229a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 387/824] gnu: r-dirichletmultinomial: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e4f040a36..68ee7a6624 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5077,14 +5077,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) + "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) From 3a15509cb62170161d2641180de4c32c557f9172 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 388/824] gnu: r-dittoseq: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-dittoseq): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68ee7a6624..ee42697acc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5104,13 +5104,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4")))) + "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs From bd76f479de43c71ddc53993466d68280ecbafe44 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 389/824] gnu: r-edaseq: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-edaseq): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee42697acc..5dc846a018 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5148,14 +5148,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) + "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs From 4eb513e7dff1a422622b7083d926282be7f684c1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:09 +0100 Subject: [PATCH 390/824] gnu: r-edger: Update to 3.40.0. * gnu/packages/bioconductor.scm (r-edger): Update to 3.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5dc846a018..2e54aaf557 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5188,13 +5188,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.38.4") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6")))) + "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs From aad9a5337c46dc28b9db51b221f4155a9df6c965 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 391/824] gnu: r-ensembldb: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e54aaf557..ed5c38fe80 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5213,14 +5213,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc")))) + "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 3ff9f819f7268c1ebe61f8397f2bf035fc2605b6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 392/824] gnu: r-fastseg: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-fastseg): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed5c38fe80..77479105c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5258,14 +5258,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) + "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges From 0c1edd86f2abe07c382989aadaca955a8a1b5b1e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 393/824] gnu: r-gage: Update to 2.48.0. * gnu/packages/bioconductor.scm (r-gage): Update to 2.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 77479105c4..e815e74d4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5285,14 +5285,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.46.1") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl")))) + "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) From b6117c18376174cb0909d5395d176f4473481437 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 394/824] gnu: r-genefilter: Update to 1.80.0. * gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e815e74d4a..178f6dda23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5313,14 +5313,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) + "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) From 533a3d991437b452a10190a941b3226f70e685b5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 395/824] gnu: r-geneoverlap: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 178f6dda23..fbba61675b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5337,13 +5337,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) + "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) From 4e501fbb67f0119f93a77cc0abefc786424a4c88 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 396/824] gnu: r-genomation: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-genomation): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbba61675b..aca0622f1e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5356,13 +5356,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) + "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings From c7c3bfa2500f94f198036f75080ad23f291ce70e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 397/824] gnu: r-genomeinfodb: Update to 1.34.3. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aca0622f1e..116893e53e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5403,13 +5403,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.4") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v")))) + "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From d7e456cc1314eec5236b72b249e7af57a394525a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 398/824] gnu: r-genomicalignments: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 116893e53e..8ebc1453c7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5430,13 +5430,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz")))) + "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) From f2910e5604c153019074d529e6c08c00e67ab731 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 399/824] gnu: r-genomicfeatures: Update to 1.50.2. * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ebc1453c7..63d96e73d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5463,13 +5463,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.4") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v")))) + "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) From 437ad93ce70593865c0a02d2748f2971ad0b8a16 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 400/824] gnu: r-genomicfiles: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63d96e73d9..07bd111c67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5507,14 +5507,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) + "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs From 169c0b7fa18c049e840b4ab09b4751de08146d09 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 401/824] gnu: r-genomicranges: Update to 1.50.1. * gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.50.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07bd111c67..e7472601ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5541,13 +5541,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.48.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) + "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) From 25c5901adcccaf80a6cc8965f7fc43cb46f65a87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 402/824] gnu: r-gostats: Update to 2.64.0. * gnu/packages/bioconductor.scm (r-gostats): Update to 2.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7472601ac..8db8db22b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5568,14 +5568,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) + "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs From 60724024de37ca8cb17c5570893ab6c755521877 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 403/824] gnu: r-gseabase: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-gseabase): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8db8db22b9..06e8b2ab8b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5599,14 +5599,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) + "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs From aa0e18c1be20be15ab87b9a10f74169981a1dc5a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:10 +0100 Subject: [PATCH 404/824] gnu: r-hpar: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 06e8b2ab8b..51c62d8082 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5628,14 +5628,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) + "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4")))) (build-system r-build-system) (native-inputs (list r-knitr)) From ce2688cd3b55fb7b139731a70c4cf1b4caf5e34b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 405/824] gnu: r-rhtslib: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-rhtslib): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51c62d8082..eda692f087 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5648,14 +5648,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.28.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) + "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, From aa25663162f29d5a4323f7c4fd5643906e76c463 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 406/824] gnu: r-impute: Update to 1.72.1. * gnu/packages/bioconductor.scm (r-impute): Update to 1.72.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eda692f087..f8ec6b674b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5677,13 +5677,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.70.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) + "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) (native-inputs (list gfortran)) (build-system r-build-system) From 1ba8e9e75c1c261c51836b69b424c5ed025db38a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 407/824] gnu: r-interactivedisplaybase: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f8ec6b674b..d3562f45ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5697,14 +5697,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) + "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) From 6bf50ca57a6d6a98946460a25c7601a4fc753bd4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 408/824] gnu: r-keggrest: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-keggrest): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3562f45ce..732fefd78e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5722,14 +5722,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.36.3") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni")))) + "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs From 413f96c95f122ac2ab79440a230f64c38977e16b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 409/824] gnu: r-lfa: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 732fefd78e..a1664b4c51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5746,13 +5746,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) + (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) From 0a699ea1820810ea268fcb9e8c22957db52227b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 410/824] gnu: r-limma: Update to 3.54.0. * gnu/packages/bioconductor.scm (r-limma): Update to 3.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1664b4c51..ee67171697 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5767,13 +5767,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.52.4") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h")))) + "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") From 4fd64b03b4276a625e329f1d83002768c2cfa710 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 411/824] gnu: r-made4: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-made4): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee67171697..ec35709503 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5786,13 +5786,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-made4 (package (name "r-made4") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5")))) + "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs From fa0eda6e3f92113eb9f6f4772a3e960d6cb0d5ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 412/824] gnu: r-methylkit: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-methylkit): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec35709503..ae33cd6120 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5815,13 +5815,13 @@ datasets (coinertia analysis).") (define-public r-methylkit (package (name "r-methylkit") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) + "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs From cb7e5ebd548819921eb8f169564633d9273b8b77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 413/824] gnu: r-muscat: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-muscat): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae33cd6120..be80567407 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5889,14 +5889,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd")))) + "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs From a7936348db6c609636c5366b6276898f5d149173 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 414/824] gnu: r-mutationalpatterns: Update to 3.8.0. * gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be80567407..2c93f79ffe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5939,14 +5939,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) + "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 66edbf1635f02c6891454061107d510e8076d9b7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 415/824] gnu: r-msnbase: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-msnbase): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c93f79ffe..3bc4d2048b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5985,14 +5985,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) + "16apm4qn7sbv06pk2i8k5z7qgkv0yq0h8ri32vikdplqxxh7h0cz")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs From 57ae5f71966da19ad7fb2c562070f59fc1c56f40 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 416/824] gnu: r-msnid: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-msnid): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bc4d2048b..f36378178e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6030,14 +6030,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) + "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments From 8735f1099568fab671e11f435eed09b7919ad096 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:11 +0100 Subject: [PATCH 417/824] gnu: r-mzid: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-mzid): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f36378178e..c645d94913 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6087,14 +6087,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) + "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs From 0fbb12153b46c2c966dacef07cb77dae2b917cef Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 418/824] gnu: r-mzr: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-mzr): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c645d94913..c53ed569fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6118,14 +6118,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) + "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) From 66f1939df5b654066b52a9fa827839d186c42b31 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 419/824] gnu: r-organism-dplyr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-organism-dplyr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c53ed569fc..cd1fd1cec9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6169,14 +6169,14 @@ previously been used in XCMS.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs From 7c8829ae33b8ac70bc31264e1e22c4d0a0b7ff3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 420/824] gnu: r-organismdbi: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd1fd1cec9..0a3475af54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6208,14 +6208,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) + "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs From 34b615e3e755861762f9d6ad97daed47227549df Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 421/824] gnu: r-pcaexplorer: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a3475af54..1f9613164f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6240,14 +6240,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) + "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs From cf106821f527ead0a3f26d91eaf367051e87a9a4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 422/824] gnu: r-pcamethods: Update to 1.90.0. * gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.90.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f9613164f..ee62d6da28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6295,14 +6295,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.88.0") + (version "1.90.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) + "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs From dd27fffd32d252699809680842a574698058f917 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 423/824] gnu: r-protgenerics: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee62d6da28..6a2b97f226 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6364,14 +6364,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) + "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") From 4e861e7f9a1a29fa68fda2ef803143c9dcfd9a34 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 424/824] gnu: r-rbgl: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-rbgl): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a2b97f226..7f3dea4d3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6384,14 +6384,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) + "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs From b7ec827477ed4a7d050fa73eda583981843fce60 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 425/824] gnu: r-rcas: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-rcas): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7f3dea4d3d..7582823bcf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6406,13 +6406,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) + "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs From 607eae1e56e74a76958dee160a04005e3264ff87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 426/824] gnu: r-regioner: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7582823bcf..2ec3b7096b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6456,14 +6456,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) + "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs From c45dc1e27347143334d36068602df1da962dd708 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 427/824] gnu: r-reportingtools: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ec3b7096b..1a33a3a438 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6487,14 +6487,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) + "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) From dfec056be2b6e4c7caeff097fe5eb2cfb80ebade Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 428/824] gnu: r-rhdf5: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a33a3a438..ba65a12d41 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6537,13 +6537,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) + "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) From a7afc50aa3eff5fc316cd2e2cce88d7433a2ffec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 429/824] gnu: r-rhdf5filters: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba65a12d41..e48aca38fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6564,14 +6564,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) + "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs From 39c52a42bda3e72324282fce1acd7b6a5936c29b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 430/824] gnu: r-rsamtools: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e48aca38fa..b7301b548d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6590,13 +6590,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) + "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) From 855ea2a8f1b37131e0590adbce114131b1ac4d9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:12 +0100 Subject: [PATCH 431/824] gnu: r-rtracklayer: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7301b548d..e920111b24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6655,13 +6655,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) + "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk")))) (build-system r-build-system) (arguments `(#:phases From d6fac1138fb7f09f4d34739d96cb4156db8e487a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 432/824] gnu: r-scannotatr: Update to 1.4.0. * gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e920111b24..4529213c04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6734,13 +6734,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) + (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs From 4d8a2f5562eb8901543380d8773f9fccacdcc414 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 433/824] gnu: r-scdblfinder: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4529213c04..c95b0fa304 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6771,13 +6771,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) + (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs From 6fb3733394d1bbd684b20b79c4d8fd633481c84f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 434/824] gnu: r-scmap: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c95b0fa304..3e0e5da87b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6816,13 +6816,13 @@ comprehensive scDblFinder method.") (define-public r-scmap (package (name "r-scmap") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs From 06856951557e0b31e7c2653459ba98fabe72168c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 435/824] gnu: r-scry: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-scry): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e0e5da87b..e4470ea30e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6858,13 +6858,13 @@ different experiment.") (define-public r-scry (package (name "r-scry") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193")))) + "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs From 59e810b232eb248f567eb582f5549320abfc3eb3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 436/824] gnu: r-seqlogo: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4470ea30e..5a220a8558 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6890,14 +6890,14 @@ single-cell RNA-seq.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) + "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs From 1ca80ed5a5aa494e70ac02f7a38da5d2cfe24ece Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 437/824] gnu: r-seqpattern: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5a220a8558..e289ead24f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6913,13 +6913,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) + "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) From 94af5e4e968456440599051efb8dd413e261f04b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 438/824] gnu: r-shortread: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e289ead24f..70be2c7a77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6936,14 +6936,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) + "0z700mjll3zv3451rd6p5195w0g3rmw17xddc5qwflwm8dnhdmll")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs From e5e22f33526ef2c1c27e1845d47e8e0622b9dd9c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 439/824] gnu: r-simplifyenrichment: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 70be2c7a77..a99a5e2490 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6979,14 +6979,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) + "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) From 2c821d2ce56ba65b30f240b7b64c5666d8d5023c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 440/824] gnu: r-transcriptr: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a99a5e2490..fd357c2d0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7020,13 +7020,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) + (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs From c07b603d6474ae89b0bc04c2bbb281600975c379 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 441/824] gnu: r-trajectoryutils: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd357c2d0b..b345a33a6f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7070,14 +7070,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) + "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) From e4e4b97a67ff08c03f148f2afb7f09ac6d439ac6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 442/824] gnu: r-slingshot: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-slingshot): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b345a33a6f..71eb6128ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7097,13 +7097,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) + "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33")))) (build-system r-build-system) (propagated-inputs (list r-igraph From 3f307e6ebc6eb4bad878aa5fc744d401b105f4a7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 443/824] gnu: r-stager: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-stager): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71eb6128ac..1a5f81d3bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7129,13 +7129,13 @@ graph construction.") (define-public r-stager (package (name "r-stager") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) + (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) From 3b89c301db466712dd9c5d4b00b2bd291048d93c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:13 +0100 Subject: [PATCH 444/824] gnu: r-stringdb: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-stringdb): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1a5f81d3bf..41066c6050 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7152,13 +7152,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) + (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs From f87a87eee849d246dd8adcc86a86a28585c67691 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 445/824] gnu: r-structuralvariantannotation: Update to 1.13.0. * gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.13.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 41066c6050..8e1ee34adb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7185,13 +7185,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) + (base32 "11z3acsbaifrxkghd7i8503ki9s1lc6c22880yna6qcfprlzb44g")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From ab4f54d5f9e8377398179f3a1e1f0feb2ce1cd3f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 446/824] gnu: r-summarizedexperiment: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e1ee34adb..498cf7bf03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7222,13 +7222,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) + "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) From adedfb51fa84c084a4633d6a766c005942eedb3f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 447/824] gnu: r-sva: Update to 3.46.0. * gnu/packages/bioconductor.scm (r-sva): Update to 3.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 498cf7bf03..38c914c71b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7256,14 +7256,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) + "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g")))) (build-system r-build-system) (propagated-inputs (list r-edger From 8ded00c7dacf7f7b92ecb03def20e190e1da5c4b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 448/824] gnu: r-systempiper: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-systempiper): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 38c914c71b..87b6c90d40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7287,14 +7287,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) + "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs From 88440606c76f027e3aa3d3214648f4af305e45c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 449/824] gnu: r-topgo: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-topgo): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87b6c90d40..714b3dae4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7330,13 +7330,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) + "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) From c1790d17fc5ca62f25c3d93c002aa4c27b2639fa Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 450/824] gnu: r-tximport: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-tximport): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 714b3dae4e..7eb5ec5541 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7363,13 +7363,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) + "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 9501ec8c4c7521ae42e375c2bcd6d1bf7d1c7b64 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 451/824] gnu: r-variantannotation: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7eb5ec5541..4d5d9f5428 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7421,13 +7421,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) + "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs From 32afcf9b90b2b34720db14dc3fa232d1cd193072 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 452/824] gnu: r-vsn: Update to 3.66.0. * gnu/packages/bioconductor.scm (r-vsn): Update to 3.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4d5d9f5428..29ea4b313b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7459,14 +7459,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.64.0") + (version "3.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) + "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) From e03bff40fcebc2e27c1aa1e923d126b8a3f7ba2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 453/824] gnu: r-xina: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-xina): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29ea4b313b..b29bc13957 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7528,13 +7528,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) + (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs From 8fe91b692a8ec5845a751560bd5597c1e848bd2a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 454/824] gnu: r-xmapbridge: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-xmapbridge): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b29bc13957..8ba60a2821 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7564,13 +7564,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) + (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") From 9a707db7eeec0e68862bc3b7e0480ae3dc80fb93 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 455/824] gnu: r-xvector: Update to 0.38.0. * gnu/packages/bioconductor.scm (r-xvector): Update to 0.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ba60a2821..a3c3b0594a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7591,13 +7591,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) + "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) From 7a0c779a91244af71de1ef0825582a1cfcb31ce3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 456/824] gnu: r-zlibbioc: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3c3b0594a..976ca0d1c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7625,13 +7625,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) + "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) From 44ec429d483f6fba07c93b023ae5357f507d085a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 457/824] gnu: r-zellkonverter: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 976ca0d1c8..b1ded1bfb5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7644,13 +7644,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.5") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6")))) + (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs From 7db100f21fba0020be304b5c33b9f92db098b93f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:14 +0100 Subject: [PATCH 458/824] gnu: r-geneplotter: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1ded1bfb5..6e1a7e7b08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7676,14 +7676,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) + "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava")))) (build-system r-build-system) (propagated-inputs (list r-annotate From 4fba8d9d7cb92e5a5ae9bcc2ee45ed02d7270451 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 459/824] gnu: r-oligoclasses: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6e1a7e7b08..f03ed0a87b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7701,14 +7701,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) + "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs From c05ab729668d302667c003a9f6f34ee5bb890470 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 460/824] gnu: r-oligo: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f03ed0a87b..ab9d08069e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7736,14 +7736,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) + "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) From 11c4bc08db3afe687fa0a200642e23909fe9b1ff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 461/824] gnu: r-qvalue: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-qvalue): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab9d08069e..53d2be265f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7772,14 +7772,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) + "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) From 9bb55dfa8d106648028db91f4ba807d17c46683d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 462/824] gnu: r-apeglm: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-apeglm): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53d2be265f..247db3c8e1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7827,13 +7827,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) + "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs From 6f68e3f42d13dab8cfccf4d6dd6ab6bacdc93f9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 463/824] gnu: r-greylistchip: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 247db3c8e1..71221d0995 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7854,13 +7854,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) + "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs From c5b66701679af103c2b1309f36b2e0e1ae6536b7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 464/824] gnu: r-diffbind: Update to 3.8.1. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71221d0995..51d7bde15c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7881,14 +7881,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.4") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr")))) + "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs From d4d9ce28010197e54d0264814fd481463531d505 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 465/824] gnu: r-mbkmeans: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51d7bde15c..0853ae35d3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7959,13 +7959,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) + "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 77d10366d469100306ee8330e57facb5e878b954 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 466/824] gnu: r-multtest: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0853ae35d3..f05ecdb04a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7991,14 +7991,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) + "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) From 7a11e32dae9753f097d179ac6e13f741e2cd97ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 467/824] gnu: r-graph: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f05ecdb04a..fb95f42251 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8026,13 +8026,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) + "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) From 73add01b2293b18d2c74905d4ddc58e890831b77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 468/824] gnu: r-chippeakanno: Update to 3.32.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb95f42251..baa6d9fc14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8119,14 +8119,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.30.1") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y")))) + "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs From 03862582db4b8bd81c18fd010345fc0e15248f93 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 469/824] gnu: r-matrixgenerics: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index baa6d9fc14..e43cb7277b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8173,13 +8173,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f")))) + "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) From 78d4b00882bfe42a19617e84bfa0aa3126c6b003 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 470/824] gnu: r-marray: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e43cb7277b..6cfb5e5549 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8200,12 +8200,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) + (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs")))) (build-system r-build-system) (propagated-inputs (list r-limma)) From 67799955b442926c87a7eb6c621f78746767fb9a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 471/824] gnu: r-cghbase: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6cfb5e5549..10524349ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8219,12 +8219,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) + (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs From 564afa20fb1f2093279af7cdde23335bee1ee0b6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:15 +0100 Subject: [PATCH 472/824] gnu: r-cghcall: Update to 2.60.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10524349ac..ba3f3a6dd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8238,12 +8238,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) + (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs From 7803ed86fe27e7e0d66ceb468dc6d5436c3e8f03 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 473/824] gnu: r-qdnaseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba3f3a6dd6..6249b010c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8257,12 +8257,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) + (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs From 721c125de4352ae56afc08e9aa43f188078eb376 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 474/824] gnu: r-bayseq: Update to 2.31.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.31.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6249b010c0..462bc1a23b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8289,14 +8289,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) + "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs From 5d32e4a62a941a94f3c1771f4669f9c0f145d55c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 475/824] gnu: r-chipcomp: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 462bc1a23b..796e3ffc7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8313,14 +8313,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) + "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs From a0465bd1162ba8a46acef4d0feadb201c48ea656 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 476/824] gnu: r-riboprofiling: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 796e3ffc7e..95d78ea246 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,14 +8347,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) + "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs From e4ab1ac23e26f9aadd1de57b1edb5b5a0c4f0a9d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 477/824] gnu: r-riboseqr: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 95d78ea246..24e0db5a79 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8388,14 +8388,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) + "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs From e7393c32f4d0a389e11e825858792014ede42769 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 478/824] gnu: r-interactionset: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24e0db5a79..42bc16b013 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8416,14 +8416,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) + "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) From 8d62cfc7d103b3e3514bd91c87e84f661e5ddcb2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 479/824] gnu: r-genomicinteractions: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42bc16b013..779d03b055 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8450,14 +8450,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) + "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) From 74852cb46ddad51b1c092494fd1e862939089752 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 480/824] gnu: r-ctc: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 779d03b055..19b1e7a4b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8491,14 +8491,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) + "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") From 7bf9521e85229245e1d235534607d5c9b7839643 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 481/824] gnu: r-goseq: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19b1e7a4b5..31d3256484 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8511,14 +8511,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) + "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 9b615c408f2b047f0bd1de8c035e47d7141f0b98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 482/824] gnu: r-glimma: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 2.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31d3256484..11e92771da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8537,14 +8537,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) + "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs From 870a334f6d4b900c571899121a73f9f425975812 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 483/824] gnu: r-rots: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11e92771da..751657051a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8570,14 +8570,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) + "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs From 83ff82481c9758a586f15533958e5ad063f088bf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 484/824] gnu: r-plgem: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-plgem): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 751657051a..84d128d92c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8593,14 +8593,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) + "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) From 45616713a7ee3b568cf88eed950cedb9169e67c5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:16 +0100 Subject: [PATCH 485/824] gnu: r-inspect: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84d128d92c..43afa6db13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8617,14 +8617,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) + "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs From 7146ee20d967f27c33d368cc8bd4790266ccccad Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 486/824] gnu: r-dnabarcodes: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 43afa6db13..7a8a1ed0b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8663,14 +8663,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) + "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs From c3b6219435b8dc137b6912a29ef645e68dd04d4a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 487/824] gnu: r-ruvseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a8a1ed0b2..7fe05ca620 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8690,14 +8690,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) + "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs From ccd857d8cfaa11579dfe908859e49a5666079c18 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 488/824] gnu: r-biocneighbors: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7fe05ca620..be519958d2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8715,14 +8715,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) + "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs From b711b25c09b5a7bc0ac35dfb7264e6b88bcb13ce Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 489/824] gnu: r-scaledmatrix: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be519958d2..fd6007e1b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8743,14 +8743,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz")))) + "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs From 0bb3b953eb347febb52d1c060929205259fde525 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 490/824] gnu: r-treeio: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-treeio): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd6007e1b9..827bc9593a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8769,14 +8769,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1")))) + "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs From 3e7dbe7804b2ca9dd4c16893feb408c34578efcb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 491/824] gnu: r-ggtree: Update to 3.6.2. * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.6.2. [propagated-inputs]: Add r-cli. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 827bc9593a..0fc9f1f937 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8801,19 +8801,20 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.4") + (version "3.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5")))) + "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs (list r-ape r-aplot + r-cli r-dplyr r-ggfun r-ggplot2 From c4df4af6baccf207299410838e3c23fecda026d2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 492/824] gnu: r-metapod: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-metapod): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fc9f1f937..58b32d8101 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8839,14 +8839,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) + "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs From c733f330e1bb5beddeb6594909ef9444e2c1d730 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 493/824] gnu: r-biocsingular: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58b32d8101..829947266b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8868,14 +8868,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) + "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs From 1517a8fd4ffc24bd44fc495d59ef1d2503625885 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 494/824] gnu: r-destiny: Update to 3.12.0. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 829947266b..28d4a88816 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8903,14 +8903,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) + "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 1dfad3e535bb058633f98df138126cfd5dc4ec8d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 495/824] gnu: r-savr: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-savr): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28d4a88816..8d4d71cae8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8947,14 +8947,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) + "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs From c7f24274bf365af2458de89a22235a94c456254e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 496/824] gnu: r-chipexoqual: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d4d71cae8..6781d5be30 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8969,14 +8969,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) + "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs From 3a731c1b28660a5742ad435032ebd23e86194710 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 497/824] gnu: r-copynumber: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-copynumber): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6781d5be30..b9c5b01c5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9009,13 +9009,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) + "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) From 9fcaa4e3d85025b16a44c79c8f3cf86f82642eef Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 498/824] gnu: r-dnacopy: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b9c5b01c5c..b4253f6f8f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9029,14 +9029,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) + "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) From c9dc9b10e844729b5a7087d84bae2a07287e09f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:17 +0100 Subject: [PATCH 499/824] gnu: r-ebseq: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-ebseq): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4253f6f8f..ecd2387c66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9127,14 +9127,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) + "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs From f60faec932b564b93d09251945a1abf6dda84855 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 500/824] gnu: r-karyoploter: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecd2387c66..5870950f00 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9149,13 +9149,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) + "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From e8e7990b881206f04258ca73986f0c9915b04363 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 501/824] gnu: r-lpsymphony: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5870950f00..20bfa1eb14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9187,14 +9187,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) + "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) (build-system r-build-system) (arguments (list From 3a9e82f0f5c963895cd65c3af07e997db6ca309f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 502/824] gnu: r-ihw: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ihw): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20bfa1eb14..ee3b1e2f62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9226,14 +9226,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) + "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs From 29f0a198a5e3eb455e761288faa1904d391744f2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 503/824] gnu: r-icobra: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee3b1e2f62..d3a16b4b38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9255,14 +9255,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) + "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs From 2896e9005e995f24d87a53791de75fb5d43af39f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 504/824] gnu: r-residualmatrix: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3a16b4b38..3f6d426072 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9292,14 +9292,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd")))) + "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) From 9f49e6eee8cb7cc70f5bb63b69b25623ddfeeecd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 505/824] gnu: r-batchelor: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f6d426072..e5b1db7717 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9321,14 +9321,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc")))) + "1cdpq8zfn718qmsqjp79siddh3kzag4a90p276v261xbjvrxavjv")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs From f149c694fda4747934269f5983b1d4a4cdd74419 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 506/824] gnu: r-mast: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-mast): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5b1db7717..ac391d8b22 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9364,14 +9364,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) + "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs From 9ddd0a0ab48fb5eee11497eec8287a402d0f37d0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 507/824] gnu: r-monocle: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-monocle): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac391d8b22..4018aa54f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9399,14 +9399,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn")))) + "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 70a1e54b8be42f6a27c8ec061c0bcdf2fe5f9636 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 508/824] gnu: r-noiseq: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-noiseq): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4018aa54f1..73386d93ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9584,14 +9584,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) + "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs From 7030f66362cac69dd8a7d209184f74b5c167e53a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 509/824] gnu: r-scdd: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scdd): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 73386d93ec..0d1ece3b7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9610,14 +9610,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) + "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs From d00553da9b4f23ab3c6f4e02e92f87c4ac988097 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 510/824] gnu: r-scone: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-scone): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d1ece3b7e..1b05269c03 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9648,14 +9648,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) + "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light From 62c58299a2c5eeb992d778a703b6713ebab3637b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 511/824] gnu: r-geoquery: Update to 2.66.0. * gnu/packages/bioconductor.scm (r-geoquery): Update to 2.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b05269c03..1709ef8ca1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9692,14 +9692,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.64.2") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) + "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs From e3d4563b4fbd3db1c502cf41712f809bde6c01eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 512/824] gnu: r-illuminaio: Update to 0.40.0. * gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1709ef8ca1..eee8b84a7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9727,14 +9727,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) + "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12")))) (build-system r-build-system) (propagated-inputs (list r-base64)) From 734d40892af3f76ce6e43cc68a4e4feb6abd5b22 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:18 +0100 Subject: [PATCH 513/824] gnu: r-siggenes: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-siggenes): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eee8b84a7d..8639eebaa2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9748,14 +9748,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) + "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) From a4e446a3a3832d0ac76f4b994b38ac7becfbfcc5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 514/824] gnu: r-bumphunter: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8639eebaa2..1bb50f6019 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9772,14 +9772,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) + "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 3c1854108e1b121d14afaec6f89692bb22aecbad Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 515/824] gnu: r-microbiome: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-microbiome): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1bb50f6019..9ccb3911a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9806,13 +9806,13 @@ studies.") (define-public r-microbiome (package (name "r-microbiome") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12")))) + "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs From 59fe138fccdb03a00c3e05c9a8d4537faedfcde3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 516/824] gnu: r-milor: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-milor): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9ccb3911a4..b800c4c4bc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9843,13 +9843,13 @@ standardization of the analyses and the development of best practices.") (define-public r-milor (package (name "r-milor") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs")))) + "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs From 44a5942ce71478848f2b238eb681e5b76d96075d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 517/824] gnu: r-minfi: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-minfi): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b800c4c4bc..7a4ed12b93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9891,14 +9891,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) + "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc")))) (build-system r-build-system) (propagated-inputs (list r-beanplot From 6b9cb6256af20124964628ec860d288fea2209c7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 518/824] gnu: r-methylumi: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-methylumi): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a4ed12b93..23c3817acb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9942,14 +9942,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) + "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4")))) (build-system r-build-system) (propagated-inputs (list r-annotate From 8bd75d3ef7f6e4dd7cf15fa85a6aacd659b0f2f8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 519/824] gnu: r-lumi: Update to 2.50.0. * gnu/packages/bioconductor.scm (r-lumi): Update to 2.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 23c3817acb..12ef4d1d90 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9989,14 +9989,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) + "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq")))) (build-system r-build-system) (propagated-inputs (list r-affy From e0b3d2dda9e97b875fff38eed81906473f7404c1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 520/824] gnu: r-linnorm: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12ef4d1d90..323233af58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10028,14 +10028,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) + "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs From 4c30f1a5b51af0def6fd1f452cd28a2dfc45af83 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 521/824] gnu: r-ioniser: Update to 2.22.0. * gnu/packages/bioconductor.scm (r-ioniser): Update to 2.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 323233af58..710dd14da9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10089,14 +10089,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) + "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs From 5c2e048789151155969785c42bbaf0c87292fed1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 522/824] gnu: r-tradeseq: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 710dd14da9..b6541c80c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10185,13 +10185,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) + "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 69eb260b6fe898f2afe23411d67aabdccd7a4910 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 523/824] gnu: r-varianttools: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-varianttools): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6541c80c4..ed1dfb8f28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10254,14 +10254,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) + "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs From 83fa503de34d936b93175a579bbf874a1cb76632 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 524/824] gnu: r-heatplus: Update to 3.6.0. * gnu/packages/bioconductor.scm (r-heatplus): Update to 3.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed1dfb8f28..c6267ed444 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10294,14 +10294,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) + "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs From 9171e09d3730ee7e964f05df078bc2ac286db091 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 525/824] gnu: r-gosemsim: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c6267ed444..5ad780d66a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10319,14 +10319,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) + "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs From 368fdb08506867d6067e88c7d3457d93b3c9dd39 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:19 +0100 Subject: [PATCH 526/824] gnu: r-anota: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-anota): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ad780d66a..d47453e4de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10346,14 +10346,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) + "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) From e392bcce646ea26b1121fde0b3d4ca6800f3a552 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 527/824] gnu: r-sigpathway: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d47453e4de..b1f0ba24e7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10376,14 +10376,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) + "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") From 245ab8252246bb6695f85f09d41eaef7f05446af Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 528/824] gnu: r-fcscan: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-fcscan): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b1f0ba24e7..4a8b0ef407 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10398,13 +10398,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) + (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs From 11b8f6caf0b52262e55fb27fe7538aa233607728 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 529/824] gnu: r-fgsea: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-fgsea): Update to 1.24.0. [propagated-inputs]: Remove r-gridextra. Add r-cowplot. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a8b0ef407..9402a06b77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10431,22 +10431,22 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) + "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel + r-cowplot r-data-table r-fastmatch r-ggplot2 - r-gridextra r-matrix r-rcpp)) (native-inputs From 56fe11925730ec476eb93b927b56f869a9465cc9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 530/824] gnu: r-dose: Update to 3.24.1. * gnu/packages/bioconductor.scm (r-dose): Update to 3.24.1. [propagated-inputs]: Remove r-do-db. Add r-hdo-db. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9402a06b77..bdc729bcf9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10463,23 +10463,23 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.22.1") + (version "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i")))) + "1ai42pnd8s8ws6y9nlq5d858w2rp8gfw2vpndslspj4q8gc4dbb1")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel - r-do-db r-fgsea r-ggplot2 r-gosemsim + r-hdo-db r-qvalue r-reshape2)) (native-inputs From 7d70375aa7ef257360900f8aa6a4621f80f512a2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 531/824] gnu: r-enrichplot: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.1. [propagated-inputs]: Add r-ggnewscale and r-rlang. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdc729bcf9..31f89ec33e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10498,20 +10498,21 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.2") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss")))) + "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggplot2 r-ggraph + r-ggnewscale r-ggtree r-gosemsim r-igraph @@ -10520,6 +10521,7 @@ data.") r-purrr r-rcolorbrewer r-reshape2 + r-rlang r-scatterpie r-shadowtext r-yulab-utils)) From 26a4a1e36b548aa7406ba8656948c2b4e0620fb0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 532/824] gnu: r-clusterprofiler: Update to 4.6.0. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.6.0. [propagated-inputs]: Add r-gson. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31f89ec33e..3d2519866e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10538,14 +10538,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.4") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5")))) + "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -10557,6 +10557,7 @@ All the visualization methods are developed based on ggplot2 graphics.") r-enrichplot r-go-db r-gosemsim + r-gson r-magrittr r-plyr r-qvalue From c5c2cbe1e369d036cf3345d43c21480fe284dd5b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 533/824] gnu: r-clusterexperiment: Update to 2.18.0. * gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3d2519866e..798c5d1db9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10576,13 +10576,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) + "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) (build-system r-build-system) (native-inputs (list r-knitr)) From ed0238c59e81cc532fb06ce33fd9bd5d70f73850 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 534/824] gnu: r-mlinterfaces: Update to 1.78.0. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.78.0. [propagated-inputs]: Add r-summarizedexperiment. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 798c5d1db9..f873b787e4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10622,14 +10622,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) + "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -10652,6 +10652,7 @@ expression data sets.") r-rpart r-sfsmisc r-shiny + r-summarizedexperiment r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") From e8dc5aec69e03b52723849fd0d112a1a29fa14b4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 535/824] gnu: r-annaffy: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-annaffy): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f873b787e4..bff059f37f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10665,14 +10665,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) + "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg")))) (build-system r-build-system) (arguments `(#:phases From e65450cc4c444d41c846652a753ec52c635bef0e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 536/824] gnu: r-a4core: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4core): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bff059f37f..e03ad9b719 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10697,14 +10697,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) + "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs From 94a665b3470d270936da9935effd5c20f9fa9cfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 537/824] gnu: r-a4classif: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4classif): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e03ad9b719..fcd257d672 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10721,14 +10721,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) + "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs From 0b89230af37847a9f9522b42ffdbd185094f632d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:20 +0100 Subject: [PATCH 538/824] gnu: r-a4preproc: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fcd257d672..f1fe9f5c7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10751,14 +10751,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) + "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs From 9e1a4ae173617463e72d7ba748f79a66787bda98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 539/824] gnu: r-a4reporting: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1fe9f5c7e..11a2fea2fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10775,14 +10775,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) + "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs From a618ee00cdcfac07331433338f4dd703304ccf87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 540/824] gnu: r-a4base: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4base): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11a2fea2fa..2c8d58abeb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10799,14 +10799,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) + "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs From 8a11bd2c1eb03329484d5fa14a7f9a6d1e956cbf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 541/824] gnu: r-a4: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-a4): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2c8d58abeb..03251c938f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10830,14 +10830,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) + "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) From e09f43a15db7232b5a12030d8168fe11c14d4b4e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 542/824] gnu: r-abseqr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03251c938f..ee3d1e3397 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10851,14 +10851,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) + "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs From 621c91564da6001d839454061a41b785b6810e8c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 543/824] gnu: r-bacon: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-bacon): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee3d1e3397..d6c8162ba0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10899,14 +10899,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) + "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) From bdd122be5745686509220e86df3e124ecce8f699 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 544/824] gnu: r-rgadem: Update to 2.46.0. * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d6c8162ba0..24da7bcd91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10924,14 +10924,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.1") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q")))) + "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs From 5fd930a771160ae3acb3f057eec3307004feb5d3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 545/824] gnu: r-motifdb: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-motifdb): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 24da7bcd91..9b18594439 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10978,12 +10978,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) + (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs From 1d8e36abd902e09d934174480fff76eb2712eef8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 546/824] gnu: r-motifbreakr: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9b18594439..fe343c3c67 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11005,12 +11005,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) + (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs From 1acf7fdae3e67637ec54444e610b8c2b0bc15240 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 547/824] gnu: r-motifstack: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe343c3c67..7470d2577d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11055,14 +11055,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) + "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs From 380c5b1894b37bebf07218faae4a02d27e09f953 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 548/824] gnu: r-genomicscores: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7470d2577d..e18e85f2de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11087,14 +11087,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.8.2") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j")))) + "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs From 82015ac5b1798d7e30f2141aeb2fef4437669a2e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 549/824] gnu: r-atacseqqc: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e18e85f2de..7e02a29608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11125,14 +11125,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) + "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs From a2ec0390a774b8cf18609732b038919a7cb1c709 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 550/824] gnu: r-gofuncr: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e02a29608..47d6427d4a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11172,14 +11172,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) + "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs From d48170687b8b5d32ba909a18392cc8c8384ed605 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:21 +0100 Subject: [PATCH 551/824] gnu: r-annotationtools: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47d6427d4a..8fde74acfa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11277,14 +11277,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) + "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) From d0a0afe1daf245c36ec7938265d5724d2153b0f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 552/824] gnu: r-allelicimbalance: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fde74acfa..62d4645840 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11302,14 +11302,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) + "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) From 265c03a7bd8c28da947ed9f621b868052c8960ae Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 553/824] gnu: r-aucell: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-aucell): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62d4645840..489f426de9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11345,14 +11345,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.18.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) + "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs From c410fa50e1fe8f83f176f1d6896b052f0e75bc98 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 554/824] gnu: r-ebimage: Update to 4.40.0. * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 489f426de9..c8aacd6ae6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11385,14 +11385,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.38.0") + (version "4.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) + "1k6gbivwlai451whq2vr3c0shzs9p4g188jn5waw7973gdzdi00q")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs From 66612f9583c7590a0428c17c923d037c3f2c431e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 555/824] gnu: r-yamss: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yamss): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8aacd6ae6..d628baf558 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11424,14 +11424,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) + "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From a072ce0eccec3e1f5dc0f0d5500d952cf73b966a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 556/824] gnu: r-gtrellis: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d628baf558..a126791eb9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11457,14 +11457,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) + "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) From f1a1fed1df7d1c9bd8de5c6e7cfacc811dda1f5c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 557/824] gnu: r-somaticsignatures: Update to 2.34.0. * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a126791eb9..409c47c41b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11483,14 +11483,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) + "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) From 42b297b2951838fcb1374d9cbfea65bf1c8f2da9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 558/824] gnu: r-yapsa: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 409c47c41b..420e0d1830 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11522,14 +11522,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) + "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs From 4da41a5977d646927c2f4d5128b691fa554d7739 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 559/824] gnu: r-gcrma: Update to 2.70.0. * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 420e0d1830..7dbc7abeb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11571,14 +11571,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) + "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1")))) (build-system r-build-system) (propagated-inputs (list r-affy From 0ac185ebb40c06ce18d525b6a106aca8df8f3ac0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 560/824] gnu: r-quantro: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-quantro): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7dbc7abeb3..20f82d5e23 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11653,14 +11653,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) + "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 802db22edff6eca8f55944a2d737b8d3ec22201c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 561/824] gnu: r-yarn: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-yarn): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 20f82d5e23..da05c34cc0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11686,14 +11686,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) + "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 275fda864af90b5a6b64a8ee8de1ac61180390e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 562/824] gnu: r-roar: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-roar): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da05c34cc0..fe80294022 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11723,14 +11723,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) + "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From 61edc0f206718fa60d57a05f36342be6e6130376 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 563/824] gnu: r-massspecwavelet: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe80294022..d084b3c372 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11791,14 +11791,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) + "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) From bcc13d3642cd167767220f7ec31a85fc704ae166 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 564/824] gnu: r-xcms: Update to 3.20.0. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d084b3c372..97181dbf06 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11815,14 +11815,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) + "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 9daff4514617f7fd4d83f4228125a06651f501ec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:22 +0100 Subject: [PATCH 565/824] gnu: r-wppi: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-wppi): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 97181dbf06..645bdebf4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11856,13 +11856,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) + "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration From c7c004c36e7e4cf922c3847e210696ee67d8cf2d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 566/824] gnu: r-wrench: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-wrench): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 645bdebf4b..bdcb83bc04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11897,14 +11897,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) + "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs From 57fec18eae677e1aa0438e55ca37d2f99439ceba Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 567/824] gnu: r-wiggleplotr: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdcb83bc04..0f7a7eab59 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11921,14 +11921,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) + "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From 75ca7d19fd31ab1792c8bb1b433e3bff5819dc21 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 568/824] gnu: r-widgettools: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f7a7eab59..30fd93da0d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11955,14 +11955,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) + "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") From 36edd2b28804fd1a892388e7f10de3a1763a1e41 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 569/824] gnu: r-webbioc: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 30fd93da0d..9e99aae7c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11976,14 +11976,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) + "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2")))) (build-system r-build-system) (inputs (list netpbm perl)) From 70e32fd0bf7930d8401f85dfd067aec555d5daff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 570/824] gnu: r-zinbwave: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9e99aae7c5..f94e78f725 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12008,14 +12008,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) + "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel From f16c7d46cc8830bd1ad6b51bb5e55e22750f5ed1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 571/824] gnu: r-zfpkm: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f94e78f725..8bec5700e6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12041,14 +12041,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) + "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs From 42e093c5759360bf2fc9123c9837348dfcdf8f8e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 572/824] gnu: r-rbowtie2: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8bec5700e6..c908d49091 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12066,14 +12066,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) + "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs From 471040c5d10519aa8ab75cd092436d0f548915f5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 573/824] gnu: r-progeny: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-progeny): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c908d49091..31ff7db383 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12093,14 +12093,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) + "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 628ce9bf483fc51b813231cfaa21f5f64af0c290 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 574/824] gnu: r-arrmnormalization: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31ff7db383..51b9fd56ec 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12125,14 +12125,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) + "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) From 43b69b74d3a133eca0e420d1942a05c4807e4e97 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 575/824] gnu: r-biocfilecache: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 51b9fd56ec..6850503eca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12148,14 +12148,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) + "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs From b35b27b983c9322d74977b0012c2cb86a0202b53 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 576/824] gnu: r-iclusterplus: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6850503eca..c9ed265aed 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12181,14 +12181,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) + "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) From 0f6cd30c7af1c6f3c03bc629ad23b9983f00cb1b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 577/824] gnu: r-rbowtie: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c9ed265aed..f172d04b5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12211,14 +12211,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) + "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments From 41e534e93a0a840b5a0c42796379c98c31106050 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 578/824] gnu: r-sgseq: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-sgseq): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f172d04b5c..feb15c43bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12247,14 +12247,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) + "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs From a9dd4f8bd61d39ad58ef0caa4b8d93db2c6e3c15 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:23 +0100 Subject: [PATCH 579/824] gnu: r-rhisat2: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index feb15c43bf..a1e370e707 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12290,14 +12290,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) + "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments From 1a99e38e8d0c53e4ff3679c42d16ba8d9a13f745 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 580/824] gnu: r-quasr: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-quasr): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a1e370e707..66320d19ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12328,14 +12328,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) + "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs From afd5dfff034394e20453672eea2c234aee87bd7f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 581/824] gnu: r-rqc: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-rqc): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 66320d19ff..789a84badd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12370,14 +12370,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) + "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs From df921b1f69720544812c80f72e8570febd2fd735 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 582/824] gnu: r-birewire: Update to 3.30.0. * gnu/packages/bioconductor.scm (r-birewire): Update to 3.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 789a84badd..a0370e8195 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12413,14 +12413,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) + "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs From 812fd22ad301e6b879f859197afa352da0951f9f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 583/824] gnu: r-multidataset: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0370e8195..4cb52448f1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12466,14 +12466,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) + "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs From 8772941e80dc0b7ea83d5130d31c98e857226fdd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 584/824] gnu: r-ropls: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.30.0. [propagated-inputs]: Add r-plotly and r-ggplot2. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cb52448f1..b040ba8c89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12503,19 +12503,21 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.28.2") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) + "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-ggplot2 r-multiassayexperiment r-multidataset + r-plotly r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes From 254acb7ddc298e6866c16adc835c152efae81677 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 585/824] gnu: r-biosigner: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biosigner): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b040ba8c89..78bf2fa352 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12545,14 +12545,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) + "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj")))) (build-system r-build-system) (propagated-inputs (list r-biobase From 2aaa3f4414447f15d1449b0d18852ac179a425c4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 586/824] gnu: r-annotatr: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-annotatr): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78bf2fa352..8b19321453 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12580,14 +12580,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) + "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 9c3506a26cc462418421796e949bb69dc6aaa133 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 587/824] gnu: r-rsubread: Update to 2.12.0. * gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8b19321453..52207ab661 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12621,14 +12621,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.5") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) + "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) From 944e48a8611219d6e52692fa42581aa595bc6d19 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 588/824] gnu: r-consensusclusterplus: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 52207ab661..7d42cdedaa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12673,14 +12673,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) + "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) From e6dc952cbb4ce8b942ff9ab5af6b9d50675ff686 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 589/824] gnu: r-cytolib: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d42cdedaa..6d18e5726a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12739,14 +12739,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) + "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs From c5130dfef1f0668bf7bb79b4ec5347f56ad8396a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 590/824] gnu: r-flowcore: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-flowcore): Update to 2.10.0. [propagated-inputs]: Remove r-rcpparmadillo; add r-cpp11. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d18e5726a..85cd44bf32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12768,24 +12768,24 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) + "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-matrixstats r-rcpp - r-rcpparmadillo r-rprotobuflib r-s4vectors)) (native-inputs From 59a3f6df90eb9bd748f020a8018b0623dc40ea33 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 591/824] gnu: r-flowmeans: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 85cd44bf32..873f139043 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12800,14 +12800,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) + "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs From a87bcca9f2bd9c8aa6a3754bd46292c75791df4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:24 +0100 Subject: [PATCH 592/824] gnu: r-ncdfflow: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 873f139043..850f2faca6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12823,14 +12823,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7")))) + "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs From ffe3bfa1baea504f8de894553c0b7f3b5c0a0bec Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 593/824] gnu: r-ggcyto: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 850f2faca6..f1a9549fab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12854,14 +12854,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325")))) + "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs From 22f8c5350e74686a84e1f1cb1000ad908faf7e04 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 594/824] gnu: r-flowviz: Update to 1.62.0. * gnu/packages/bioconductor.scm (r-flowviz): Update to 1.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1a9549fab..f1e9963cdd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12891,14 +12891,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.2") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95")))) + "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs From 223fb324926f9c2cfe6a309000884a7b3a78de59 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 595/824] gnu: r-flowclust: Update to 3.36.0. * gnu/packages/bioconductor.scm (r-flowclust): Update to 3.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1e9963cdd..2d4e571a32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12922,14 +12922,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) + "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments From d029859dd293859d73684395ca06302a71251990 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 596/824] gnu: r-rprotobuflib: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d4e571a32..d1733c91ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12956,14 +12956,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) + "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments From 8a089e4e117183c3dd297bff70ae8f27a7775cbe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 597/824] gnu: r-flowworkspace: Update to 4.10.0. * gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d1733c91ff..3bea2eda02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12985,14 +12985,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.8.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) + "07w2pnnzmivfc621c8pvndqrn1k245cwjrb0nnk2i85i3si4j9c3")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs From 2061e5af92067bfeb7a5e7dbeb82d2490f00384d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 598/824] gnu: r-flowstats: Update to 4.10.0. * gnu/packages/bioconductor.scm (r-flowstats): Update to 4.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3bea2eda02..2a922b19f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13039,14 +13039,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.2") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) + "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs From 522e1136b6b6ddb5bc2f8b4ca77c52f4f66ec73b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 599/824] gnu: r-opencyto: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-opencyto): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a922b19f7..25c4257320 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13077,14 +13077,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) + "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs From 90be8abee62787cc5206c903c8460d97237bbf77 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 600/824] gnu: r-cytoml: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25c4257320..5aee1f199f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13121,14 +13121,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) + "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs From 6741cfad7c0b2fdf927f440b295073da832cee09 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 601/824] gnu: r-flowsom: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-flowsom): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5aee1f199f..36aa67ffef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13173,14 +13173,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) + "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs From f80ad8d51bf8062f18c915a46e843e37069e4cc1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 602/824] gnu: r-mixomics: Update to 6.22.0. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36aa67ffef..35684c489d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13216,14 +13216,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.20.0") + (version "6.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) + "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs From 3073f30b07c207a8ab378e25186e593e2ede9a87 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 603/824] gnu: r-depecher: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-depecher): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 35684c489d..83c3aff0d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13262,14 +13262,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) + "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs From 3857d2dd8df4c33f8964fd8af26c83d749447eab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 604/824] gnu: r-rcistarget: Update to 1.17.0. * gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.17.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 83c3aff0d9..c61bf8ff6c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13308,14 +13308,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.16.0") + (version "1.17.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) + "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs From 355400fff2cc2bdfc45fae3c1a966e20c1ca2f5b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:25 +0100 Subject: [PATCH 605/824] gnu: r-chicago: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-chicago): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c61bf8ff6c..1298fbe331 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13350,14 +13350,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) + "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs From 5adc9823f847e471766db36caf8632351087ad70 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 606/824] gnu: r-cicero: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1298fbe331..4817a3ddd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13396,14 +13396,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) + "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat From a6580915af97f1f23239b1f74ce52a92853dd1f0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 607/824] gnu: r-circrnaprofiler: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4817a3ddd6..e75ae03698 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13463,14 +13463,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) + "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) From f184b3a86bd6d9d7fd523af2e57e2bffe867bfe2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 608/824] gnu: r-genie3: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-genie3): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e75ae03698..0cda7ab027 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13598,14 +13598,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) + "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs From d29b13e9be0485b7904417a8e6148ec36be4d981 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 609/824] gnu: r-roc: Update to 1.74.0. * gnu/packages/bioconductor.scm (r-roc): Update to 1.74.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0cda7ab027..2bb4cc0497 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13622,14 +13622,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) + "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs From 1d03230dc856af37553b91e309d58a58966289bf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 610/824] gnu: r-watermelon: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-watermelon): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bb4cc0497..546f87a2ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13644,14 +13644,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) + "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs From ba535c8148a37e4c52e2374b7250bda024c139f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 611/824] gnu: r-gdsfmt: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 546f87a2ce..08f4549f29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13682,14 +13682,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) + "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. From 63b8d104dc0bfa88553887ca6961ffcf08043eab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 612/824] gnu: r-bigmelon: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08f4549f29..79f601d02c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13738,14 +13738,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) + "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs From 1f7c82bf0b1d840b34d1ee6b1aaf447cecff9899 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 613/824] gnu: r-seqbias: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-seqbias): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79f601d02c..0110db4a81 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13769,14 +13769,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) + "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs From d9b593d522ca85fc9bae0c1b1fe9572ae2e47f3a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 614/824] gnu: r-reqon: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-reqon): Update to 1.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0110db4a81..bd25da0fe5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13793,14 +13793,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) + "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs From 827abdb960cb59d78527d257ab7ddac43d20cd6e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 615/824] gnu: r-wavcluster: Update to 2.32.0. * gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bd25da0fe5..a46a78fc54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13816,14 +13816,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) + "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs From 8a2f4b7192d095f1d921dd4141bf1a486fc27d2d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 616/824] gnu: r-variantfiltering: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a46a78fc54..f5ba721d51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13904,14 +13904,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) + "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) From 30bfeccabb217f13bb02f6aacd564f65992609ca Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 617/824] gnu: r-variancepartition: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5ba721d51..60010c26a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14010,14 +14010,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) + "1mn91r0yrhz08m3vs2h3i35rcbxyc7sdfknmk6vcw1z75znjsnpl")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) From 86eddd9e14f9a5b8e05ba4dc7a1f48fa55456449 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 618/824] gnu: r-htqpcr: Update to 1.52.0. * gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.52.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 60010c26a9..e1fef9c109 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14058,14 +14058,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) + "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs From ba16a0a2ee0a4cc49dbda64fe18bebee27f31a66 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:26 +0100 Subject: [PATCH 619/824] gnu: r-unifiedwmwqpcr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e1fef9c109..a6205fe08c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14088,14 +14088,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) + "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) From ffea168d764ae7de55c6d12f4f4a29bc40239e75 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 620/824] gnu: r-universalmotif: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6205fe08c..a6d7576666 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14112,14 +14112,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr")))) + "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) From 949b5f3ddb7443b042970ebdd759cb5b250cda15 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 621/824] gnu: r-ace: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-ace): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6d7576666..aea93d74fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14160,13 +14160,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) + "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) From b5a0834c2f0c4012dcd26878f8eeb0af8a8a5d78 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 622/824] gnu: r-acgh: Update to 1.76.0. * gnu/packages/bioconductor.scm (r-acgh): Update to 1.76.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aea93d74fc..86218db20d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14189,13 +14189,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) + "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) From 5fed6cbcbce444673c48d1bf21fdb3aaf363a1d6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 623/824] gnu: r-acme: Update to 2.54.0. * gnu/packages/bioconductor.scm (r-acme): Update to 2.54.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86218db20d..f545059e82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14213,13 +14213,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) + "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) From fcde82ae09852caed0676b46843c5bbbf6815e4d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 624/824] gnu: r-acde: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-acde): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f545059e82..3c828535c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14240,13 +14240,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) + "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) From ade1bef97a75dda2e76ffaac260a15e9492ca3c9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 625/824] gnu: r-bgmix: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bgmix): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3c828535c1..b256de0da6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14333,14 +14333,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) + "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs From 16e636eccb3d276ffdfc61f131ff8bffbd4f65bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 626/824] gnu: r-bgx: Update to 1.64.0. * gnu/packages/bioconductor.scm (r-bgx): Update to 1.64.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b256de0da6..03c256705e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14355,14 +14355,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) + "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments From 02928ed15f030c3600489e18564eb82c01a5af14 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 627/824] gnu: r-bhc: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-bhc): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 03c256705e..979ffdf4f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14391,14 +14391,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) + "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") From 002ef09276b26a760242bf6ecbd32b24b1f7442b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 628/824] gnu: r-bicare: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-bicare): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 979ffdf4f5..c47103cb21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14417,14 +14417,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) + "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs From a1d8a95a0671be70d70ff8cf64f61b922ce0ae6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 629/824] gnu: r-bifet: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bifet): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c47103cb21..b39ab8f9bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14439,14 +14439,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) + "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs From 4665e589d676a551022a8072e6dabee90e5c1ac1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 630/824] gnu: r-rsbml: Update to 2.56.0. * gnu/packages/bioconductor.scm (r-rsbml): Update to 2.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b39ab8f9bd..e50395ad62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14468,14 +14468,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) + "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs From 7939489f80196e5cd9797e7a8ff3066dcc0f992f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 631/824] gnu: r-hypergraph: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e50395ad62..e332bcfdf3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14494,14 +14494,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) + "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs From b90e4cdd5623964cbfcb74cc386bf6c04de4ecc3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 632/824] gnu: r-hyperdraw: Update to 1.50.0. * gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e332bcfdf3..fe78204e26 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14516,14 +14516,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) + "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) From dae60e1c1f38a2d7f49eff3021c60d3acd2771b1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:27 +0100 Subject: [PATCH 633/824] gnu: r-biggr: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-biggr): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe78204e26..d0a006ed29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14538,14 +14538,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) + "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs From 087322f6fa5a70fb4b397b0465e653cf31ad81ea Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 634/824] gnu: r-bigpint: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bigpint): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0a006ed29..b2118bc042 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14602,14 +14602,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) + "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs From 8bbcb000c720249f86e15975bede563cd39a155f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 635/824] gnu: r-chemminer: Update to 3.50.0. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.50.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2118bc042..28c1d0a74a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14645,14 +14645,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.48.0") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) + "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs From 4cf44682fb35e17f365f392a11c7301c7582cf4c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 636/824] gnu: r-fmcsr: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-fmcsr): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28c1d0a74a..000f69c2f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14688,13 +14688,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) + (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs From a6a6f4466fc0f25a0d7709863a0e539c5d8a4d0a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 637/824] gnu: r-bioassayr: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 000f69c2f6..1de08e3630 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14717,14 +14717,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) + "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs From 828084b2cb3228c3af79b435d3d09d6e64a9127a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 638/824] gnu: r-biobroom: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-biobroom): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1de08e3630..272d1b3bb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14752,14 +14752,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) + "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs From 2cd3b140710b501d540a43fbf9968117302bdb55 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 639/824] gnu: r-graphite: Update to 1.44.0. * gnu/packages/bioconductor.scm (r-graphite): Update to 1.44.0. [propagated-inputs]: Add r-purrr. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 272d1b3bb3..1f8857d38a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14781,18 +14781,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) + "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) + (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description From 0f7ac7b091cd2b14b600e5774feefb39f565f24e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 640/824] gnu: r-reactomepa: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.42.0. [propagated-inputs]: Add r-gson. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1f8857d38a..c33bfa4d53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14804,14 +14804,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) + "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -14821,6 +14821,7 @@ symbols).") r-ggplot2 r-ggraph r-graphite + r-gson r-igraph r-reactome-db)) (native-inputs From 712bce2124b7ece8bdd315c3ea85c846d1a7dfde Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 641/824] gnu: r-ebarrays: Update to 2.62.0. * gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.62.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c33bfa4d53..cffb708e9b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14837,14 +14837,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) + "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs From 5f39d8aa867dfc293533541dd70c91b7629ee3dd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 642/824] gnu: r-bioccheck: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cffb708e9b..94a95a6ec9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14903,13 +14903,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw")))) + "0ncvxqx3irc7nv9ib93kz1c3lxyqc4y6g0g11ymxrqx7i4g3qgb8")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) From dfad35abc698394cf2a04b42306790270a5168eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 643/824] gnu: r-biocgraph: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 94a95a6ec9..abbf55e892 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14932,14 +14932,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) + "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs From dcb59af845473041eccba43a43a2b51638e9b3bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 644/824] gnu: r-biocstyle: Update to 2.26.0. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index abbf55e892..29a864fb93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14954,13 +14954,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) + "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) From d87f979e28f39176f5647949099362b96f8b56e6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 645/824] gnu: r-biocviews: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 29a864fb93..84840fc9fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14978,13 +14978,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38")))) + "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) From 97629088897c202ae1c0f481ddf16a3ad24a79ae Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:28 +0100 Subject: [PATCH 646/824] gnu: r-experimenthub: Update to 2.6.0. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 84840fc9fc..dd2e2bcd9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15006,14 +15006,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) + "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs From 55c39e29470806a1e062e557a54714f0b0796bb8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 647/824] gnu: r-grohmm: Update to 1.32.0. * gnu/packages/bioconductor.scm (r-grohmm): Update to 1.32.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd2e2bcd9e..31a8b9925f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15040,14 +15040,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) + "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs From 5557dea898f63d2165004692377e5b36f6dc1a46 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 648/824] gnu: r-multiassayexperiment: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.24.0. [propagated-inputs]: Add r-biocbaseutils and r-delayedarray. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31a8b9925f..678ffb128e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15067,20 +15067,22 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) + "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-biocbaseutils r-biocgenerics + r-delayedarray r-genomicranges r-iranges r-s4vectors From 1eaf500dd684337e4a4f6c2c5d8239cd9bc943fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 649/824] gnu: r-bioconcotk: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 678ffb128e..fbca4b0040 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15104,14 +15104,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) + "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs From 1a19353ae1dac0b08540bd9883ae0e16e1e23825 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 650/824] gnu: r-biocor: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biocor): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbca4b0040..22c62534d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15149,14 +15149,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) + "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs From c1cff36f4c30a3d8a903eeb5b02191a76786e0ed Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 651/824] gnu: r-biocpkgtools: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.16.0. [propagated-inputs]: Remove r-tidyr and r-tidyselect. Add r-rorcid. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22c62534d9..4f9838e875 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15176,14 +15176,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd")))) + "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -15203,11 +15203,10 @@ gene selection, testing relationships, and so on.") r-rbgl r-readr r-rlang + r-rorcid r-rvest r-stringr r-tibble - r-tidyr - r-tidyselect r-xml2)) (native-inputs (list r-knitr)) From ec4583b1d203a2139d98b6198f6cbdd3a789e9fe Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 652/824] gnu: r-biocset: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biocset): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f9838e875..619b6721fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15223,14 +15223,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) + "197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs From 3e451b9415528732582087c7d9875accfd54ae5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 653/824] gnu: r-biocworkflowtools: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 619b6721fa..7c6f950a5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15261,14 +15261,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) + "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) From 29c12faa8736af26c9d20492b2bc734c2a1f6a7c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 654/824] gnu: r-biodist: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-biodist): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c6f950a5f..1e56317e8a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15294,14 +15294,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) + "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs From 4f3b6abb5f1b2763bbc7917767aee357949c2a3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 655/824] gnu: r-pcatools: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-pcatools): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e56317e8a..f4daeb867d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15316,14 +15316,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) + "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs From c705fcaaa5800f5dc781898fee5d017568a488cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 656/824] gnu: r-rgreat: Update to 2.0.1. * gnu/packages/bioconductor.scm (r-rgreat): Update to 2.0.1. [propagated-inputs]: Add r-annotationdbi, r-circlize, r-digest, r-doparallel, r-dt, r-foreach, r-genomeinfodb, r-genomicfeatures, r-globaloptions, r-go-db, r-org-hs-eg-db, r-progress, r-rcolorbrewer, r-rcpp, r-s4vectors, r-shiny, r-txdb-hsapiens-ucsc-hg19-knowngene, and r-txdb-hsapiens-ucsc-hg38-knowngene. --- gnu/packages/bioconductor.scm | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f4daeb867d..71a060be87 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15362,18 +15362,40 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.28.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) + "1s1xx15ilamcyd8f7cnsgdc3r3izhx9wxmb8amamrmr9bzijjvhi")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (list r-annotationdbi + r-circlize + r-digest + r-doparallel + r-dt + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-getoptlong + r-globaloptions + r-go-db + r-iranges + r-org-hs-eg-db + r-progress + r-rcolorbrewer + r-rcurl + r-rcpp + r-rjson + r-s4vectors + r-shiny + r-txdb-hsapiens-ucsc-hg19-knowngene + r-txdb-hsapiens-ucsc-hg38-knowngene)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") From 79c096cb2e88ef386f62ac078c849faa645d2e6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 657/824] gnu: r-m3c: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-m3c): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71a060be87..55d34f2a6e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15408,14 +15408,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) + "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs From a02007bd88bf00dbcdad098d4a0acd4da864d938 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:29 +0100 Subject: [PATCH 658/824] gnu: r-icens: Update to 1.70.0. * gnu/packages/bioconductor.scm (r-icens): Update to 1.70.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d34f2a6e..9f6d794e9c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15441,14 +15441,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) + "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs From 4737a25691f7f845200ffda1ef3caa4d25f0ba5c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 659/824] gnu: r-preprocesscore: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f6d794e9c..158de128a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15564,14 +15564,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) + "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) From 96cd3b4bcff89fd8317505fb29505ec6f8119e9e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 660/824] gnu: r-s4vectors: Update to 0.36.0. * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 158de128a1..58baa4dd3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15585,13 +15585,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) + "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) From f074346f2cfd4b97329e24c811c050d390c4c886 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 661/824] gnu: r-rgraphviz: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58baa4dd3a..e915145f7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15652,14 +15652,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) + "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments From 65866be416001593588d9e1d2c49f0a3267ad80c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 662/824] gnu: r-fishpond: Update to 2.4.0. * gnu/packages/bioconductor.scm (r-fishpond): Update to 2.4.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e915145f7e..7b9f814a19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15690,13 +15690,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (inputs (list zlib)) From 06c18fde52f9e9e211420758af94f2d3ccab966f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 663/824] gnu: r-fithic: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-fithic): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b9f814a19..bc58bea7d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15728,13 +15728,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) + "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs From ab92277de4c5ff4622558feffb9627643883a450 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 664/824] gnu: r-hitc: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-hitc): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc58bea7d7..a90766ee19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15752,13 +15752,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) + "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs From 9e45f2c18346d2dec417919312c029b2c49f7caf Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 665/824] gnu: r-hdf5array: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a90766ee19..e13009209b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15781,14 +15781,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9")))) + "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs From 2a5fb31db95c02741b36c290241463723accda92 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 666/824] gnu: r-rhdf5lib: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e13009209b..08d853dcdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15812,14 +15812,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) + "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7")) (modules '((guix build utils))) (snippet '(begin From 6dfa3f50b9286fee202a594f9c1284f575b5bde4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 667/824] gnu: r-beachmat: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08d853dcdf..fa706304c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15892,14 +15892,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) + "0sa1wh997jfiz2y0dr7v12b7pvlf7icgv6arlyqy57winbnqa96m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) From 6dc8ec03589d208fa4ab1686872c3cd3361a2293 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 668/824] gnu: r-cner: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-cner): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa706304c6..a8ca442cd6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15918,13 +15918,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) + (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) From 21b32e45bd3e32d9f729441f11b2f2bb67d7c1ab Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 669/824] gnu: r-tfbstools: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a8ca442cd6..0e9e11295b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15966,14 +15966,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) + "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs From 8b332d676d06188f6dfb200099def4220106a7a3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 670/824] gnu: r-maftools: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-maftools): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0e9e11295b..76d3b57d04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16012,13 +16012,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) + (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs From 5374b55b68ad5713f97e2fc30ebcde73be00ce5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 671/824] gnu: r-motifmatchr: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 76d3b57d04..d6b1836449 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16041,14 +16041,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) + "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs From 64ccd0ff3cbf23ef05ae031456434eb8dbca41eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:30 +0100 Subject: [PATCH 672/824] gnu: r-chromvar: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-chromvar): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d6b1836449..f9ea235018 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16075,13 +16075,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) + (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs From d748ae3d00039d9747cf3f54c2e2a950ab8031b8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 673/824] gnu: r-singlecellexperiment: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f9ea235018..45d831bdfc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16122,14 +16122,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) + "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) From 54a67ddf86e7dcd8769c9fa01e62c2df39e040c2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 674/824] gnu: r-singler: Update to 2.0.0. * gnu/packages/bioconductor.scm (r-singler): Update to 2.0.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 45d831bdfc..501628ff93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16150,13 +16150,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) + (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs From 3fa18b550480ca4b8b3d63e9eef8c4f601a4ff81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 675/824] gnu: r-scuttle: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 501628ff93..d73de67236 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16182,14 +16182,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671")))) + "1z9pigcqfqyp5n6n9gbmw3ix4f1v0ayxi4xmxj7c4d0vdm5c8c2s")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs From 14e3905c6e5c4a3d4b56b22488e4f8a6ff88f537 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 676/824] gnu: r-scater: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-scater): Update to 1.26.1. [propagated-inputs]: Add r-ggrastr, r-pheatmap, and r-uwot. --- gnu/packages/bioconductor.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d73de67236..cbb9123595 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16217,13 +16217,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) + "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -16236,8 +16236,10 @@ of other packages.") r-ggbeeswarm r-ggplot2 r-ggrepel + r-ggrastr r-gridextra r-matrix + r-pheatmap r-rcolorbrewer r-rcppml r-rlang @@ -16246,6 +16248,7 @@ of other packages.") r-scuttle r-singlecellexperiment r-summarizedexperiment + r-uwot r-viridis)) (native-inputs (list r-knitr)) From c73d3e9bad9f1c21b4cda6f827a2e3eaec001e48 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 677/824] gnu: r-scran: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-scran): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cbb9123595..b565f83f55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16262,14 +16262,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni")))) + "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) (build-system r-build-system) (propagated-inputs (list r-beachmat From 2dc26068eba6de2133b4b8fd71e65bfb30a6fd9a Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 678/824] gnu: r-sparsematrixstats: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b565f83f55..d2faf65077 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16305,14 +16305,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) + "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) From 377a9b2177cdd7a1e614b6aade1cf34fdec9302c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 679/824] gnu: r-delayedmatrixstats: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2faf65077..2a0e2db1d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16330,14 +16330,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv")))) + "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) From b5a0d814489534ad3bee09703480846c6a729e67 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 680/824] gnu: r-mscoreutils: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a0e2db1d1..4cfaa23442 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16366,14 +16366,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) + "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs From 0640f750b425b2cacc3f8609bbf953c702f00739 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 681/824] gnu: r-msfeatures: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cfaa23442..7230882fa7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16395,13 +16395,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) + (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs From 94a86e7e39c7db7ee75d780b29865bee47b09fff Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 682/824] gnu: r-biocio: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-biocio): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7230882fa7..ac0023a9be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16425,14 +16425,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) + "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs From 5c6c7831d62b4160dcf34a953acb74321f245176 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 683/824] gnu: r-msmseda: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-msmseda): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac0023a9be..2e6ae69fe4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16458,14 +16458,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) + "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs From 01e78296bc3286f0ed3322c726fce31d0c64f2ce Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 684/824] gnu: r-msmstests: Update to 1.36.0. * gnu/packages/bioconductor.scm (r-msmstests): Update to 1.36.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2e6ae69fe4..c8159010a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16481,14 +16481,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) + "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs From dbeb05e6a3bbe2eaeb62b8198b2d8c3464235ad8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:31 +0100 Subject: [PATCH 685/824] gnu: r-catalyst: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-catalyst): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c8159010a2..39898e97a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16510,14 +16510,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) + "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs From 77f2aa3fa4dae5329f3bba522d0f328b828b9084 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 686/824] gnu: r-erma: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-erma): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39898e97a4..15eab6a923 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16573,14 +16573,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) + "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From 34867ac9cf0d5a882b3a70223df51c7317b3737d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 687/824] gnu: r-ggbio: Update to 1.46.0. * gnu/packages/bioconductor.scm (r-ggbio): Update to 1.46.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15eab6a923..3558a37ad3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16613,14 +16613,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg")))) + "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g")))) (build-system r-build-system) (arguments `(#:phases From 5f3ff4f884f83455fbc25c291cf482da7245bf81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 688/824] gnu: r-gviz: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3558a37ad3..d9e0e4e14a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16781,14 +16781,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) + "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs From b6e56ceeb990a417b9a88118ed0c4021de6ffb1f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 689/824] gnu: r-gwascat: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-gwascat): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9e0e4e14a..c62bb4fe2c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16830,14 +16830,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) + "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi From db290bf5b991cf9d7b34b3699c211fdb748a94df Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 690/824] gnu: r-kegggraph: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62bb4fe2c..0fcced71a4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16864,13 +16864,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) + (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs From 1315c532de6850f983bb83163f021012995224b8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 691/824] gnu: r-ldblock: Update to 1.28.0. * gnu/packages/bioconductor.scm (r-ldblock): Update to 1.28.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0fcced71a4..7a736fdc3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16888,14 +16888,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) + "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics From ddc7edf0b3ec4f7a7dba863364592b2180315f39 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 692/824] gnu: r-pathview: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-pathview): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a736fdc3c..1e76ac9158 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17012,13 +17012,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71")))) + (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs From 1ff0bc4e7b4685d13c2e3c6603a80410ef94e483 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 693/824] gnu: r-snpstats: Update to 1.48.0. * gnu/packages/bioconductor.scm (r-snpstats): Update to 1.48.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e76ac9158..d7d0ca6920 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17046,14 +17046,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) + "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) From 5950a171ba9f89b918d2fc4c842855ee381c3e7c Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 694/824] gnu: r-chromstar: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-chromstar): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d7d0ca6920..6f9b5dcee9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17070,14 +17070,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) + "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs From 3ca58a4ff35e06487d55810fd8222e90ce359869 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 695/824] gnu: r-guitar: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-guitar): Update to 2.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6f9b5dcee9..69b722c8b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17108,14 +17108,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) + "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs From 3823aa40a34426e7d9c07ab1e9b75290765a0c5f Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 696/824] gnu: r-ballgown: Update to 2.30.0. * gnu/packages/bioconductor.scm (r-ballgown): Update to 2.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69b722c8b6..7af742b3f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17161,14 +17161,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) + "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs From 5604f64c342b04f6e8f06cad6fca15d6108d72c6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 697/824] gnu: r-megadepth: Update to 1.8.0. * gnu/packages/bioconductor.scm (r-megadepth): Update to 1.8.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7af742b3f6..aba0a43e1d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17195,14 +17195,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) + "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) From 81cea8424d8ca7a9189b3920b83cb5e34a75716e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:32 +0100 Subject: [PATCH 698/824] gnu: r-beclear: Update to 2.14.0. * gnu/packages/bioconductor.scm (r-beclear): Update to 2.14.0. [propagated-inputs]: Add r-ids. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aba0a43e1d..5536954335 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17228,14 +17228,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) + "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -17244,6 +17244,7 @@ regions or annotations of your choice from BigWig files.") r-data-table r-dixontest r-futile-logger + r-ids r-matrix r-rcpp r-rdpack)) From 3912f43996883094a30ba28d1c3b24f716cc9f8b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 699/824] gnu: r-bgeecall: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5536954335..cba1d09841 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17262,14 +17262,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil")))) + "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs From 009ac4e3a93475e2665d18cc4ee5c5b8ab898975 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 700/824] gnu: r-bgeedb: Update to 2.24.0. * gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cba1d09841..7afc365b04 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17298,14 +17298,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.22.3") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k")))) + "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs From 8ba466faff5154a879dffc9fd0ea63af7ddbf2f1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 701/824] gnu: r-biobtreer: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7afc365b04..635ca45724 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17332,14 +17332,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) + "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs From dbaad2365aa0899522965725cd82b55ad7006bf5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 702/824] gnu: r-minet: Update to 3.56.0. * gnu/packages/bioconductor.scm (r-minet): Update to 3.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 635ca45724..9724e94075 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17356,14 +17356,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) + "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs From 727cd07d1a6f69d9f8846c9e43a5e5587e3bd1eb Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 703/824] gnu: r-genetclassifier: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9724e94075..3b03612045 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17378,14 +17378,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) + "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) From 925642f837a5c9d4fc7ce45dc715e6a7ca7453d4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 704/824] gnu: r-dir-expiry: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3b03612045..b348f15405 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17403,14 +17403,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) + "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) From f5a514b60576a87821fbf2389b2550f05c95dd27 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 705/824] gnu: r-basilisk-utils: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b348f15405..3218e3fc32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17427,14 +17427,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) + "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) From 3aea2c40d8caafdf032a5a51b59173d7b25c2cfd Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 706/824] gnu: r-basilisk: Update to 1.10.2. * gnu/packages/bioconductor.scm (r-basilisk): Update to 1.10.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3218e3fc32..a96ade0f14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17451,14 +17451,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk")))) + "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs From 4fcf1f08ec9a34beab41018ba577903a7549fba8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 707/824] gnu: r-biocthis: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-biocthis): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a96ade0f14..eef6919fda 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17477,14 +17477,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) + "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments From efc663040bc6a8eadc7856713aa306afaf04488e Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 708/824] gnu: r-biocdockermanager: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eef6919fda..f5666b0005 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17511,14 +17511,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d")))) + "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) From ffd5e53e8729702c6db237817df1a2c7da24c20b Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 709/824] gnu: r-biodb: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-biodb): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f5666b0005..0c62f98bf9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17541,14 +17541,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1")))) + "08ahz3v2xbhwfh89dbnhhcdm0x5qv4hibi8wknlqf5x8gqm5j5w6")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs From 4875f37cb6a8a5f2203cbad943d517b512546a59 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 710/824] gnu: r-biomformat: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-biomformat): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c62f98bf9..40d7a65608 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17586,14 +17586,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) + "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs From 3879ddbdb98bf65a1593756301629e7ef38eaa34 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 711/824] gnu: r-mvcclass: Update to 1.72.0. * gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.72.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40d7a65608..301aadeb73 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17615,14 +17615,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) + "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") From c0412736d88cd7ef5d0f848aefba3255fa7ab760 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:33 +0100 Subject: [PATCH 712/824] gnu: r-biomvcclass: Update to 1.66.0. * gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.66.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 301aadeb73..ca40129dff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17635,14 +17635,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) + "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs From 858d9ccd9bb38be880f64cad603c4a201931feed Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 713/824] gnu: r-biomvrcns: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca40129dff..af9b15f5a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17657,14 +17657,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) + "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs From 1118d6e85672e7335d4dfa88c71832d4aa308571 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 714/824] gnu: r-bionero: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-bionero): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af9b15f5a9..597618fb7c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17682,14 +17682,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp")))) + "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs From 01fb7c35e7580bd8b015c073476a6724f25c7a18 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 715/824] gnu: r-bionet: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-bionet): Update to 1.58.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 597618fb7c..47a4cd5c60 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17738,14 +17738,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) + "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs From 219b98fee9402ac9810198ecfb281c8cfb448ca4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 716/824] gnu: r-bionetstat: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47a4cd5c60..c1f29ab421 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17767,14 +17767,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2")))) + "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs From f230df5f4fac80460ff1b6298af2608646c7e377 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 717/824] gnu: r-bioqc: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-bioqc): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1f29ab421..c39f5ecba6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17809,14 +17809,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) + "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs From 3ed0a63106cbe2ad5f4406b115da73afbd5e1489 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 718/824] gnu: r-biotip: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biotip): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c39f5ecba6..ea2e1fec58 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17835,14 +17835,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) + "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs From 3b8df103f725332c0409c5beb856391558133019 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 719/824] gnu: r-biotmle: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-biotmle): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea2e1fec58..857ede1403 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17865,14 +17865,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) + "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs From c2c91d9dfe9b767f3a808aaefd87c3f31a808383 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 720/824] gnu: r-bsseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-bsseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 857ede1403..752662fb93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17907,14 +17907,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) + "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs From 95792cda899aeb69c5c0952fa05bfa47bd5d0f11 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 721/824] gnu: r-dada2: Update to 1.26.0. * gnu/packages/bioconductor.scm (r-dada2): Update to 1.26.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 752662fb93..72f5ccb6e1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17953,13 +17953,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs From e524c12e063eac2b560b6f7b6216ae6edca59dda Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 722/824] gnu: r-dmrseq: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72f5ccb6e1..a2bb6b33d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17990,14 +17990,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) + "1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs From 3f5845473954dddfea7c9343e7bd97cde4b223c0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 723/824] gnu: r-omicade4: Update to 1.38.0. * gnu/packages/bioconductor.scm (r-omicade4): Update to 1.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a2bb6b33d5..687fc4cbb7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18036,13 +18036,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj")))) + "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) From 926fe78f73bbde29b9311cc5363f18a6c6719c5d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 724/824] gnu: r-omnipathr: Update to 3.5.25. * gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.5.25. [propagated-inputs]: Add r-rmarkdown and r-rvest. --- gnu/packages/bioconductor.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 687fc4cbb7..5032eb8a91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18055,13 +18055,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.4.0") + (version "3.5.25") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) + (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -18081,12 +18081,14 @@ interest on transformed methylation proportions.") r-later r-logger r-magrittr + r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang + r-rvest r-stringr r-tibble r-tidyr From dde0da5a950e171853fb0e9a71c2b35cb27ca8d3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:34 +0100 Subject: [PATCH 725/824] gnu: r-biscuiteer: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5032eb8a91..246ac591c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18110,14 +18110,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) + "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs From 7a33311bfdd4030cc0ce32f713cd52c512b5d9f9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: [PATCH 726/824] gnu: r-tcgabiolinks: Update to 2.25.3. * gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.25.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 246ac591c8..e4a235edad 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18162,13 +18162,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.24.3") + (version "2.25.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms")))) + (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs From 5140be4c8147615495ac99bfb1f6f64a2065757d Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: [PATCH 727/824] gnu: r-tricycle: Update to 1.6.0. * gnu/packages/bioconductor.scm (r-tricycle): Update to 1.6.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4a235edad..15c408185e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18217,13 +18217,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) + "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs From 9988c60ea31991ec841a205d1d44153235b1b5cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: [PATCH 728/824] gnu: r-tximeta: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 15c408185e..aa47ce0a2e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18256,14 +18256,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8")))) + "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs From 54afdb3de18f4a0665ebfc451f788be9a553bd82 Mon Sep 17 00:00:00 2001 From: zimoun Date: Thu, 17 Nov 2022 03:50:35 +0100 Subject: [PATCH 729/824] gnu: r-phyloseq: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa47ce0a2e..1b1a007c1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18297,13 +18297,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) + (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs From f3004710faded7a605bb9dd585214e4e77b3363b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Nov 2022 16:51:06 +0100 Subject: [PATCH 730/824] gnu: r-ggtern: Update to 3.4.0. * gnu/packages/cran.scm (r-ggtern): Update to 3.4.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d67b72892d..91e05373bb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3651,13 +3651,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.3.5") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd")))) + (base32 "01j1rvff3vz72vwqsy3bh81aav7gfymg4sbvc267vg0r3a16ywcg")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs From ffe149ccc5a1c0d06b4e6b81f970808fbf4025e8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Nov 2022 18:59:56 +0100 Subject: [PATCH 731/824] gnu: r-with-tests: Drop labels from input lists. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Drop input labels. [inputs]: Same. (r-minimal)[arguments]: Remove lookup of "texlive" package. --- gnu/packages/statistics.scm | 84 ++++++++++++++++++------------------- 1 file changed, 41 insertions(+), 43 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ba937e8c4b..02c3b98ae6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -366,48 +366,48 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; As the JDK is a rather large input with only very limited effects on R, ;; we decided to drop it. (native-inputs - `(("bzip2" ,bzip2) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) ; for building HTML manuals - ("texlive" ,(texlive-updmap.cfg (list texlive-ae - texlive-inconsolata - texlive-fonts-ec - texlive-grfext - texlive-amsfonts - texlive-latex-base - texlive-latex-fancyvrb - texlive-latex-graphics - texlive-hyperref - texlive-oberdiek - texlive-latex-tools - texlive-latex-upquote - texlive-url - texlive-latex-xkeyval))) - ("tzdata" ,tzdata-for-tests) - ("xz" ,xz))) + (list bzip2 + perl + pkg-config + texinfo ; for building HTML manuals + (texlive-updmap.cfg (list texlive-ae + texlive-inconsolata + texlive-fonts-ec + texlive-grfext + texlive-amsfonts + texlive-latex-base + texlive-latex-fancyvrb + texlive-latex-graphics + texlive-hyperref + texlive-oberdiek + texlive-latex-tools + texlive-latex-upquote + texlive-url + texlive-latex-xkeyval)) + tzdata-for-tests + xz)) (inputs - `(;; We need not only cairo here, but pango to ensure that tests for the - ;; "cairo" bitmapType plotting backend succeed. - ("pango" ,pango) - ("coreutils" ,coreutils) - ("curl" ,curl) - ("openblas" ,openblas) - ("gfortran" ,gfortran) - ("icu4c" ,icu4c) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxt" ,libxt) - ("pcre2" ,pcre2) - ("readline" ,readline) - ;; This avoids a reference to the ungraftable static bash. R uses the - ;; detected shell for the "system" procedure. - ("bash" ,bash-minimal) - ("tcl" ,tcl) - ("tk" ,tk) - ("which" ,which) - ("zlib" ,zlib))) + (list coreutils + curl + openblas + gfortran + icu4c + libjpeg-turbo + libpng + libtiff + libxt + ;; We need not only cairo here, but pango to ensure that tests for the + ;; "cairo" bitmapType plotting backend succeed. + pango + pcre2 + readline + tcl + tk + which + zlib + ;; This avoids a reference to the ungraftable static bash. R uses the + ;; detected shell for the "system" procedure. + bash-minimal)) (native-search-paths (list (search-path-specification (variable "R_LIBS_SITE") @@ -452,8 +452,6 @@ available, greatly increasing its breadth and scope.") "|" (assoc-ref inputs "perl") "|" - (assoc-ref inputs "texlive") - "|" (assoc-ref inputs "texlive-bin") "|" (assoc-ref inputs "texinfo") From eeeca2341d76a71951773245b279cc89025441c7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Nov 2022 21:42:20 +0100 Subject: [PATCH 732/824] gnu: r-with-tests: Update to 4.2.2. * gnu/packages/statistics.scm (r-with-tests): Update to 4.2.2. [arguments]: Patch DESCRIPTION file of "tools" package to avoid non-deterministic line break. --- gnu/packages/statistics.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 02c3b98ae6..75f19de4f3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -206,7 +206,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -214,7 +214,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0gv4di1x835i4nsy21vqw66c0blmmmvyjkixc5a8x117dm4dnljd")))) + "1x9xjl6fyzs8r72zigirp905ki50wzyw9rxf7iqsbbsixi12pxhg")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -310,7 +310,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (("\\(2008\\)\n") "(2008) ") ((" ``Software") "``Software") (("Data Analysis:.") "Data Analysis:\n") - (("Programming with R") " Programming with R")))) + (("Programming with R") " Programming with R")) + (substitute* "src/library/tools/DESCRIPTION.in" + (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") + "codetools, methods, xml2, curl, commonmark, + knitr, xfun, mathjaxr")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") From a8082fefe01ee2694888e61311889fe553387823 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Nov 2022 21:43:29 +0100 Subject: [PATCH 733/824] gnu: r-minimal: Use %store-directory instead of /gnu/store. * gnu/packages/statistics.scm (r-minimal)[arguments]: Use %store-directory instead of hard-coding "/gnu/store" prefix. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 75f19de4f3..caae27b0f9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -463,7 +463,8 @@ available, greatly increasing its breadth and scope.") (assoc-ref inputs "xz") "|" (format #false - "/gnu/store/[^-]+-(~{~a~^|~})-[^/]+" + "~a/[^-]+-(~{~a~^|~})-[^/]+" + (%store-directory) '("glibc-utf8-locales" "libselinux" "libsepol" @@ -472,7 +473,8 @@ available, greatly increasing its breadth and scope.") "util-macros" "graphite2")) "|" - "/gnu/store/[^-]+-glibc-[^-]+-static" + (format #false "~a/[^-]+-glibc-[^-]+-static" + (%store-directory)) ")/lib")) "")))))))))))) (define-public rmath-standalone From 4c0449ba8fc0934665de730e660dcb18365ec70a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Nov 2022 21:44:29 +0100 Subject: [PATCH 734/824] gnu: r-minimal: Simplify build phase. * gnu/packages/statistics.scm (r-minimal)[arguments]: Simplify phase "remove-extraneous-references". --- gnu/packages/statistics.scm | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index caae27b0f9..6196d6bd69 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -452,26 +452,20 @@ available, greatly increasing its breadth and scope.") (substitute* (string-append out "/lib/R/bin/libtool") (((string-append "(-L)?(" - (assoc-ref inputs "bzip2") - "|" - (assoc-ref inputs "perl") - "|" - (assoc-ref inputs "texlive-bin") - "|" - (assoc-ref inputs "texinfo") - "|" - (assoc-ref inputs "xz") - "|" (format #false "~a/[^-]+-(~{~a~^|~})-[^/]+" (%store-directory) - '("glibc-utf8-locales" + '("bzip2" + "file" + "glibc-utf8-locales" + "graphite2" "libselinux" "libsepol" - "file" + "perl" + "texinfo" "texlive-bin" "util-macros" - "graphite2")) + "xz")) "|" (format #false "~a/[^-]+-glibc-[^-]+-static" (%store-directory)) From 04340b27bae6355b90c7bdf3f3d39c99bc0d03ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:16 +0100 Subject: [PATCH 735/824] gnu: r-bambu: Update to 3.0.2. * gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b1a007c1b..ac1876afa0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2923,13 +2923,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "08vh0vbmjn1kzp10yrinn0p0ab2cjhgiagx1vhci5sf4s6p20vy4")))) + "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs From d3696e71a985930b54f0dbbd2722cb0a6530cf96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: [PATCH 736/824] gnu: r-deconvr: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-deconvr): Update to 1.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ac1876afa0..19924b3f77 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3507,13 +3507,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "14cxrcv5q6w20bq2pbxj75c0lzz96dxwqh1hqh2cl8nvvfi70jsv")))) + "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs From 3bc54ddeab1e5a28d4844ab8c5441155ca205381 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: [PATCH 737/824] gnu: r-chipseeker: Update to 1.34.1. * gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.34.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19924b3f77..9466dbc130 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4772,13 +4772,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1s90q73lldnmh2nxyb36hv44s3pj2l7pr0qka0z27b3cmnhqh50z")))) + "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r")))) (build-system r-build-system) (native-inputs (list r-knitr)) From a5ee462b7a3d014abb21c9a00969bb2989b0eaef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: [PATCH 738/824] gnu: r-shortread: Update to 1.56.1. * gnu/packages/bioconductor.scm (r-shortread): Update to 1.56.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9466dbc130..e308b9041d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6936,14 +6936,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0z700mjll3zv3451rd6p5195w0g3rmw17xddc5qwflwm8dnhdmll")))) + "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs From f9747ecc2c81fcec187d0a0f81dba2bbdb4a8410 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:21 +0100 Subject: [PATCH 739/824] gnu: r-dose: Update to 3.24.2. * gnu/packages/bioconductor.scm (r-dose): Update to 3.24.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e308b9041d..6d2b9f9021 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10463,14 +10463,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.24.1") + (version "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1ai42pnd8s8ws6y9nlq5d858w2rp8gfw2vpndslspj4q8gc4dbb1")))) + "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs From 8bfac375aa5f28d14e99faa1e8a19119cae576ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: [PATCH 740/824] gnu: r-bioccheck: Update to 1.34.2. * gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.34.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d2b9f9021..bca34e2cdc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14903,13 +14903,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0ncvxqx3irc7nv9ib93kz1c3lxyqc4y6g0g11ymxrqx7i4g3qgb8")))) + "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) From a2ad5b53bfc660a8ca4a44f307f2eed1bcdb9fcf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: [PATCH 741/824] gnu: r-rgreat: Update to 2.0.2. * gnu/packages/bioconductor.scm (r-rgreat): Update to 2.0.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bca34e2cdc..dd9405affc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -15362,14 +15362,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "1s1xx15ilamcyd8f7cnsgdc3r3izhx9wxmb8amamrmr9bzijjvhi")))) + "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs From f43a41d1966638b0b75a46276c76642cb89e3023 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 12:30:22 +0100 Subject: [PATCH 742/824] gnu: r-scuttle: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd9405affc..19b17651b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16182,14 +16182,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1z9pigcqfqyp5n6n9gbmw3ix4f1v0ayxi4xmxj7c4d0vdm5c8c2s")))) + "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs From 13e8930efb855f3332045f38b558fecab50ac7fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 20 Jun 2022 00:33:46 +0200 Subject: [PATCH 743/824] gnu: Add r-arrayexpress. * gnu/packages/bioconductor.scm (r-arrayexpress): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19b17651b2..da7420d9f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2472,6 +2472,31 @@ reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayexpress + (package + (name "r-arrayexpress") + (version "1.56.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ArrayExpress" version)) + (sha256 + (base32 + "0v2v7v0gim0bsg34ciplapz6mjih68yqhcgzdlhcyj2d6vrgiad5")))) + (properties `((upstream-name . "ArrayExpress"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-limma + r-oligo + r-xml)) + (home-page "https://bioconductor.org/packages/ArrayExpress") + (synopsis "Building R objects from ArrayExpress datasets") + (description + "This package offers the possibility to access the ArrayExpress repository +at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data +structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") + (license license:artistic2.0))) + (define-public r-aseb (package (name "r-aseb") From c2cba91ac9b8f8d4ff860f9993280c35acc6cff7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 14:54:41 +0100 Subject: [PATCH 744/824] gnu: r-arrayexpress: Update to 1.57.0. * gnu/packages/bioconductor.scm (r-arrayexpress): Update to 1.57.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da7420d9f2..12a28dd6a6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2475,13 +2475,13 @@ tumor samples from healthy controls.") (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.56.0") + (version "1.57.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "0v2v7v0gim0bsg34ciplapz6mjih68yqhcgzdlhcyj2d6vrgiad5")))) + "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs From 01124e5a109bcae5ad59670eb855d479251acb9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 22 Jun 2022 15:45:33 +0200 Subject: [PATCH 745/824] gnu: Add r-asafe. * gnu/packages/bioconductor.scm (r-asafe): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 12a28dd6a6..9c876704a0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2497,6 +2497,29 @@ at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (license license:artistic2.0))) +(define-public r-asafe + (package + (name "r-asafe") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be +used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate +ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an +@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry +pairs.") + (license license:artistic2.0))) + (define-public r-aseb (package (name "r-aseb") From c706a0a2afd6ea2fa1905758970797cddeb150a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:02:41 +0100 Subject: [PATCH 746/824] gnu: r-asafe: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-asafe): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9c876704a0..4ac69d1a89 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2500,13 +2500,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (define-public r-asafe (package (name "r-asafe") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) (native-inputs (list r-knitr)) From 6c7f0849c1e01bd9a3252643a7dd4442c4d9fc14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 16 Jun 2022 18:35:02 +0200 Subject: [PATCH 747/824] gnu: Add r-alphabeta. * gnu/packages/bioconductor.scm (r-alphabeta): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ac69d1a89..92a3bc5a15 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2301,6 +2301,45 @@ paired or unpaired study designs.") ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alphabeta + (package + (name "r-alphabeta") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlphaBeta" version)) + (sha256 + (base32 + "1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag")))) + (properties `((upstream-name . "AlphaBeta"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AlphaBeta") + (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants") + (description + "The package @code{AlphaBeta} is a computational method for estimating +epimutation rates and spectra from high-throughput DNA methylation data in +plants. The method has been specifically designed to: + +@itemize +@item analyze @emph{germline} epimutations in the context of + multi-generational mutation accumulation lines; +@item analyze @emph{somatic} epimutations in the context of plant development + and aging. +@end itemize") + (license license:gpl3))) + (define-public r-alpine (package (name "r-alpine") From 610616d4489fe9c066ffab4bc17f95f5cec40339 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:13:50 +0100 Subject: [PATCH 748/824] gnu: r-alphabeta: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92a3bc5a15..330ab8c77d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,13 +2304,13 @@ paired or unpaired study designs.") (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag")))) + "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs From 5dc82a7f8b08d0e7816107e60625badb090ad97a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Thu, 16 Jun 2022 18:16:50 +0200 Subject: [PATCH 749/824] gnu: Add r-alevinqc. * gnu/packages/bioconductor.scm (r-alevinqc): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 330ab8c77d..975e36bb54 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2301,6 +2301,40 @@ paired or unpaired study designs.") ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alevinqc + (package + (name "r-alevinqc") + (version "1.12.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alevinQC" version)) + (sha256 + (base32 + "0g75qnz7ah0widdjn99lhvnacz38vgl9j86n65wyswsf413hz3bb")))) + (properties `((upstream-name . "alevinQC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-rcpp + r-rjson + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-tximport)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/csoneson/alevinQC") + (synopsis "Quality control reports for @code{Alevin} output") + (description + "The package @code{r-alevinqc} generates quality control reports +summarizing the output from an @code{alevin} run. The reports can be +generated as HTML or PDF files, or as Shiny applications.") + (license license:expat))) + (define-public r-alphabeta (package (name "r-alphabeta") From 6f39e161241931f101f3c7924bfa4ece34959604 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:28:15 +0100 Subject: [PATCH 750/824] gnu: r-alevinqc: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.14.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 975e36bb54..cd9fa0d2fe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,13 +2304,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "0g75qnz7ah0widdjn99lhvnacz38vgl9j86n65wyswsf413hz3bb")))) + "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs From 2e85d26ebb5be6f7c52a9f2d780e0ae34fd40692 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 2 May 2022 11:49:55 +0200 Subject: [PATCH 751/824] gnu: Add r-aims. * gnu/packages/bioconductor.scm (r-aims): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cd9fa0d2fe..179551c2f0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2107,6 +2107,30 @@ using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aims + (package + (name "r-aims") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AIMS" version)) + (sha256 + (base32 + "1z7yzaizyzcv556w8880603nd947k0d6raadjm42mdl66mma0cdx")))) + (properties `((upstream-name . "AIMS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071)) + (home-page "https://git.bioconductor.org/packages/AIMS") + (synopsis + "Absolute assignment of breast cancer intrinsic molecular subtype") + (description + "This package contains an implementation of @code{AIMS} -- Absolute +Intrinsic Molecular Subtyping. It contains necessary functions to assign the +five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, +Basal-like, Normal-like). Assignments could be done on individual samples as +well as on dataset of gene expression data.") + (license license:artistic2.0))) + (define-public r-airpart (package (name "r-airpart") From fa59a22140bcb98fa6e5cf895deaa5f2fbdb9bcf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 15:36:18 +0100 Subject: [PATCH 752/824] gnu: r-aims: Update to 1.30.0. * gnu/packages/bioconductor.scm (r-aims): Update to 1.30.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 179551c2f0..61f312e17f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2110,13 +2110,13 @@ objects are used so that other packages could be used as well.") (define-public r-aims (package (name "r-aims") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "1z7yzaizyzcv556w8880603nd947k0d6raadjm42mdl66mma0cdx")))) + "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) From a8c36bf8c49d1f790d4132a47e95972bba793c89 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 23 Nov 2022 21:30:02 -0500 Subject: [PATCH 753/824] gnu: linux-libre 4.19: Update to 4.19.266. * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.266. (linux-libre-4.19-pristine-source): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a984b45fbc..263772da7b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -418,7 +418,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.265") +(define-public linux-libre-4.19-version "4.19.266") (define-public linux-libre-4.19-gnu-revision "gnu1") (define deblob-scripts-4.19 (linux-libre-deblob-scripts @@ -428,7 +428,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "00i91lx938nqlgy63hiricqd0fnbbf26vgya9c5lb7m1f4x324im"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1l5cdpgng1gci1p1gdr2jzqw486h3w56gpyc7fbq74hlc6nnwh1p"))) + (hash (base32 "0qfgvdzf8mwx0vhz6v6vkdch3hilh6qrl24gmy5z1vpwbxjvc4kv"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) From 8d3bd8e4b08fef0ea7fac48296191d3e6e342e9c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Sun, 19 Jun 2022 22:42:01 +0200 Subject: [PATCH 754/824] gnu: Add r-ancombc. * gnu/packages/bioconductor.scm (r-ancombc): New variable. --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61f312e17f..d9303b5873 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2284,6 +2284,52 @@ of Medical Research. The goal is to provide a standard library for quantitative analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) +(define-public r-ancombc + (package + (name "r-ancombc") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANCOMBC" version)) + (sha256 + (base32 + "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq")))) + (properties `((upstream-name . "ANCOMBC"))) + (build-system r-build-system) + (propagated-inputs + (list r-desctools + r-doparallel + r-dorng + r-dplyr + r-energy + r-foreach + r-hmisc + r-magrittr + r-mass + r-microbiome + r-nlme + r-nloptr + r-phyloseq + r-rdpack + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FrederickHuangLin/ANCOMBC") + (synopsis "Analysis of compositions of microbiomes with bias correction") + (description + "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA) +and correlation analyses for microbiome data. Specifically, the package +includes @dfn{Analysis of Compositions of Microbiomes with Bias +Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM) +for DA analysis, and @dfn{Sparse Estimation of Correlations among +Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically +subject to two sources of biases: unequal sampling fractions (sample-specific +biases) and differential sequencing efficiencies (taxon-specific biases). +Methodologies included in the @code{ANCOMBC} package were designed to correct +these biases and construct statistically consistent estimators.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") From 8b1bee45f7fe37fd46e449910ff4ceb421e8ad87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:00:32 +0100 Subject: [PATCH 755/824] gnu: Add r-osqp. * gnu/packages/cran.scm (r-osqp): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 91e05373bb..88600988c4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19251,6 +19251,28 @@ authoring books and technical documents with R Markdown.") that accept short and long options.") (license license:gpl2+))) +(define-public r-osqp + (package + (name "r-osqp") + (version "0.6.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "osqp" version)) + (sha256 + (base32 + "00w2hr0pagnvpsk84z99c7alhv7xvs9wpcmkzbcg3qs14g888rgf")))) + (properties `((upstream-name . "osqp"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-r6 r-rcpp)) + (home-page "https://osqp.org") + (synopsis "Quadratic Programming Solver using the OSQP Library") + (description + "This package provides bindings to the OSQP solver. The OSQP +solver is a numerical optimization package or solving convex quadratic +programs written in C and based on the alternating direction method of +multipliers. See for details.") + (license (list license:asl2.0)))) + (define-public r-kernlab (package (name "r-kernlab") From 697a0f8ca486842e73cd81ac3157b0ab5ad70fc5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:01:02 +0100 Subject: [PATCH 756/824] gnu: Add r-scs. * gnu/packages/cran.scm (r-scs): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 88600988c4..daa1249892 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21017,6 +21017,30 @@ errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) +(define-public r-scs + (package + (name "r-scs") + (version "3.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "scs" version)) + (sha256 + (base32 + "04srf33zw4dxv22b1h5qwjch5yg7hrvk4iq8yvxqnbr8qzp1x26n")))) + (properties `((upstream-name . "scs"))) + (build-system r-build-system) + (home-page "https://github.com/FlorianSchwendinger/scs") + (synopsis "Splitting conic solver") + (description + "This package solves convex cone programs via operator splitting. +It can solve: linear programs, second-order cone programs, +semidefinite programs, exponential cone programs, and power cone +programs, or problems with any combination of those cones. SCS uses +AMD (a set of routines for permuting sparse matrices prior to +factorization) and LDL (a sparse LDL factorization and solve package) +from SuiteSparse.") + (license license:gpl3))) + (define-public r-sctransform (package (name "r-sctransform") From bde758150ffba188afa32cc436ec7b7c5f1124ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:16:13 +0100 Subject: [PATCH 757/824] gnu: Add r-ecosolver. * gnu/packages/cran.scm (r-ecosolver): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index daa1249892..10d7411b88 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1922,6 +1922,30 @@ excellent candidate for labeling of a polygon.") @code{dplyr} and the wider @code{tidyverse} using only @code{base}.") (license license:expat))) +(define-public r-ecosolver + (package + (name "r-ecosolver") + (version "0.5.4") + (source (origin + (method url-fetch) + (uri (cran-uri "ECOSolveR" version)) + (sha256 + (base32 + "0973m346vakgddp92dzqlky0wa196hj341r9y7rz67bc2zl8jx2x")))) + (properties `((upstream-name . "ECOSolveR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bnaras.github.io/ECOSolveR/") + (synopsis "Embedded conic solver in R") + (description + "This package provides an R interface to the @dfn{Embedded COnic +Solver} (ECOS), an efficient and robust C library for convex problems. +Conic and equality constraints can be specified in addition to integer +and boolean variable constraints for mixed-integer problems. This R +interface is inspired by the Python interface and has similar calling +conventions.") + (license license:gpl3+))) + (define-public r-ecp (package (name "r-ecp") From efb965a4fabb09d0a4af7a9ff176d4af509ee134 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:21:41 +0100 Subject: [PATCH 758/824] gnu: Add r-cvxr. * gnu/packages/cran.scm (r-cvxr): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 10d7411b88..ad0657ef3b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5711,6 +5711,43 @@ testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) +(define-public r-cvxr + (package + (name "r-cvxr") + (version "1.0-11") + (source (origin + (method url-fetch) + (uri (cran-uri "CVXR" version)) + (sha256 + (base32 + "0alp1g4bszxqcrjbn54bz1zswg8y10372fwwlbi0jjazycw9cap9")))) + (properties `((upstream-name . "CVXR"))) + (build-system r-build-system) + (propagated-inputs + (list r-bit64 + r-ecosolver + r-gmp + r-matrix + r-osqp + r-r6 + r-rcpp + r-rcppeigen + r-rmpfr + r-scs)) + (native-inputs (list r-knitr)) + (home-page "https://cvxr.rbind.io") + (synopsis "Disciplined convex optimization") + (description + "This package provides an object-oriented modeling language for +@dfn{disciplined convex programming} (DCP) as described in Fu, +Narasimhan, and Boyd (2020, ). It allows +the user to formulate convex optimization problems in a natural way +following mathematical convention and DCP rules. The system analyzes +the problem, verifies its convexity, converts it into a canonical +form, and hands it off to an appropriate solver to obtain the +solution. Interfaces to solvers on CRAN and elsewhere are provided.") + (license license:asl2.0))) + (define-public r-squarem (package (name "r-squarem") From 90d8ac279fcffe12969e0bdd43a07363c212942e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:28:28 +0100 Subject: [PATCH 759/824] gnu: Add r-treesummarizedexperiment. * gnu/packages/bioconductor.scm (r-treesummarizedexperiment): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d9303b5873..17d5195ce5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8989,6 +8989,39 @@ heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.") (license license:artistic2.0))) +(define-public r-treesummarizedexperiment + (package + (name "r-treesummarizedexperiment") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "TreeSummarizedExperiment" version)) + (sha256 + (base32 + "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2")))) + (properties `((upstream-name . "TreeSummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-iranges + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-treeio)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment") + (synopsis "S4 class for data with tree structures") + (description + "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to +include hierarchical information on the rows or columns of the rectangular +data.") + (license license:gpl2+))) + (define-public r-ggtree (package (name "r-ggtree") From 139da51753717a06692bd87a754f54b4e60f4fcd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 17:59:52 +0100 Subject: [PATCH 760/824] gnu: Add r-mia. * gnu/packages/bioconductor.scm (r-mia): New variable. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 17d5195ce5..0d4110bc20 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10027,6 +10027,54 @@ to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) +(define-public r-mia + (package + (name "r-mia") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "mia" version)) + (sha256 + (base32 + "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync")))) + (properties `((upstream-name . "mia"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-decipher + r-decontam + r-delayedarray + r-delayedmatrixstats + r-dirichletmultinomial + r-dplyr + r-iranges + r-mass + r-multiassayexperiment + r-rlang + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/microbiome/mia") + (synopsis "Microbiome analysis") + (description + "The mia package implements tools for microbiome analysis based on the +@code{SummarizedExperiment}, @code{SingleCellExperiment} and +@code{TreeSummarizedExperiment} infrastructure. Data wrangling and analysis +in the context of taxonomic data is the main scope. Additional functions for +common task are implemented such as community indices calculation and +summarization.") + (license license:artistic2.0))) + (define-public r-microbiome (package (name "r-microbiome") From c29d999a34d7dbb447446e0abd376ec3a27fdf54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 18:00:09 +0100 Subject: [PATCH 761/824] gnu: r-ancombc: Update to 2.0.1. * gnu/packages/bioconductor.scm (r-ancombc): Update to 2.0.1. [propagated-inputs]: Remove r-microbiome, r-nlme, and r-phyloseq; add r-cvxr, r-emmeans, r-lme4, r-lmertest, r-mia, r-rngtools, r-s4vectors, r-singlecellexperiment, r-summarizedexperiment, and r-treesummarizedexperiment. --- gnu/packages/bioconductor.scm | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0d4110bc20..bb319a13e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2287,33 +2287,40 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "1.6.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq")))) + "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs - (list r-desctools + (list r-cvxr + r-desctools r-doparallel r-dorng r-dplyr + r-emmeans r-energy r-foreach r-hmisc + r-lme4 + r-lmertest r-magrittr r-mass - r-microbiome - r-nlme + r-mia r-nloptr - r-phyloseq r-rdpack r-rlang + r-rngtools + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment r-tibble - r-tidyr)) + r-tidyr + r-treesummarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/FrederickHuangLin/ANCOMBC") (synopsis "Analysis of compositions of microbiomes with bias correction") From 3174c4c17d184982a21207d65173b0121a050653 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:47:55 +0100 Subject: [PATCH 762/824] gnu: emacs-org-modern: Update to 0.6. * gnu/packages/emacs-xyz.scm (emacs-org-modern): Update to 0.6. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 7436322ae8..fdb5f015cf 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33577,7 +33577,7 @@ Fennel code within Emacs.") (define-public emacs-org-modern (package (name "emacs-org-modern") - (version "0.5") + (version "0.6") (source (origin (method git-fetch) @@ -33585,7 +33585,7 @@ Fennel code within Emacs.") (url "https://github.com/minad/org-modern") (commit version))) (sha256 - (base32 "1gny2p3w6ck5sarv6vap2y1lj6h9qaxbh7r7bzszb9qj8rhapk6q")) + (base32 "03zpwb475rpbhq1s6101clj0j9mcxdg033clvvybp0p7hm4inwaz")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (home-page "https://github.com/minad/org-modern") From b8eb99f8174f0090f48fd6e7da41e7d762236621 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:48:53 +0100 Subject: [PATCH 763/824] gnu: emacs-detached: Update to 0.10.0. * gnu/packages/emacs-xyz.scm (emacs-detached): Update to 0.10.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index fdb5f015cf..a7838e2d3d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26262,7 +26262,7 @@ according to their use.") (define-public emacs-detached (package (name "emacs-detached") - (version "0.9.2") + (version "0.10.0") (source (origin (method git-fetch) (uri (git-reference @@ -26271,7 +26271,7 @@ according to their use.") (file-name (git-file-name name version)) (sha256 (base32 - "0bcrqqim6is75d4zadswxp162m9gd34xmb2wxsx9rhvkwq0ln35k")))) + "13vssywna281dr4r0hqp85xdi3xnajmdahqy7kf147jvgazkqbmd")))) (arguments (list #:tests? #t From 49cfa7d8bd6e482248aec676ee5ffd36abd242e5 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:52:45 +0100 Subject: [PATCH 764/824] gnu: emacs-eldev: Update to 1.3. * gnu/packages/emacs-xyz.scm (emacs-eldev): Update to 1.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a7838e2d3d..3ce794d141 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -20056,7 +20056,7 @@ according to a parsing expression grammar.") (define-public emacs-eldev (package (name "emacs-eldev") - (version "1.2.2") + (version "1.3") (source (origin (method git-fetch) @@ -20065,7 +20065,7 @@ according to a parsing expression grammar.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0d6wbfim0q81sm5m45fjc6n0v6nk32qrgas5nzrs0vslym4bfxna")))) + (base32 "112jv9rz6brglffwsablnhafhhnfnq89k9vh8xzbbi6i4xz2l1ak")))) (build-system emacs-build-system) (arguments (list From 95aa64e9feaf4715bb631beea7d5d72a6a5dad0a Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:53:45 +0100 Subject: [PATCH 765/824] gnu: emacs-vertico: Update to 0.29. * gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.29. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3ce794d141..f54275ef26 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33073,7 +33073,7 @@ and preferred services can easily be configured.") (define-public emacs-vertico (package (name "emacs-vertico") - (version "0.28") + (version "0.29") (source (origin (method git-fetch) @@ -33082,7 +33082,7 @@ and preferred services can easily be configured.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yybwj32k74c5c4rzlpmkq540b8ax0ihn5v7krnri83wn50hr272")))) + (base32 "0gqfq7yni470yys9blarmsinjgf1025azlr09g1842w20hwrs7hc")))) (build-system emacs-build-system) (arguments `(#:phases From 071d0cac8032556bb10e5322a674aca47631353d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:55:20 +0100 Subject: [PATCH 766/824] gnu: emacs-kind-icon: Update to 0.1.8. * gnu/packages/emacs-xyz.scm (emacs-kind-icon): Update to 0.1.8. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index f54275ef26..2753888cf0 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21137,14 +21137,14 @@ or expressions with SVG rounded box labels that are fully customizable.") (define-public emacs-kind-icon (package (name "emacs-kind-icon") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/kind-icon-" version ".tar")) (sha256 - (base32 "02imi2qj329yrqvs23d4z7fv8bbaz0fvya6zdswb38blpdri4cn1")))) + (base32 "0m0jpgk3iv0p8fzmx1nyfd1l7i803lm4mzlpp47kn7v0z09pxaph")))) (build-system emacs-build-system) (propagated-inputs (list emacs-svg-lib)) (home-page "https://github.com/jdtsmith/kind-icon") From 826d862eb31da45b21a1a6cbf94ff1614215a172 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:57:58 +0100 Subject: [PATCH 767/824] gnu: emacs-projectile: Update to 2.7.0. * gnu/packages/emacs-xyz.scm (emacs-projectile): Update to 2.7.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2753888cf0..22e3339149 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11835,7 +11835,7 @@ like @code{org-edit-src-code} but for arbitrary regions.") (define-public emacs-projectile (package (name "emacs-projectile") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/bbatsov" @@ -11843,7 +11843,7 @@ like @code{org-edit-src-code} but for arbitrary regions.") (file-name (string-append "projectile-" version ".el")) (sha256 (base32 - "12crymgri4sg7fvnh692f96cm0krmmcnz6x3ypxgq8da84rl34p4")))) + "1jd1csrvafy49dcfag0ccpqbdn5my183h325bv6j4x4c3a6qbp98")))) (build-system emacs-build-system) (propagated-inputs (list emacs-dash emacs-pkg-info)) From b438e1f2311a06c309f7b4cf29683463bf446da1 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 12:59:08 +0100 Subject: [PATCH 768/824] gnu: emacs-projectile: Improve description. * gnu/packages/emacs-xyz.scm (emacs-projectile)[description]: Use proper capitalization, expand some words, add Texinfo markup, remove fancy typography. --- gnu/packages/emacs-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 22e3339149..0132193197 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11851,10 +11851,10 @@ like @code{org-edit-src-code} but for arbitrary regions.") (synopsis "Manage and navigate projects in Emacs easily") (description "This library provides easy project management and navigation. The -concept of a project is pretty basic - just a folder containing special file. -Currently git, mercurial and bazaar repos are considered projects by default. -If you want to mark a folder manually as a project just create an empty -.projectile file in it.") +concept of a project is pretty basic: just a folder containing special file. +Currently Git, Mercurial and Bazaar repositories are considered projects by +default. If you want to mark a folder manually as a project just create an +empty @file{.projectile} file in it.") (license license:gpl3+))) (define-public emacs-skeletor From 8f3e10ae819aabbe8216bfee6cd3e7857bc27293 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 18:03:06 +0100 Subject: [PATCH 769/824] gnu: emacs-projectile: Activate tests. * gnu/packages/emacs-xyz.scm (emacs-projectile)[source]: Use Git repository instead of released tarball to get the test file. [arguments]: Activate tests, and fix a failing one. --- gnu/packages/emacs-xyz.scm | 30 ++++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 0132193197..2eef75925a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -11836,15 +11836,29 @@ like @code{org-edit-src-code} but for arbitrary regions.") (package (name "emacs-projectile") (version "2.7.0") - (source (origin - (method url-fetch) - (uri (string-append "https://raw.githubusercontent.com/bbatsov" - "/projectile/v" version "/projectile.el")) - (file-name (string-append "projectile-" version ".el")) - (sha256 - (base32 - "1jd1csrvafy49dcfag0ccpqbdn5my183h325bv6j4x4c3a6qbp98")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbatsov/projectile") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ybd41iss8vd56qv6czpxqq7a99s4h7i3a2r4khy4rf5blj5zdqi")))) (build-system emacs-build-system) + (arguments + (list + #:tests? #t + #:test-command #~(list "buttercup" "-L" ".") + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'fix-failing-test + (lambda _ + (substitute* "test/projectile-test.el" + (("user-emacs-directory") "\".\""))))))) + (native-inputs + (list emacs-buttercup)) (propagated-inputs (list emacs-dash emacs-pkg-info)) (home-page "https://github.com/bbatsov/projectile") From 9381e14536cf4370ab1f567839636f21c3eb9f12 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 8 Nov 2022 20:56:04 -0500 Subject: [PATCH 770/824] gnu: Add qttranslations. * gnu/packages/qt.scm (qttranslations): New variable. --- gnu/packages/qt.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 30bf429897..3784d01eaf 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1878,6 +1878,27 @@ that helps in Qt development.") ;; LICENSES/Qt-GPL-exception-1.0.txt). (license (list license:gpl3)))) +(define-public qttranslations + (package + (name "qttranslations") + (version "6.3.1") + (source (origin + (method url-fetch) + (uri (qt-urls name version)) + (sha256 + (base32 + "15yvvxw1vngnjlly6cady05ljamg01qiaqn2vh0xkph855gdbgfp")))) + (build-system cmake-build-system) + (arguments (list #:tests? #f)) + (native-inputs (list qtbase qttools)) + (home-page (package-home-page qtbase)) + (synopsis "Qt translation catalogs") + (description "This package contains the translations for Qt contributed by +the Qt community.") + ;; GPL 3 only with Qt GPL exception 1.0 (see: + ;; LICENSES/Qt-GPL-exception-1.0.txt). + (license (list license:gpl3)))) + (define-public qtscript (package (inherit qtsvg-5) (name "qtscript") From d1dc2c47fef2102a479f797244e542af6eaf9865 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Wed, 9 Nov 2022 09:00:40 -0500 Subject: [PATCH 771/824] gnu: Add clazy. * gnu/packages/qt.scm (clazy): New variable. --- gnu/packages/qt.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 3784d01eaf..009626d6d9 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -4563,6 +4563,31 @@ authentication on behalf of its clients.") "This plugin for the Accounts-SSO SignOn daemon handles the OAuth 1.0 and 2.0 authentication protocols.") (license license:lgpl2.1+))) + +(define-public clazy + (package + (name "clazy") + (version "1.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KDE/clazy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1y0n1jknq566z1rifkgdm1yqb0mw564lp51jidfz7q9w91spijci")))) + (build-system cmake-build-system) + (native-inputs (list python)) + (inputs (list clang llvm)) + (home-page "https://github.com/KDE/clazy/") + (synopsis "Qt-oriented static code analyzer") + (description "clazy is a compiler plugin which allows @command{clang} to +understand Qt semantics. It can emit more than fifty (50) Qt-related compiler +warnings, ranging from unneeded memory allocations to misuses of the API, +including @i{fix-its} for automatic refactoring.") + (license license:lgpl2.0+))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar From 085831010cc389888facb9f30fb10c5faff18ec9 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Thu, 10 Nov 2022 12:40:38 -0500 Subject: [PATCH 772/824] gnu: qttools: Add clang-15 as input. * gnu/packages/qt.scm (qttools) [inputs]: Add clang-15, so that the qdoc command can be built. [phases] {sanity-check}: New phase, to guard against a problem that proved difficult to isolate. --- gnu/packages/qt.scm | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 009626d6d9..2e44a6256a 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1866,9 +1866,22 @@ that helps in Qt development."))) (list ;; The build system attempts to fetch online resources and fails when ;; building the test suite. - #:configure-flags #~(list "-DQT_BUILD_TESTS=OFF"))) + #:configure-flags #~(list "-DQT_BUILD_TESTS=OFF") + #:phases #~(modify-phases %standard-phases + (add-after 'install 'sanity-check + (lambda* (#:key outputs #:allow-other-keys) + ;; This validation exists to validate that the dynamic + ;; library for Clang works as intended; there was + ;; originally problems due to left-overs patching the + ;; value of BUILD_SHARED_LIBS in CLANG-FROM-LLVM that + ;; would cause the following error: "CommandLine Error: + ;; Option 'filter' registered more than once!" + (invoke/quiet (search-input-file outputs "bin/qdoc") + "--help")))))) (native-inputs (list perl qtdeclarative vulkan-headers)) - (inputs (list libxkbcommon mesa qtbase)) + ;; Use clang-15, which is built using as a single shared library, which is + ;; what the build system of qttools expects. + (inputs (list clang-15 libxkbcommon mesa qtbase)) (home-page (package-home-page qtbase)) (synopsis "Qt Tools and Designer modules") (description "The Qt Tools module provides a set of applications to browse From 4c9e94a453fc377fc9f2344d9644df422a0ed315 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 8 Nov 2022 15:23:04 -0500 Subject: [PATCH 773/824] gnu: Add qt-creator. * gnu/packages/qt.scm (qt-creator): New variable. wip --- gnu/packages/qt.scm | 129 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 129 insertions(+) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 2e44a6256a..7694334a2c 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -64,15 +64,18 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages cups) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages documentation) + #:use-module (gnu packages elf) #:use-module (gnu packages enchant) #:use-module (gnu packages fontutils) #:use-module (gnu packages flex) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gcc) + #:use-module (gnu packages gdb) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -4601,6 +4604,132 @@ warnings, ranging from unneeded memory allocations to misuses of the API, including @i{fix-its} for automatic refactoring.") (license license:lgpl2.0+))) +(define-public qt-creator + (package + (name "qt-creator") + (version "9.0.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.qt.io/official_releases/qtcreator/" + (version-major+minor version) "/" version + "/qt-creator-opensource-src-" version ".tar.gz")) + (modules '((guix build utils))) + (snippet '(begin + (for-each + delete-file-recursively + ;; Remove bundled libraries, where supported. + ;; TODO: package and unbundle litehtml + '("src/libs/3rdparty/yaml-cpp" + "src/shared/qbs/src/shared/qtscript/src/3rdparty" + "tests/unit/unittest/3rdparty" + ;; Marketplace recommends nonfree extensions; + ;; remove it. + "src/plugins/marketplace")) + (substitute* "src/plugins/CMakeLists.txt" + (("add_subdirectory\\(marketplace).*") "")) + (substitute* "src/plugins/plugins.qbs" + ((".*marketplace/marketplace.qbs.*") "")))) + (sha256 + (base32 + "1adyxs0cnqx14gwzkvh909c52449ia6y87n1r4qf6wwydhch43cs")))) + (build-system qt-build-system) + (arguments + (list + #:qtbase qtbase + #:configure-flags + #~(list "-DWITH_DOCS=ON" + "-DBUILD_DEVELOPER_DOCS=ON" + "-DCMAKE_VERBOSE_MAKEFILE=ON" + "-DWITH_TESTS=ON" + ;; Extend the RUNPATH with lib/qtcreator, which contains + ;; multiple shared objects. + (string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath=" + #$output "/lib/qtcreator")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests-build + (lambda _ + ;; Add a missing link directive (see: + ;; https://bugreports.qt.io/browse/QTCREATORBUG-28434). + (substitute* "src/libs/tracing/CMakeLists.txt" + (("DEPENDS Utils Qt5::Qml Qt5::Quick") + "DEPENDS Utils Qt5::Quick") + (("PUBLIC_DEPENDS Qt5::Widgets") + "PUBLIC_DEPENDS Qt5::Widgets Qt5::Qml")))) + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/libs/utils/commandline.cpp" + "src/libs/utils/deviceshell.cpp") + (("/bin/sh") + (search-input-file inputs "bin/sh"))) + (substitute* "src/libs/utils/qtcprocess.cpp" + (("/usr/bin/env") + (search-input-file inputs "bin/env"))) + (substitute* "tests/auto/utils/qtcprocess/tst_qtcprocess.cpp" + (("/bin/sh") + (which "sh"))))) + (add-before 'build 'build-doc + (lambda _ + (invoke "cmake" "--build" "." "--target=docs" "-v"))) + (add-after 'build-doc 'install-doc + (lambda _ + (invoke "cmake" "--install" "." "--prefix" #$output + "--component=qch_docs") + (invoke "cmake" "--install" "." "--prefix" #$output + "--component=html_docs"))) + (replace 'check + ;; Loosely based on .github/workflows/build_cmake.yml. + (lambda* (#:key tests? parallel-tests? #:allow-other-keys) + (when tests? + (invoke "xvfb-run" ;for the 'renderpass' tests + "ctest" "-j" (if parallel-tests? + (number->string (parallel-job-count)) + "1") + "--label-exclude" "exclude_from_precheck" + "--exclude-regex" "tst_perfdata")))) + (add-after 'qt-wrap 'wrap-bin + ;; Make a few well-integrated tools readily available. + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (search-input-file outputs "bin/qtcreator") + `("PATH" suffix ,(map (lambda (c) + (dirname (search-input-file inputs c))) + '("bin/clang-tidy" + "bin/clazy-standalone" + "bin/gdb" + "bin/valgrind"))))))))) + (native-inputs + (list googletest + pkg-config + python + qttools + qttranslations + vulkan-headers + xvfb-run)) + (inputs + (list bash-minimal + coreutils-minimal + clang + clazy + elfutils + gdb + libxkbcommon + llvm + qt5compat + qtdeclarative + qtshadertools + qtsvg + yaml-cpp + valgrind + vulkan-loader + `(,zstd "lib"))) + (home-page "https://www.qt.io/") + (synopsis "Integrated development environment (IDE) for Qt") + (description "Qt Creator is an IDE tailored to the needs of Qt developers. +It includes features such as an advanced code editor, a visual debugger and a +@acronym{GUI, Graphical User Interface} designer.") + (license license:gpl3+))) ;with the Qt Company GPL Exception 1.0 + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar From 564dcaa1fa06254aeedb0934b4f3bd1c26f9f53c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 23 Nov 2022 22:18:20 +0200 Subject: [PATCH 774/824] gnu: python-brotlicffi: Unbundle brotli. * gnu/packages/python-compression.scm (python-brotlicffi)[source]: Add snippet to delete bundled libbrotli. [arguments]: Add phase to configure using shared libbrotli. [inputs]: Add brotli. --- gnu/packages/python-compression.scm | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 9eef74c71b..c483d68b5f 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2017, 2019, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2017 Nikita ;;; Copyright © 2017 Julien Lepiller -;;; Copyright © 2018, 2019, 2020 Efraim Flashner +;;; Copyright © 2018-2020, 2022 Efraim Flashner ;;; Copyright © 2020 Nicolas Goaziou ;;; Copyright © 2020, 2022 Marius Bakke ;;; Copyright © 2021 Brendan Tildesley @@ -134,9 +134,21 @@ Jump conversion filter by CFFI for Python.") (uri (pypi-uri "brotlicffi" version)) (sha256 (base32 - "15kxgdiqcg0cm6h5xq3vkbhw7674673hcx3n2yicd3wx29l8l90c")))) + "15kxgdiqcg0cm6h5xq3vkbhw7674673hcx3n2yicd3wx29l8l90c")) + (snippet + #~(begin + (use-modules (guix build utils)) + (delete-file-recursively "libbrotli"))))) (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-shared-brotli + (lambda _ + (setenv "USE_SHARED_BROTLI" "1")))))) (propagated-inputs (list python-cffi)) + (inputs (list brotli)) (home-page "https://github.com/python-hyper/brotlicffi") (synopsis "Python CFFI bindings to the Brotli library") (description "This package provides Python CFFI bindings to the Brotli From 255450bed2b24b9dd21745e2675aa0ecf38a2a79 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 24 Nov 2022 10:02:51 +0200 Subject: [PATCH 775/824] gnu: arm-trusted-firmware: Update to 2.8. * gnu/packages/firmware.scm (make-arm-trusted-firmware): Update to 2.8. [arguments]: Remove trailing #t from phases. Clean up regexes. --- gnu/packages/firmware.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index d192671eec..9f6c957113 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2017 David Craven -;;; Copyright © 2017, 2018 Efraim Flashner +;;; Copyright © 2017, 2018, 2022 Efraim Flashner ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2018 Vagrant Cascadian ;;; Copyright © 2019 Mathieu Othacehe @@ -645,7 +645,7 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (define* (make-arm-trusted-firmware platform #:optional (arch "aarch64")) (package (name (string-append "arm-trusted-firmware-" platform)) - (version "2.6") + (version "2.8") (source (origin (method git-fetch) @@ -656,7 +656,7 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (file-name (git-file-name "arm-trusted-firmware" version)) (sha256 (base32 - "1j0rn33pwgmksqliwf2npm2px84qmbyma9iq8zpllwfc7dsl6gx9")))) + "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3")))) (build-system gnu-build-system) (arguments `(#:phases @@ -667,16 +667,15 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (lambda _ (for-each (lambda (file) (delete-file file)) - (find-files "." ".*\\.bin$")))) + (find-files "." "\\.bin$")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) - (bin (find-files "." ".*\\.(bin|elf)$"))) + (bin (find-files "." "\\.(bin|elf)$"))) (for-each (lambda (file) (install-file file out)) - bin)) - #t))) + bin))))) #:make-flags (list (string-append "PLAT=" ,platform) ,@(if (and (not (string-prefix? "aarch64" (%current-system))) From b3beeaa30981e49070ff28434b69aa234069bd2d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 24 Nov 2022 10:17:11 +0200 Subject: [PATCH 776/824] gnu: arm-trusted-firmware: Remove blobs in a snippet. * gnu/packages/firmware.scm (make-arm-trusted-firmware)[source]: Add snippet to remove binary blobs. [arguments]: Remove related phase. --- gnu/packages/firmware.scm | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 9f6c957113..e9bb3ed450 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -656,18 +656,19 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (file-name (git-file-name "arm-trusted-firmware" version)) (sha256 (base32 - "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3")))) + "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Remove binary blobs which do not contain source or proper license. + (for-each (lambda (file) + (delete-file file)) + (find-files "." "\\.bin$")))))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) ; no configure script - ;; Remove binary blobs which do not contain source or proper license. - (add-after 'unpack 'remove-binary-blobs - (lambda _ - (for-each (lambda (file) - (delete-file file)) - (find-files "." "\\.bin$")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) From 5f8c11d48e4949aa77d7aaa1e7e25568bd8dfa97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2022 22:31:50 +0100 Subject: [PATCH 777/824] gnu: emacs-s: Do not use full-fledged Emacs to run tests. * gnu/packages/emacs-xyz.scm (emacs-s)[arguments]: Use emacs-minimal. --- gnu/packages/emacs-xyz.scm | 1 - 1 file changed, 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2eef75925a..3e4c8b38bc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -4700,7 +4700,6 @@ which is restored where possible when the file is loaded again.") (build-system emacs-build-system) (arguments `(#:tests? #t - #:emacs ,emacs ; FIXME: tests fail with emacs-minimal #:test-command '("./run-tests.sh"))) (home-page "https://github.com/magnars/s.el") (synopsis "Emacs string manipulation library") From 82c43b276dd5e60c81ad2c040a9d945befc4bc88 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 15 Nov 2022 14:05:36 -0500 Subject: [PATCH 778/824] gnu: linux-libre: Enable building info doc. * gnu/packages/patches/linux-libre-infodocs-target.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/linux.scm (linux-libre-6.0-source, linux-libre-5.15-source) (linux-libre-5.10-source): Apply above patch. (doc-supported?): New procedure. (make-linux-libre) [DOC-SUPPORTED?]: Add new patch in the default patches used. Add a BUILD-DOC? argument. (make-linux-libre*): Add a BUILD-DOC? argument. Validate BUILD-DOC? for supported VERSION. [arguments]: Conditionally add the build-doc and install-doc phases. [native-inputs]: Conditionally add fontconfig, graphviz, python-wrapper, python-sphinx, texinfo and which. --- gnu/local.mk | 3 +- gnu/packages/linux.scm | 273 ++++++++++-------- .../patches/linux-libre-infodocs-target.patch | 88 ++++++ 3 files changed, 250 insertions(+), 114 deletions(-) create mode 100644 gnu/packages/patches/linux-libre-infodocs-target.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3b0e6b0c2c..7278c50e4f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1482,7 +1482,8 @@ dist_patch_DATA = \ %D%/packages/patches/lierolibre-remove-arch-warning.patch \ %D%/packages/patches/lierolibre-try-building-other-arch.patch \ %D%/packages/patches/linbox-fix-pkgconfig.patch \ - %D%/packages/patches/linphone-desktop-without-sdk.patch \ + %D%/packages/patches/linphone-desktop-without-sdk.patch \ + %D%/packages/patches/linux-libre-infodocs-target.patch \ %D%/packages/patches/linux-libre-support-for-Pinebook-Pro.patch \ %D%/packages/patches/linux-pam-no-setfsuid.patch \ %D%/packages/patches/linuxdcpp-openssl-1.1.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 263772da7b..8727ddd76a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -33,7 +33,7 @@ ;;; Copyright © 2018, 2019 Pierre Langlois ;;; Copyright © 2018 Vasile Dumitrascu ;;; Copyright © 2019 Tim Gesthuizen -;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer +;;; Copyright © 2019, 2020, 2021, 2022 Maxim Cournoyer ;;; Copyright © 2019 Stefan Stefanović ;;; Copyright © 2019-2022 Brice Waegeneire ;;; Copyright © 2019 Kei Kebreau @@ -108,8 +108,9 @@ #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) - #:use-module (gnu packages flex) #:use-module (gnu packages file) + #:use-module (gnu packages flex) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -119,6 +120,7 @@ #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) #:use-module (gnu packages gperf) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-apps) @@ -494,17 +496,20 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (define-public linux-libre-6.0-source (source-with-patches linux-libre-6.0-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.15-source (source-with-patches linux-libre-5.15-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.10-source (source-with-patches linux-libre-5.10-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.4-source (source-with-patches linux-libre-5.4-pristine-source @@ -759,6 +764,11 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ;;; Kernel package utilities. ;;; +(define (doc-supported? version) + ;; Versions older than 5.10 have different enough build scripts that the + ;; infodocs patch doesn't apply. + (version>=? version "5.10")) + (define* (make-linux-libre version gnu-revision hash-string supported-systems #:key (extra-version #f) @@ -767,7 +777,13 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (configuration-file #f) (defconfig "defconfig") (extra-options %default-extra-linux-options) - (patches (list %boot-logo-patch))) + (build-doc? (doc-supported? version)) + (patches + `(,%boot-logo-patch + ,@(if build-doc? + (list (search-patch + "linux-libre-infodocs-target.patch")) + '())))) (make-linux-libre* version gnu-revision (origin (method url-fetch) @@ -778,7 +794,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." #:extra-version extra-version #:configuration-file configuration-file #:defconfig defconfig - #:extra-options extra-options)) + #:extra-options extra-options + #:build-doc? build-doc?)) (define* (make-linux-libre* version gnu-revision source supported-systems #:key @@ -787,7 +804,10 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ;; See kernel-config for an example. (configuration-file #f) (defconfig "defconfig") - (extra-options %default-extra-linux-options)) + (extra-options %default-extra-linux-options) + (build-doc? (doc-supported? version))) + (when (and build-doc? (not (doc-supported? version))) + (error "unsupported 'build-doc?' for kernels <5.10")) (package (name (if extra-version (string-append "linux-libre-" extra-version) @@ -796,11 +816,127 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (source source) (supported-systems supported-systems) (build-system gnu-build-system) + (arguments + (list + #:modules '((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1) + (srfi srfi-26) + (ice-9 ftw) + (ice-9 match)) + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/pwd + (lambda _ + (substitute* (find-files + "." "^Makefile(\\.include)?$") + (("/bin/pwd") "pwd")))) + #$@(if build-doc? + #~((add-before 'configure 'build-doc + (lambda _ + (substitute* "Documentation/Makefile" + ;; Remove problematic environment check script. + ((".*scripts/sphinx-pre-install.*") "")) + (invoke "make" "infodocs"))) + (add-after 'build-doc 'install-doc + (lambda _ + (with-directory-excursion "Documentation/output" + (invoke "make" "-C" "texinfo" "install-info" + (string-append "infodir=" #$output + "/share/info")))))) + #~()) + (replace 'configure + (lambda* (#:key inputs target #:allow-other-keys) + ;; Avoid introducing timestamps. + (setenv "KCONFIG_NOTIMESTAMP" "1") + (setenv "KBUILD_BUILD_TIMESTAMP" (getenv "SOURCE_DATE_EPOCH")) + + ;; Other variables useful for reproducibility. + (setenv "KBUILD_BUILD_USER" "guix") + (setenv "KBUILD_BUILD_HOST" "guix") + + ;; Set ARCH and CROSS_COMPILE. + (let ((arch #$(platform-linux-architecture + (lookup-platform-by-target-or-system + (or (%current-target-system) + (%current-system)))))) + (setenv "ARCH" arch) + (format #t "`ARCH' set to `~a'~%" (getenv "ARCH")) + + (when target + (setenv "CROSS_COMPILE" (string-append target "-")) + (format #t "`CROSS_COMPILE' set to `~a'~%" + (getenv "CROSS_COMPILE")))) + + (setenv "EXTRAVERSION" + #$(and extra-version + (string-append "-" extra-version))) + + (let ((config (assoc-ref inputs "kconfig"))) + + ;; Use a custom kernel configuration file or a default + ;; configuration file. + (if config + (begin + (copy-file config ".config") + (chmod ".config" #o666)) + (invoke "make" #$defconfig)) + + ;; Appending works even when the option wasn't in the + ;; file. The last one prevails if duplicated. + (let ((port (open-file ".config" "a")) + (extra-configuration #$(config->string extra-options))) + (display extra-configuration port) + (close-port port)) + + (invoke "make" "oldconfig")))) + (replace 'install + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (let ((moddir (string-append #$output "/lib/modules")) + (dtbdir (string-append #$output "/lib/dtbs"))) + ;; Install kernel image, kernel configuration and link map. + (for-each (lambda (file) (install-file file #$output)) + (find-files "." "^(\\.config|bzImage|zImage|Image\ +|vmlinuz|System\\.map|Module\\.symvers)$")) + ;; Install device tree files + (unless (null? (find-files "." "\\.dtb$")) + (mkdir-p dtbdir) + (invoke "make" (string-append "INSTALL_DTBS_PATH=" dtbdir) + "dtbs_install")) + ;; Install kernel modules + (mkdir-p moddir) + (invoke "make" + ;; Disable depmod because the Guix system's + ;; module directory is an union of potentially + ;; multiple packages. It is not possible to use + ;; depmod to usefully calculate a dependency + ;; graph while building only one of them. + "DEPMOD=true" + (string-append "MODULE_DIR=" moddir) + (string-append "INSTALL_PATH=" #$output) + (string-append "INSTALL_MOD_PATH=" #$output) + "INSTALL_MOD_STRIP=1" + "modules_install") + (let* ((versions (filter (lambda (name) + (not (string-prefix? "." name))) + (scandir moddir))) + (version (match versions + ((x) x)))) + ;; There are symlinks to the build and source directory. + ;; Both will point to target /tmp/guix-build* and thus + ;; not be useful in a profile. Delete the symlinks. + (false-if-file-not-found + (delete-file + (string-append moddir "/" version "/build"))) + (false-if-file-not-found + (delete-file + (string-append moddir "/" version "/source")))))))))) (native-inputs `(("perl" ,perl) ("bc" ,bc) ("openssl" ,openssl) - ("elfutils" ,elfutils) ; Needed to enable CONFIG_STACK_VALIDATION + ("elfutils" ,elfutils) ;needed to enable CONFIG_STACK_VALIDATION ("flex" ,flex) ("bison" ,bison) @@ -809,6 +945,18 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ("mpfr" ,mpfr) ("mpc" ,mpc) + ;; For generating the documentation. + ,@(if build-doc? + ;; TODO: remove fontconfig after the 5.10 kernel is dropped. + ;; Also replace python-wrapper by python at that time. + `(("fontconfig" ,fontconfig) + ("graphviz" ,graphviz) + ("python" ,python-wrapper) + ("python-sphinx" ,python-sphinx) + ("texinfo" ,texinfo) + ("which" ,which)) + '()) + ,@(match (let ((arch (platform-linux-architecture (lookup-platform-by-target-or-system (or (%current-target-system) @@ -817,115 +965,14 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (configuration-file arch #:variant (version-major+minor version)))) - (#f ;no config for this platform + (#f ;no config for this platform '()) ((? string? config) `(("kconfig" ,config)))))) - (arguments - (list #:modules '((guix build gnu-build-system) - (guix build utils) - (srfi srfi-1) - (srfi srfi-26) - (ice-9 ftw) - (ice-9 match)) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'patch-/bin/pwd - (lambda _ - (substitute* (find-files "." "^Makefile(\\.include)?$") - (("/bin/pwd") "pwd")))) - (replace 'configure - (lambda* (#:key inputs target #:allow-other-keys) - ;; Avoid introducing timestamps. - (setenv "KCONFIG_NOTIMESTAMP" "1") - (setenv "KBUILD_BUILD_TIMESTAMP" - (getenv "SOURCE_DATE_EPOCH")) - - ;; Other variables useful for reproducibility. - (setenv "KBUILD_BUILD_USER" "guix") - (setenv "KBUILD_BUILD_HOST" "guix") - - ;; Set ARCH and CROSS_COMPILE. - (let ((arch #$(platform-linux-architecture - (lookup-platform-by-target-or-system - (or (%current-target-system) - (%current-system)))))) - (setenv "ARCH" arch) - (format #t "`ARCH' set to `~a'~%" (getenv "ARCH")) - - (when target - (setenv "CROSS_COMPILE" (string-append target "-")) - (format #t "`CROSS_COMPILE' set to `~a'~%" - (getenv "CROSS_COMPILE")))) - - (setenv "EXTRAVERSION" - #$(and extra-version - (string-append "-" extra-version))) - - (let ((config (assoc-ref inputs "kconfig"))) - - ;; Use a custom kernel configuration file or a default - ;; configuration file. - (if config - (begin - (copy-file config ".config") - (chmod ".config" #o666)) - (invoke "make" #$defconfig)) - - ;; Appending works even when the option wasn't in the - ;; file. The last one prevails if duplicated. - (let ((port (open-file ".config" "a")) - (extra-configuration #$(config->string extra-options))) - (display extra-configuration port) - (close-port port)) - - (invoke "make" "oldconfig")))) - (replace 'install - (lambda* (#:key inputs native-inputs #:allow-other-keys) - (let ((moddir (string-append #$output "/lib/modules")) - (dtbdir (string-append #$output "/lib/dtbs"))) - ;; Install kernel image, kernel configuration and link map. - (for-each (lambda (file) (install-file file #$output)) - (find-files "." "^(\\.config|bzImage|zImage|Image|vmlinuz|System\\.map|Module\\.symvers)$")) - ;; Install device tree files - (unless (null? (find-files "." "\\.dtb$")) - (mkdir-p dtbdir) - (invoke "make" (string-append "INSTALL_DTBS_PATH=" dtbdir) - "dtbs_install")) - ;; Install kernel modules - (mkdir-p moddir) - (invoke "make" - ;; Disable depmod because the Guix system's - ;; module directory is an union of potentially - ;; multiple packages. It is not possible to use - ;; depmod to usefully calculate a dependency - ;; graph while building only one of them. - "DEPMOD=true" - (string-append "MODULE_DIR=" moddir) - (string-append "INSTALL_PATH=" #$output) - (string-append "INSTALL_MOD_PATH=" #$output) - "INSTALL_MOD_STRIP=1" - "modules_install") - (let* ((versions (filter (lambda (name) - (not (string-prefix? "." name))) - (scandir moddir))) - (version (match versions - ((x) x)))) - ;; There are symlinks to the build and source directory. - ;; Both will point to target /tmp/guix-build* and thus - ;; not be useful in a profile. Delete the symlinks. - (false-if-file-not-found - (delete-file - (string-append moddir "/" version "/build"))) - (false-if-file-not-found - (delete-file - (string-append moddir "/" version "/source")))))))) - #:tests? #f)) (home-page "https://www.gnu.org/software/linux-libre/") (synopsis "100% free redistribution of a cleaned Linux kernel") - (description - "GNU Linux-Libre is a free (as in freedom) variant of the Linux kernel. -It has been modified to remove all non-free binary blobs.") + (description "GNU Linux-Libre is a free (as in freedom) variant of the +Linux kernel. It has been modified to remove all non-free binary blobs.") (license license:gpl2) (properties '((max-silent-time . 3600))))) ;don't timeout on blob scan. diff --git a/gnu/packages/patches/linux-libre-infodocs-target.patch b/gnu/packages/patches/linux-libre-infodocs-target.patch new file mode 100644 index 0000000000..e9e6495c26 --- /dev/null +++ b/gnu/packages/patches/linux-libre-infodocs-target.patch @@ -0,0 +1,88 @@ +Upstream status: https://marc.info/?l=linux-doc&m=166861669723994&w=2 + +From 7edb5b278ee383ff9bed525329b2cdbe22317bf2 Mon Sep 17 00:00:00 2001 +From: Maxim Cournoyer +Date: Mon, 14 Nov 2022 22:51:11 -0500 +Subject: [PATCH] doc: add texinfodocs and infodocs targets + +Sphinx supports generating Texinfo sources and Info documentation, +which can be navigated easily and is convenient to search (via the +indexed nodes or anchors, for example). + +This change also causes the html output to appear under its own output +sub-directory, which makes it easier to install, since it's clean from +.doctrees or other output formats. + +Signed-off-by: Maxim Cournoyer +--- + Documentation/Makefile | 13 ++++++++++++- + Documentation/userspace-api/media/Makefile | 3 ++- + Makefile | 2 +- + 3 files changed, 15 insertions(+), 3 deletions(-) + +diff --git a/Documentation/Makefile b/Documentation/Makefile +index 64d44c1ecad3..bd8dac560633 100644 +--- a/Documentation/Makefile ++++ b/Documentation/Makefile +@@ -93,7 +93,16 @@ quiet_cmd_sphinx = SPHINX $@ --> file://$(abspath $(BUILDDIR)/$3/$4) + + htmldocs: + @$(srctree)/scripts/sphinx-pre-install --version-check +- @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,html,$(var),,$(var))) ++ @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,html,$(var),html,$(var))) ++ ++texinfodocs: ++ @$(srctree)/scripts/sphinx-pre-install --version-check ++ @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,texinfo,$(var),texinfo,$(var))) ++ ++# Note: the 'info' Make target is generated by sphinx itself when ++# running the texinfodocs target define above. ++infodocs: texinfodocs ++ $(MAKE) -C $(BUILDDIR)/texinfo info + + linkcheckdocs: + @$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,linkcheck,$(var),,$(var))) +@@ -143,6 +152,8 @@ cleandocs: + dochelp: + @echo ' Linux kernel internal documentation in different formats from ReST:' + @echo ' htmldocs - HTML' ++ @echo ' texinfodocs - Texinfo' ++ @echo ' infodocs - Info' + @echo ' latexdocs - LaTeX' + @echo ' pdfdocs - PDF' + @echo ' epubdocs - EPUB' +diff --git a/Documentation/userspace-api/media/Makefile b/Documentation/userspace-api/media/Makefile +index 00922aa7efde..3d8aaf5c253b 100644 +--- a/Documentation/userspace-api/media/Makefile ++++ b/Documentation/userspace-api/media/Makefile +@@ -47,10 +47,11 @@ $(BUILDDIR)/lirc.h.rst: ${UAPI}/lirc.h ${PARSER} $(SRC_DIR)/lirc.h.rst.exception + + # Media build rules + +-.PHONY: all html epub xml latex ++.PHONY: all html texinfo epub xml latex + + all: $(IMGDOT) $(BUILDDIR) ${TARGETS} + html: all ++texinfo: all + epub: all + xml: all + latex: $(IMGPDF) all +diff --git a/Makefile b/Makefile +index 58cd4f5e1c3a..b3266c408b6c 100644 +--- a/Makefile ++++ b/Makefile +@@ -1785,7 +1785,7 @@ $(help-board-dirs): help-%: + # Documentation targets + # --------------------------------------------------------------------------- + DOC_TARGETS := xmldocs latexdocs pdfdocs htmldocs epubdocs cleandocs \ +- linkcheckdocs dochelp refcheckdocs ++ linkcheckdocs dochelp refcheckdocs texinfodocs infodocs + PHONY += $(DOC_TARGETS) + $(DOC_TARGETS): + $(Q)$(MAKE) $(build)=Documentation $@ + +base-commit: 81e7cfa3a9eb4ba6993a9c71772fdab21bc5d870 +-- +2.38.1 + From 84136e95b27753eae010ea183a77b653c80f134d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 18:12:11 +0100 Subject: [PATCH 779/824] gnu: emacs-inspector: Fix base version. * gnu/packages/emacs-xyz.scm (emacs-inspector)[version]: Use "0.8" as base version, which is the version from "inspector.el" instead of "tree-inspector.el". --- gnu/packages/emacs-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3e4c8b38bc..cde1725185 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -559,7 +559,7 @@ configuration language which makes it trivial to write your own themes.") (revision "0")) (package (name "emacs-inspector") - (version (git-version "0.3" revision commit)) + (version (git-version "0.8" revision commit)) (source (origin (uri (git-reference From fa5701964d8946d87b999e1eb18f7881b047c54e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 23:29:10 +0100 Subject: [PATCH 780/824] gnu: emacs-inspector: Activate tests. * gnu/packages/emacs-xyz.scm (emacs-inspector)[arguments]: Add tests. Skip failing test. Fix compatibility with Emacs 28 and older. --- gnu/packages/emacs-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index cde1725185..3f6f69c3c4 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -570,6 +570,28 @@ configuration language which makes it trivial to write your own themes.") (base32 "0n72sqn29b5sya686cicgp40mkk5x5821b7bw4zs6dcl82cyij5n")) (file-name (git-file-name name version)))) (build-system emacs-build-system) + (arguments + (list + #:tests? #t + #:test-command #~(list "emacs" "-Q" "--batch" + "-L" "." + "-l" "inspector-tests.el" + "-l" "tree-inspector-tests.el" + "-f" "ert-run-tests-batch-and-exit") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'preserve-emacs-28-compatibility + ;; XXX: `cl-constantly' function is defined in "cl-lib" starting + ;; from Emacs 29+. For now, replace it with its definition. + (lambda _ + (substitute* "tree-inspector.el" + (("cl-constantly") "lambda (_)")))) + (add-before 'check 'skip-failing-test + (lambda _ + (substitute* "tree-inspector-tests.el" + (("\\(ert-deftest inspector-tests--inspect-struct-test.*" all) + (string-append all " (skip-unless nil)")))))))) + (native-inputs (list emacs-ert-runner)) (propagated-inputs (list emacs-treeview)) (home-page "https://github.com/mmontone/emacs-inspector") (synopsis "Inspection tool for Emacs Lisp objects") From d858714ffc9095999a5538815e44dc453516fd0c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 23:36:03 +0100 Subject: [PATCH 781/824] gnu: burgerspace: Update to 1.9.5. * gnu/packages/games.scm (burgerspace): Update to 1.9.5. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 78327956be..495fdf0f2d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -10451,14 +10451,14 @@ get high scores.") (define-public burgerspace (package (name "burgerspace") - (version "1.9.4") + (version "1.9.5") (source (origin (method url-fetch) (uri (string-append "http://perso.b2b2c.ca/~sarrazip/dev/" "burgerspace-" version ".tar.gz")) (sha256 - (base32 "1xb4immzmd419aa08lgkzf7ibxa6ax238zb2l5iw9nkgvzlh1v6l")))) + (base32 "1r2albqv2ygs58rwcldsx1mp2vy96j7k4yw5jjmvwgnxjmddq7wr")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) From 94907932b8492a9b8373b09c335e0a228427cc83 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 23:45:05 +0100 Subject: [PATCH 782/824] gnu: emacs-flymake-mypy: Update to 0.3.0. * gnu/packages/emacs-xyz.scm (emacs-flymake-mypy): Update to 0.3.0. --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3f6f69c3c4..3db632d4a3 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -34026,16 +34026,16 @@ into the current buffer.") (revision "0")) (package (name "emacs-flymake-mypy") - (version (git-version "0.2.0" revision commit)) + (version "0.3.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/com4/flymake-mypy") - (commit commit))) + (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "124pfa1kwrapwylbrvkzg3jwcmlsvfklg33ms9ki32khvglmff5h")))) + "1zaa2kljsmm13layqmb7dwd7l2x3a5ymzzmzjjhykc67kbyjvvkk")))) (build-system emacs-build-system) (home-page "https://github.com/com4/flymake-mypy") (synopsis "Flymake checker for mypy") From 5eb2995c006283fc0b649f10a6d002580ccac8d6 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Thu, 24 Nov 2022 23:47:32 +0100 Subject: [PATCH 783/824] gnu: emacs-popon: Update to 0.12. * gnu/packages/emacs-xyz.scm (emacs-popon): Update to 0.12. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3db632d4a3..5d6f4d040f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33820,7 +33820,7 @@ with popups, which also work in the terminal.") (define-public emacs-popon (package (name "emacs-popon") - (version "0.11") + (version "0.12") (source (origin (method git-fetch) @@ -33830,7 +33830,7 @@ with popups, which also work in the terminal.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "14hf1n9d7rqfzr58kjsvjq63v3iamk3szvcn6zms7ry8x70v3lmv")))) + (base32 "0wkydg326ql8cvvmibq1nf6y40d1b0ax0p892pwncmi7awnf20gr")))) (build-system emacs-build-system) (home-page "https://codeberg.org/akib/emacs-popon/") (synopsis "Pop floating text on a window") From d524ec6fb595adbd33d3efda562041bb59d7505a Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 21 Nov 2022 14:49:04 -0500 Subject: [PATCH 784/824] doc: Add a security keys section to the cookbook. * doc/guix-cookbook.texi (Top): Register new menu. (System Configuration): Likewise. (Using security keys): New section. --- doc/guix-cookbook.texi | 62 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/doc/guix-cookbook.texi b/doc/guix-cookbook.texi index f371364746..af08d4ed54 100644 --- a/doc/guix-cookbook.texi +++ b/doc/guix-cookbook.texi @@ -21,6 +21,7 @@ Copyright @copyright{} 2020 Brice Waegeneire@* Copyright @copyright{} 2020 André Batista@* Copyright @copyright{} 2020 Christine Lemmer-Webber@* Copyright @copyright{} 2021 Joshua Branson@* +Copyright @copyright{} 2022 Maxim Cournoyer* Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or @@ -95,6 +96,7 @@ System Configuration * Auto-Login to a Specific TTY:: Automatically Login a User to a Specific TTY * Customizing the Kernel:: Creating and using a custom Linux kernel on Guix System. * Guix System Image API:: Customizing images to target specific platforms. +* Using security keys:: How to use security keys with Guix System. * Connecting to Wireguard VPN:: Connecting to a Wireguard VPN. * Customizing a Window Manager:: Handle customization of a Window manager on Guix System. * Running Guix on a Linode Server:: Running Guix on a Linode Server. Running Guix on a Linode Server @@ -1380,6 +1382,7 @@ reference. * Auto-Login to a Specific TTY:: Automatically Login a User to a Specific TTY * Customizing the Kernel:: Creating and using a custom Linux kernel on Guix System. * Guix System Image API:: Customizing images to target specific platforms. +* Using security keys:: How to use security keys with Guix System. * Connecting to Wireguard VPN:: Connecting to a Wireguard VPN. * Customizing a Window Manager:: Handle customization of a Window manager on Guix System. * Running Guix on a Linode Server:: Running Guix on a Linode Server @@ -1883,6 +1886,65 @@ guix system image --image-type=hurd-qcow2 my-hurd-os.scm will instead produce a Hurd QEMU image. +@node Using security keys +@section Using security keys +@cindex 2FA, two-factor authentication +@cindex U2F, Universal 2nd Factor +@cindex security key, configuration + +The use of security keys can improve your security by providing a second +authentication source that cannot be easily stolen or copied, at least +for a remote adversary (something that you have), to the main secret (a +passphrase -- something that you know), reducing the risk of +impersonation. + +The example configuration detailed below showcases what minimal +configuration needs to be made on your Guix System to allow the use of a +Yubico security key. It is hoped the configuration can be useful for +other security keys as well, with minor adjustments. + +@subsection Configuration for use as a two-factor authenticator (2FA) + +To be usable, the udev rules of the system should be extended with +key-specific rules. The following shows how to extend your udev rules +with the @file{lib/udev/rules.d/70-u2f.rules} udev rule file provided by +the @code{libfido2} package from the @code{(gnu packages +security-token)} module and add your user to the @samp{"plugdev"} group +it uses: + +@lisp +(use-package-modules ... security-token ...) +... +(operating-system + ... + (users (cons* (user-account + (name "your-user") + (group "users") + (supplementary-groups + '("wheel" "netdev" "audio" "video" + "plugdev")) ;<- added system group + (home-directory "/home/your-user")) + %base-user-accounts)) + ... + (services + (cons* + ... + (udev-rules-service 'fido2 libfido2 #:groups '("plugdev"))))) +@end lisp + +After re-configuring your system and re-logging in your graphical +session so that the new group is in effect for your user, you can verify +that your key is usable by launching: + +@example +guix shell ungoogled-chromium -- chromium chrome://settings/securityKeys +@end example + +and validating that the security key can be reset via the ``Reset your +security key'' menu. If it works, congratulations, your security key is +ready to be used with applications supporting two-factor authentication +(2FA). + @node Connecting to Wireguard VPN @section Connecting to Wireguard VPN From 77fe40060da0f6dd2db0e3dabe5c24ed616d84af Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 25 Nov 2022 09:51:46 +0100 Subject: [PATCH 785/824] gnu: p2pool: Update to 2.5. * gnu/packages/finance.scm (p2pool): Update to 2.5. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index c8f3ee9d1d..d068ef0b5f 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -2190,7 +2190,7 @@ mining.") (define-public p2pool (package (name "p2pool") - (version "2.2.1") + (version "2.5") (source (origin (method git-fetch) @@ -2199,7 +2199,7 @@ mining.") (commit (string-append "v" version)) (recursive? #t))) (file-name (git-file-name name version)) - (sha256 (base32 "19pn7axj96yvza2x7678rs79c2vgmhl8d7f9ki72v2n6l2630fw8")) + (sha256 (base32 "1kdsxh6f24zp7h7bwkrin2mc81ysfny5wprzgy41h2bc6dpq067w")) (modules '((guix build utils))) (snippet #~(for-each delete-file-recursively From 4777c104beaa9f3f75db5476432b26557d2325c2 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 25 Nov 2022 09:54:08 +0100 Subject: [PATCH 786/824] gnu: xmrig: Update to 6.18.1. * gnu/packages/finance.scm (xmrig): Update to 6.18.1. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index d068ef0b5f..0866688ea3 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -2134,7 +2134,7 @@ and manipulation.") (define-public xmrig (package (name "xmrig") - (version "6.18.0") + (version "6.18.1") (source (origin (method git-fetch) @@ -2142,7 +2142,7 @@ and manipulation.") (url "https://github.com/xmrig/xmrig") (commit (string-append "v" version)))) (file-name (git-file-name name version)) - (sha256 (base32 "1ncnfjpjwjdv29plyiam2nh01bfni49sgfi3qkijygi1450w71dx")) + (sha256 (base32 "0f0kly374pkgnpnx60hac0bg9297a5zhycss6p37iavayn28jg39")) (modules '((guix build utils))) (snippet ;; TODO: Try to use system libraries instead of bundled ones in From 753a88c980ddba4ee30118d7c01b3ad75ef8922d Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 25 Nov 2022 09:58:51 +0100 Subject: [PATCH 787/824] gnu: electron-cash: Update to 4.2.12. * gnu/packages/finance.scm (electron-cash): Update to 4.2.12. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 0866688ea3..3a94666728 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -628,7 +628,7 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (define-public electron-cash (package (name "electron-cash") - (version "4.2.11") + (version "4.2.12") (source (origin (method git-fetch) @@ -637,7 +637,7 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1g0xnb63c52l379zrqkfhxlkg1d2hf2dgjs2swspa0vah845r282")))) + (base32 "1bfnfpdyi3q5zq0zj07dq82aj3cihnr7j82gy4ch97182lsl6nms")))) (build-system python-build-system) (arguments (list From 045b86826111f163e170ab528c831dd81ff21db8 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 25 Nov 2022 10:03:39 +0100 Subject: [PATCH 788/824] gnu: electrum: Update to 4.3.2. * gnu/packages/finance.scm (electrum): Update to 4.3.2. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 3a94666728..ae63fbd9b0 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -553,7 +553,7 @@ do so.") (define-public electrum (package (name "electrum") - (version "4.2.1") + (version "4.3.2") (source (origin (method url-fetch) @@ -561,7 +561,7 @@ do so.") version "/Electrum-" version ".tar.gz")) (sha256 - (base32 "0w41411zq07kx0351wxkmpn0wr42wd2nx0m6v0iwvpsggx654b6r")) + (base32 "1kbyinm9fnxpx9chkyd11yr9rxvcxvw3ml7kzvxcfa8v7jnl0dmx")) (modules '((guix build utils))) (snippet '(begin From 63374ef9b9c7ebd374bed6630783b020e45e576f Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 25 Nov 2022 01:42:52 +0000 Subject: [PATCH 789/824] gnu: Add cl-concurrent-hash-tables. * gnu/packages/lisp-xyz.scm (sbcl-concurrent-hash-tables, cl-concurrent-hash-tables, ecl-concurrent-hash-tables): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 270d55af67..61de232697 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -14232,6 +14232,39 @@ directly.") (define-public ecl-custom-hash-table (sbcl-package->ecl-package sbcl-custom-hash-table)) +(define-public sbcl-concurrent-hash-tables + (let ((commit "1b9f0b5da54fece4f42296e1bdacfcec0c370a5a") + (revision "0")) + (package + (name "sbcl-concurrent-hash-tables") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/no-defun-allowed/concurrent-hash-tables") + (commit commit))) + (file-name (git-file-name "cl-concurrent-hash-tables" version)) + (sha256 + (base32 "03g24ycr1ngzg8bv10iwp1bmnldz5bxbfdqrzhfxhicpibh49r96")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-atomics sbcl-bordeaux-threads)) + (home-page "https://github.com/no-defun-allowed/concurrent-hash-tables") + (synopsis "Portability library for concurrent hash tables in Common Lisp") + (description "@code{concurrent-hash-tables} is a Common Lisp portability +library wrapping some implementations of concurrent hash tables which do not +have to be entirely locked in their operation, including +@code{42nd-at-threadmill}, @code{luckless}, and a fallback, segmented hash +table.") + (license license:bsd-2)))) + +(define-public cl-concurrent-hash-tables + (sbcl-package->cl-source-package sbcl-concurrent-hash-tables)) + +(define-public ecl-concurrent-hash-tables + (sbcl-package->ecl-package sbcl-concurrent-hash-tables)) + (define-public sbcl-collectors (let ((commit "13acef25d8422d1d82e067b1861e513587c166ee")) (package From fe09d32e34d30c92587536b581361e8c9be850f2 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 25 Nov 2022 06:58:38 +0000 Subject: [PATCH 790/824] gnu: Add cl-atomichron. * gnu/packages/lisp-xyz.scm (sbcl-atomichron, cl-atomichron, ecl-atomichron): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 61de232697..190061b855 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -15376,6 +15376,40 @@ determine the cost of certain actions on a given platform and implementation.") (define-public ecl-the-cost-of-nothing (sbcl-package->ecl-package sbcl-the-cost-of-nothing)) +(define-public sbcl-atomichron + (let ((commit "5b3578bbad8c37ab559e56924d98c373efe11de5") + (revision "0")) + (package + (name "sbcl-atomichron") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/no-defun-allowed/atomichron") + (commit commit))) + (file-name (git-file-name "cl-atomichron" version)) + (sha256 + (base32 "1fmmhb3pbv7j4d1cc02zv24bpd0kd2agfjjcj46w3gmv1bb0hva1")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-atomics sbcl-bordeaux-threads)) + (home-page "https://github.com/no-defun-allowed/atomichron") + (synopsis "Atomic metering library for Common Lisp") + (description + "@code{atomichron} is a Common Lisp library which implements a time +meter which tracks how many times a form is evaluated, and how long evaluation +takes. It uses atomic instructions so that meters will present correct +results in the presence of multiple threads, while trying to minimize +synchronization latency.") + (license license:bsd-2)))) + +(define-public cl-atomichron + (sbcl-package->cl-source-package sbcl-atomichron)) + +(define-public ecl-atomichron + (sbcl-package->ecl-package sbcl-atomichron)) + (define-public sbcl-glyphs (let ((commit "1ff5714e8c1dca327bc604dfe3e3d1f4b7755373")) (package From 5c93d5136622df41ca799d122a4d1d6cfd6b28d5 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 25 Nov 2022 07:12:23 +0000 Subject: [PATCH 791/824] gnu: Add cl-marray. * gnu/packages/lisp-xyz.scm (sbcl-marray, cl-marray): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 190061b855..aee311c2dd 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -13061,6 +13061,44 @@ than a few Kb.") (define-public ecl-mmap (sbcl-package->ecl-package sbcl-mmap)) +(define-public sbcl-marray + (let ((commit "0352f316b6830f0b119088ba9be836e4726bd7d8") + (revision "0")) + (package + (name "sbcl-marray") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/death/marray") + (commit commit))) + (file-name (git-file-name "cl-marray" version)) + (sha256 + (base32 "0l4kvzpiw14vqhlsaflp3c7y51vznjjgbdi0q3axqk1wxvzy1zlx")))) + (build-system asdf-build-system/sbcl) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda _ + (substitute* "marray.asd" + ((":components") + ":depends-on (#+sbcl \"sb-posix\")\n :components"))))))) + (home-page "https://github.com/death/marray") + (synopsis "Memory-mapped files as Common Lisp arrays") + (description + "MARRAY is a library which provides access to memory-mapped files +through Common Lisp arrays.") + (license license:expat)))) + +(define-public cl-marray + (sbcl-package->cl-source-package sbcl-marray)) + +;; ECL support not implemented yet. +;; (define-public ecl-marray +;; (sbcl-package->ecl-package sbcl-marray)) + (define-public sbcl-3bz (let ((commit "569614c40408f3aefc77ba233e0e4bd66d3850ad") (revision "1")) From 13eafd67301b37b6490d666c4f78d6c26337c052 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 25 Nov 2022 07:29:56 +0000 Subject: [PATCH 792/824] gnu: Add cl-file-notify. * gnu/packages/lisp-xyz.scm (sbcl-file-notify, cl-file-notify, ecl-file-notify): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index aee311c2dd..56178a82cd 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -490,6 +490,39 @@ interface to the Linux inotify API.") (define-public ecl-cl-inotify (sbcl-package->ecl-package sbcl-cl-inotify)) +(define-public sbcl-file-notify + (let ((commit "f12dc2f2aae5fee13355cd93a8cae0c4c412b76d") + (revision "0")) + (package + (name "sbcl-file-notify") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/file-notify") + (commit commit))) + (file-name (git-file-name "cl-file-notify" version)) + (sha256 + (base32 "0788d98rqm1krl8nbfh8qshvyf6g336i9bqrdhkx06cfvbh0wcny")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-cffi + sbcl-documentation-utils + sbcl-trivial-features)) + (home-page "https://github.com/Shinmera/file-notify") + (synopsis "Get notifications for file accesses and changes") + (description + "File-Notify is a Common Lisp library for getting notifications for file +accesses and changes.") + (license license:zlib)))) + +(define-public cl-file-notify + (sbcl-package->cl-source-package sbcl-file-notify)) + +(define-public ecl-file-notify + (sbcl-package->ecl-package sbcl-file-notify)) + (define-public sbcl-bodge-queue (let ((commit "948c9a501dcd412689952d09eb7453ec2722336a") (revision "0")) From d0b4baf51f8a3b79923de5348f3d4a5cdf164e33 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Fri, 25 Nov 2022 07:48:02 +0000 Subject: [PATCH 793/824] gnu: Add cl-system-load. * gnu/packages/lisp-xyz.scm (sbcl-system-load, cl-system-load, ecl-system-load): New variables. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 56178a82cd..ad2da5fa82 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -16966,6 +16966,35 @@ return the CPU count of the current system.") (define-public cl-cpus (sbcl-package->cl-source-package sbcl-cl-cpus)) +(define-public sbcl-system-load + (let ((commit "3ff1a40be55866cc5316ac7a530d872b12510294") + (revision "0")) + (package + (name "sbcl-system-load") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/system-load") + (commit commit))) + (file-name (git-file-name "cl-system-load" version)) + (sha256 + (base32 "08d8kr8j5l2m8p69f47iklxhna394vx9mrys0sgplf5f2bqb7xcv")))) + (build-system asdf-build-system/sbcl) + (home-page "https://github.com/Shinmera/system-load") + (synopsis "Access system's CPU and memory usage from Common Lisp") + (description + "System-Load is a Common Lisp library for accessing the system's CPU and +memory usage.") + (license license:zlib)))) + +(define-public cl-system-load + (sbcl-package->cl-source-package sbcl-system-load)) + +(define-public ecl-system-load + (sbcl-package->ecl-package sbcl-system-load)) + (define-public sbcl-fof (let ((commit "522879e7da110ecf2e841998b197b34062c54b29") (revision "1")) From 79e40b6ce8e4f5f499ea338aede75a0810a210c1 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Fri, 25 Nov 2022 10:52:16 +0100 Subject: [PATCH 794/824] gnu: bitcoin-core: Update to 23.0. According to , versions 0.20 and 0.21 have passed end of life. * gnu/packages/finance.scm (bitcoin-core): Update to 23.0. (bitcoin-core-23.0): New variable. (bitcoin-core-0.20, bitcoin-core-0.21): Remove variables. --- gnu/packages/finance.scm | 21 ++++----------------- 1 file changed, 4 insertions(+), 17 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index ae63fbd9b0..feb533eca7 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -129,10 +129,10 @@ #:use-module (gnu packages xml) #:use-module (gnu packages gnuzilla)) -(define-public bitcoin-core-0.21 +(define-public bitcoin-core-23.0 (package (name "bitcoin-core") - (version "0.21.2") + (version "23.0") (source (origin (method url-fetch) (uri @@ -140,7 +140,7 @@ version "/bitcoin-" version ".tar.gz")) (sha256 (base32 - "17nvir1yc6mf4wr1fn4xsabw49cd5p9vig8wj77vv4anzi8zfij1")))) + "01fcb90pqip3v77kljykx51cmg7jdg2cmp7ys0a40svdkps8nx16")))) (build-system gnu-build-system) (native-inputs (list autoconf @@ -207,23 +207,10 @@ of the bitcoin protocol. This package provides the Bitcoin Core command line client and a client based on Qt.") (license license:expat))) -(define-public bitcoin-core-0.20 - (package - (inherit bitcoin-core-0.21) - (version "0.20.2") - (source (origin - (method url-fetch) - (uri - (string-append "https://bitcoincore.org/bin/bitcoin-core-" - version "/bitcoin-" version ".tar.gz")) - (sha256 - (base32 - "14smp5vmh7baabl856wlg7w7y5910jhx6c02mlkm4hkywf3yylky")))))) - ;; The support lifetimes for bitcoin-core versions can be found in ;; . -(define-public bitcoin-core bitcoin-core-0.21) +(define-public bitcoin-core bitcoin-core-23.0) (define-public hledger (package From b095dac8e0aeb9a61ecffd53bfa6f60f49b31f54 Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Fri, 25 Nov 2022 11:03:05 +0100 Subject: [PATCH 795/824] gnu: Add r-btools. * gnu/packages/bioinformatics.scm (r-btools): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d7097c42c..6c6ff3e25a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Felix Gruber +;;; Copyright © 2022 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; @@ -535,6 +536,42 @@ BED, GFF/GTF, VCF.") and utilities for PacBio C++ applications.") (license license:bsd-3)))) +(define-public r-btools + (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") + (revision "1")) + (package + (name "r-btools") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbattaglia/btools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bca593dnxz6xdywpdi0ipli0paln2b3bfxxj0csnmj55ryrz428")))) + (properties `((upstream-name . "btools"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomformat + r-coin + r-deseq2 + r-dplyr + r-genefilter + r-phyloseq + r-picante + r-plotly + r-reshape2 + r-stringr + r-vegan)) + (home-page "https://github.com/twbattaglia/btools") + (synopsis "R functions for microbial diversity analyses") + (description + "This package provides an assortment of R functions that is suitable +for all types of microbial diversity analyses.") + (license license:expat)))) + (define-public pbbam (package (name "pbbam") From 123e6f5f2422f573673a5fdce88d88014bcbe0f1 Mon Sep 17 00:00:00 2001 From: Ahriman Date: Thu, 24 Nov 2022 15:15:05 +0000 Subject: [PATCH 796/824] gnu: Add raider. * gnu/packages/gnome.scm (raider): New variable. Signed-off-by: Christopher Baines --- gnu/packages/gnome.scm | 51 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 9cebf618e0..f81b44cca2 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4961,6 +4961,57 @@ GLibproxyResolver, and a GNOME GProxyResolver that uses the proxy information from the GSettings schemas in gsettings-desktop-schemas.") (license license:lgpl2.1+))) +(define-public raider + (package + (name "raider") + (version "1.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ADBeveridge/raider/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ll9220d6qf9m7wdi5xhq69p8h8whs7l5h5nzdhlbn99qh5388bz")))) + (build-system meson-build-system) + (arguments + (list #:meson meson-0.63 + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "data/com.github.ADBeveridge.Raider.gschema.xml" + (("/usr/bin/shred") + (which "shred"))))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/raider") + `("GSETTINGS_SCHEMA_DIR" = + (,(string-append (assoc-ref outputs "out") + "/share/glib-2.0/schemas"))))))))) + (native-inputs + (list gettext-minimal + pkg-config + cmake + `(,glib "bin") + desktop-file-utils + itstool + gobject-introspection + blueprint-compiler + `(,gtk "bin"))) + (inputs + (list libadwaita + gtk)) + (home-page "https://github.com/ADBeveridge/raider") + (synopsis "Securely delete your files") + (description + "Raider is a simple shredding program built for GNOME. Also known as +File Shredder, it uses the GNU Core Utility called shred to securely delete +files.") + (license license:gpl3+))) + (define-public rest (package (name "rest") From 6827d76d383be2a0ef655767fb1420cf641f9790 Mon Sep 17 00:00:00 2001 From: conses Date: Thu, 24 Nov 2022 17:21:26 +0100 Subject: [PATCH 797/824] gnu: Add portfolio. * gnu/packages/gnome-xyz.scm (portfolio): New variable. Signed-off-by: Christopher Baines --- gnu/packages/gnome-xyz.scm | 54 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index b7e10100fb..0368ccc223 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -55,6 +55,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages build-tools) #:use-module (gnu packages check) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) @@ -304,6 +305,59 @@ and products. Plots is designed to integrate well with the GNOME desktop and takes advantage of modern hardware using OpenGL.") (license license:gpl3+))) +(define-public portfolio + (package + (name "portfolio") + (version "0.9.14") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchx84/Portfolio") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0h09v8lhz3kv6qmwjhx3gr7rp6ccfhrzm54gjnaixl4dcg9zddls")))) + (arguments + (list #:glib-or-gtk? #t + #:imported-modules `(,@%meson-build-system-modules + (guix build python-build-system)) + #:modules '((guix build meson-build-system) + ((guix build python-build-system) + #:prefix python:) + (guix build utils)) + #:phases #~(modify-phases %standard-phases + (add-after 'install 'rename-executable + (lambda _ + (with-directory-excursion (string-append #$output + "/bin") + (symlink "dev.tchx84.Portfolio" "portfolio")))) + (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (search-input-file outputs + "bin/dev.tchx84.Portfolio") + `("GUIX_PYTHONPATH" = + (,(getenv "GUIX_PYTHONPATH") ,(python:site-packages + inputs + outputs))) + `("GI_TYPELIB_PATH" = + (,(getenv "GI_TYPELIB_PATH"))))))))) + (build-system meson-build-system) + (inputs (list bash-minimal python-pygobject gtk+ libhandy)) + (native-inputs + (list desktop-file-utils + gettext-minimal + `(,glib "bin") + `(,gtk+ "bin") + python)) + (home-page "https://github.com/tchx84/Portfolio") + (synopsis "Minimalist file manager for Linux mobile devices") + (description + "Portfolio is a minimalist file manager for those who want to use Linux +mobile devices. Tap to activate and long press to select, to browse, open, +copy, move, delete, or edit your files.") + (license license:gpl3+))) + (define-public gnome-shell-extension-unite-shell (package (name "gnome-shell-extension-unite-shell") From 3271fa1f402e497ff1de9cc2dbc2b09e1a32078f Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 24 Nov 2022 11:24:37 +0000 Subject: [PATCH 798/824] gnu: Add python-drms. * gnu/packages/astronomy.scm (python-drms): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index d450d1dd94..fb45a83b34 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1142,6 +1142,43 @@ attempting to maintain ISTP compliance @end itemize") (license license:expat))) +(define-public python-drms + (package + (name "python-drms") + (version "0.6.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "drms" version)) + (sha256 + (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? + #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (setenv "JSOC_EMAIL" "jsoc@sunpy.org") + (invoke "python" "-m" "pytest" "-vv"))))))) + (native-inputs + (list python-astropy + python-pytest-astropy + python-pytest + python-setuptools-scm)) + (propagated-inputs (list python-numpy python-pandas)) + (home-page "https://sunpy.org") + (synopsis "Access astronomical HMI, AIA and MDI data with Python") + (description + "DRMS module provides an easy-to-use interface for accessing HMI, AIA and +MDI data with Python. It uses the publicly accessible +JSOC (@url{http://jsoc.stanford.edu/}) DRMS server by default, but can also be +used with local NetDRMS sites.") + (license license:bsd-2))) + (define-public python-ephem (package (name "python-ephem") From 0458cbd84c03068241dfaf293b0594ec07dc2019 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 24 Nov 2022 11:24:38 +0000 Subject: [PATCH 799/824] gnu: Add python-mpl-animators. * gnu/packages/astronomy.scm (python-mpl-animators): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index fb45a83b34..e9409cbade 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1202,6 +1202,32 @@ for a table giving the position of a planet, asteroid, or comet for a series of dates.") (license license:expat))) +(define-public python-mpl-animators + (package + (name "python-mpl-animators") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mpl_animators" version)) + (sha256 + (base32 "12kjmj7rn3pk9ly82h5s5hn0kl3kxkr7bgkz9zr9k59pir8z1r8b")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest + python-pytest-mpl + python-setuptools-scm)) + (propagated-inputs + (list python-astropy + python-matplotlib + python-numpy)) + (home-page "https://sunpy.org") + (synopsis "Interactive animations with matplotlib") + (description + "The @code{mpl_animators} package provides a set of classes which allow +the easy construction of interactive matplotlib widget based animations.") + (license license:bsd-3))) + (define-public python-photutils (package (name "python-photutils") From 0575012803683ebacd43029530683af7bdf791f9 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 24 Nov 2022 11:24:39 +0000 Subject: [PATCH 800/824] gnu: Add python-hvpy. * gnu/packages/astronomy.scm (python-hvpy): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index e9409cbade..492b871e12 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1202,6 +1202,27 @@ for a table giving the position of a planet, asteroid, or comet for a series of dates.") (license license:expat))) +(define-public python-hvpy + (package + (name "python-hvpy") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "hvpy" version)) + (sha256 + (base32 "0r0asyflz2sw9zn5vgs138nh81m0rbwbakmrncbc1ghdr3g6jahv")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org + (propagated-inputs (list python-pydantic python-requests)) + (native-inputs (list python-pytest python-pytest-astropy)) + (home-page "https://helioviewer.org/") + (synopsis "Helioviewer Python API Wrapper") + (description "@code{hvpy} is a Python API wrapper around the formal +@url{Helioviewer API, https://api.helioviewer.org/docs/v2/}.") + (license license:bsd-2))) + (define-public python-mpl-animators (package (name "python-mpl-animators") From a3d85918f90e31118bc9b7e483520d0ae6192e3d Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 24 Nov 2022 11:24:40 +0000 Subject: [PATCH 801/824] gnu: Add python-reproject. * gnu/packages/astronomy.scm (python-reproject): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 56 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 492b871e12..b5f37232a3 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1355,6 +1355,62 @@ Virtual observatory (VO) using Python.") (description "Regions is an Astropy package for region handling.") (license license:bsd-3))) +(define-public python-reproject + (package + (name "python-reproject") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "reproject" version)) + (sha256 + (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55")))) + (build-system pyproject-build-system) + (arguments + (list + ;; FIXME: Failing tests + ;; + ;; reproject/adaptive/core.py:7: in + ;; from .deforest import map_coordinates + ;; E ModuleNotFoundError: No module named 'reproject.adaptive.deforest' + ;; + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'writable-compiler + (lambda _ + (make-file-writable "reproject/_compiler.c"))) + (add-before 'check 'writable-compiler + (lambda _ + (make-file-writable "reproject/_compiler.c"))) + (add-before 'check 'writable-home + (lambda _ + (setenv "HOME" (getcwd))))))) + (propagated-inputs + (list python-astropy + python-astropy-healpix + python-numpy + python-scipy)) + (native-inputs + (list python-asdf + python-cython + python-extension-helpers + python-gwcs + python-pytest-astropy + python-pyvo + python-semantic-version + python-pytest + python-setuptools-scm + python-shapely)) + (home-page "https://reproject.readthedocs.io") + (synopsis "Astronomical image reprojection in Python") + (description + "This package provides a functionality to reproject astronomical images using +various techniques via a uniform interface, where reprojection is the +re-gridding of images from one world coordinate system to another e.g. +changing the pixel resolution, orientation, coordinate system.") + (license license:bsd-3))) + (define-public python-astral (package (name "python-astral") From 78ee6dcfe13c1561ff1d5cdfc2c2d4fa8afe0883 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 24 Nov 2022 11:24:41 +0000 Subject: [PATCH 802/824] gnu: Add python-sunpy. * gnu/packages/astronomy.scm (python-sunpy): New variable. Signed-off-by: Christopher Baines --- gnu/packages/astronomy.scm | 85 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index b5f37232a3..767b4c4d96 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages databases) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) @@ -1411,6 +1412,90 @@ re-gridding of images from one world coordinate system to another e.g. changing the pixel resolution, orientation, coordinate system.") (license license:bsd-3))) +(define-public python-sunpy + (package + (name "python-sunpy") + (version "4.0.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sunpy" version)) + (sha256 + (base32 "0aiirb6l8zshdrpsvh6d5ki759ah9zfm9gbl0in985hprwwxyrq1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'writable-compiler + (lambda _ + (make-file-writable "sunpy/_compiler.c"))) + (add-before 'check 'prepare-test-environment + (lambda _ + (setenv "HOME" "/tmp") + (make-file-writable "sunpy/_compiler.c") + ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests + (substitute* "sunpy/image/tests/test_transform.py" + (("def test_clipping") "def __off_test_clipping") + (("def test_nans") "def __off_test_nans") + (("def test_endian") "def __off_test_endian")) + (substitute* "sunpy/map/tests/test_mapbase.py" + (("def test_derotating_nonpurerotation_pcij") + "def __off_test_derotating_nonpurerotation_pcij")) + (substitute* "sunpy/map/sources/tests/test_mdi_source.py" + (("def test_synoptic_source") + "def __off_test_synoptic_source")) + (substitute* "sunpy/tests/tests/test_self_test.py" + (("def test_main_nonexisting_module") + "def __off_test_main_nonexisting_module") + (("def test_main_stdlib_module") + "def __off_test_main_stdlib_module"))))))) + (native-inputs + (list python-aiohttp + python-extension-helpers + python-hvpy + python-packaging + python-pytest + python-pytest-astropy + python-pytest-doctestplus + python-pytest-mock + python-pytest-mpl + python-pytest-xdist + python-setuptools-scm)) + (propagated-inputs + (list parfive + python-asdf + python-asdf-astropy + python-astropy + python-beautifulsoup4 + python-cdflib + python-dask + python-dateutil + python-drms + python-glymur + python-h5netcdf + python-h5py + python-hypothesis + python-jplephem + python-matplotlib + python-mpl-animators + python-numpy + ;; python-opencv-python ; not packed yet + python-pandas + python-reproject + python-scikit-image + python-scipy + python-semantic-version + python-sqlalchemy + python-tqdm + python-zeep)) + (home-page "https://sunpy.org") + (synopsis "Python library for Solar Physics") + (description + "SunPy is package for solar physics and is meant to be a free alternative to the +SolarSoft data analysis environment.") + (license license:bsd-2))) + (define-public python-astral (package (name "python-astral") From 7e0ad0dd0f2829d6f3776648ba7c88acf9888d7a Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 25 Nov 2022 14:44:27 +0100 Subject: [PATCH 803/824] gnu: docker: Fix tests. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Edison Ibáñez * gnu/packages/linux.scm (xfsprogs-5.9): New variable. * gnu/packages/docker.scm (docker)[inputs]: Replace xfsprogs by xfsprogs-5.9. --- gnu/packages/docker.scm | 2 +- gnu/packages/linux.scm | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 184280b38f..7d109dc94c 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -580,7 +580,7 @@ runcexecutor/executor.go" util-linux lvm2 tini - xfsprogs + xfsprogs-5.9 xz)) (native-inputs (list eudev ; TODO: Should be propagated by lvm2 (.pc -> .pc) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8727ddd76a..c032fb8c32 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8550,6 +8550,20 @@ file systems.") ;; licensed under lgpl2.1. the other stuff is licensed under gpl2. (license (list license:gpl2 license:lgpl2.1)))) +(define-public xfsprogs-5.9 + (package + (inherit xfsprogs) + (name "xfsprogs") + (version "5.9.0") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kernel.org/linux/utils/fs/xfs/xfsprogs/" + "xfsprogs-" version ".tar.gz")) + (sha256 + (base32 + "13xkn9jpmwp4fm9r68vhgznkmxhnv83n2b39mhy2qdaph90w2a1l")))))) + (define-public xfsprogs/static (package (inherit xfsprogs) From 50546f9c0c044d65e99dad476637b9b8326888ef Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Wed, 9 Nov 2022 18:42:25 +0000 Subject: [PATCH 804/824] licenses: Add EUPL 1.1. * guix/licenses.scm (eupl1.1): New variable. Signed-off-by: Lars-Dominik Braun --- guix/licenses.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/guix/licenses.scm b/guix/licenses.scm index 80cf0f1114..632c9174df 100644 --- a/guix/licenses.scm +++ b/guix/licenses.scm @@ -57,6 +57,7 @@ edl1.0 epl1.0 epl2.0 + eupl1.1 eupl1.2 expat expat-0 freetype @@ -344,6 +345,11 @@ at URI, which may be a file:// URI pointing the package's tree." "https://www.eclipse.org/legal/epl-2.0/" "https://www.gnu.org/licenses/license-list#EPL2")) +(define eupl1.1 + (license "EUPL 1.1" + "https://directory.fsf.org/wiki/License:EUPL-1.1" + "https://www.gnu.org/licenses/license-list#EUPL-1.1")) + (define eupl1.2 (license "EUPL 1.2" "https://directory.fsf.org/wiki/License:EUPL-1.2" From afa5fa8d5b33e115745c720a1d06db0160d9d902 Mon Sep 17 00:00:00 2001 From: Antero Mejr Date: Wed, 9 Nov 2022 18:36:21 +0000 Subject: [PATCH 805/824] gnu: Add xkcdpass. * gnu/packages/password-utils.scm (xkcdpass): New variable. Signed-off-by: Lars-Dominik Braun --- gnu/packages/password-utils.scm | 40 +++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index c74ffe5242..3248e06d8f 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1455,3 +1455,43 @@ are not using it. It uses the same GPG key to encrypt passwords and tomb, therefore you don't need to manage more key or secret. Moreover, you can ask pass-tomb to automatically close your store after a given time.") (license license:gpl3+))) + +(define-public xkcdpass + (package + (name "xkcdpass") + (version "1.19.3") + (home-page "https://github.com/redacted/XKCD-password-generator") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "xkcdpass-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xfrmx9k2vinlagv476rfcfdp41aix1ldy6qnzzx26n985gcyk7p")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-manpage + (lambda* (#:key outputs #:allow-other-keys) + (install-file + "xkcdpass.1" + (string-append (assoc-ref outputs "out") "/share/man/man1"))))))) + (synopsis + "Generate secure multiword passwords/passphrases, inspired by XKCD") + (description + "This package provides a flexible and scriptable password generator which +generates strong passphrases, inspired by +@url{https://xkcd.com/936/,XKCD 936}.") + (license (list license:bsd-3 ;code + license:cc0 ;spanish, eff_large_de, french word lists + license:cc-by-sa3.0 ;finnish, italian word list + license:cc-by-sa4.0 ;norwegian word list + license:eupl1.1 ;finnish word list + license:gpl2 ;portuguese word list + license:gpl3 ;ger-anix word list + license:lgpl2.0 ;finnish word list + license:lgpl2.1 ;portuguese word list + license:mpl1.1)))) ;portuguese word list From bd6de843e6def9e37555a52a40c64115cf49264c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 26 Nov 2022 11:05:54 +0100 Subject: [PATCH 806/824] gnu: emacs-paredit: Update to 25. * gnu/packages/emacs-xyz.scm (emacs-paredit): Update to 25. [description]: Remove out of place emphasis markers. --- gnu/packages/emacs-xyz.scm | 43 +++++++++++++++++--------------------- 1 file changed, 19 insertions(+), 24 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 5d6f4d040f..d04b826528 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -809,36 +809,31 @@ Emacs package archive}.") (license license:gpl3+))) (define-public emacs-paredit - ;; The last tagged release is from 2014; use the latest commit, which - ;; includes many fixes such as honoring the 'fill-paragraph-function' - ;; variable. - (let ((commit "d0b1a2f42fb47efc8392763d6487fd027e3a2955") - (revision "1")) - (package - (name "emacs-paredit") - (version (git-version "24" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://mumble.net/~campbell/git/paredit.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1x91xxvwb3r3h61ff1kknlaakxm1a40r7zg2lck9j52yiza4f191")))) - (build-system emacs-build-system) - (home-page "http://mumble.net/~campbell/emacs/paredit/") - (synopsis "Emacs minor mode for editing parentheses") - (description - "ParEdit (paredit.el) is a minor mode for performing structured editing + (package + (name "emacs-paredit") + (version "25") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://mumble.net/~campbell/git/paredit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gc6lnk5xqxzl9s2m99hfi07wp4zfhh1k64c1bdrjfalv55nl998")))) + (build-system emacs-build-system) + (home-page "http://mumble.net/~campbell/emacs/paredit/") + (synopsis "Emacs minor mode for editing parentheses") + (description + "ParEdit (paredit.el) is a minor mode for performing structured editing of S-expression data. The typical example of this would be Lisp or Scheme source code. -ParEdit helps **keep parentheses balanced** and adds many keys for moving +ParEdit helps keep parentheses balanced and adds many keys for moving S-expressions and moving around in S-expressions. Its behavior can be jarring for those who may want transient periods of unbalanced parentheses, such as when typing parentheses directly or commenting out code line by line.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-puni ;; No tagged release upstream From 86e47b5ee9c5907dc2177b79a3436cfc39162e0d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 26 Nov 2022 11:07:56 +0100 Subject: [PATCH 807/824] gnu: emacs-xref: Update to 1.6.0. * gnu/packages/emacs-xyz.scm (emacs-xref): Update to 1.6.0. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index d04b826528..28c31fc162 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -32916,14 +32916,14 @@ work on alists, hash-table and arrays. All functions are prefixed with (define-public emacs-xref (package (name "emacs-xref") - (version "1.5.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/xref-" version ".tar")) (sha256 - (base32 "131jxsc1sl8q3r9drhylwyfig9qjjkj3hilv3npidp868pr7xdna")))) + (base32 "0vqs2l4gypdx475yi0yic0mnsg1f9nm698gi90kh7xfcpmkfcgb4")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/xref.html") (synopsis "Cross-referencing commands") From 203fe108b5b9c499e53ea0ce18c6c9dd6fe6d829 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 26 Nov 2022 11:09:13 +0100 Subject: [PATCH 808/824] gnu: emacs-kind-icon: Update to 0.1.9. * gnu/packages/emacs-xyz.scm (emacs-kind-icon): Update to 0.1.9. [description]: Use proper Texinfo marker. Remove useless "etc.". --- gnu/packages/emacs-xyz.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 28c31fc162..4e61df8aa8 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -21167,22 +21167,22 @@ or expressions with SVG rounded box labels that are fully customizable.") (define-public emacs-kind-icon (package (name "emacs-kind-icon") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/kind-icon-" version ".tar")) (sha256 - (base32 "0m0jpgk3iv0p8fzmx1nyfd1l7i803lm4mzlpp47kn7v0z09pxaph")))) + (base32 "0phssrcpmcidzlwy1577f3f02qwjs6hpavb416302y0n8kkhwvli")))) (build-system emacs-build-system) (propagated-inputs (list emacs-svg-lib)) (home-page "https://github.com/jdtsmith/kind-icon") (synopsis "Completion kind icons in Emacs") - (description "Kind-icon mode adds a colorful icon or text prefix based -on :company-kind for compatible completion UIs. The \"kind\" prefix is -typically used for differentiating completion candidates such as variables, -functions, etc.") + (description "Kind-icon mode adds a colorful icon or text prefix based on +@code{:company-kind} for compatible completion UIs. The ``kind'' prefix is +typically used for differentiating completion candidates such as variables or +functions.") (license license:gpl3+))) (define-public emacs-svg-icon From d223aff97db35d2ce430f4d81858691c735b599e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 26 Nov 2022 11:11:24 +0100 Subject: [PATCH 809/824] gnu: emacs-detached: Update to 0.10.1. * gnu/packages/emacs-xyz.scm (emacs-detached): Update to 0.10.1. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 4e61df8aa8..1a2819e22a 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -26292,7 +26292,7 @@ according to their use.") (define-public emacs-detached (package (name "emacs-detached") - (version "0.10.0") + (version "0.10.1") (source (origin (method git-fetch) (uri (git-reference @@ -26301,7 +26301,7 @@ according to their use.") (file-name (git-file-name name version)) (sha256 (base32 - "13vssywna281dr4r0hqp85xdi3xnajmdahqy7kf147jvgazkqbmd")))) + "0dvvyqc0nw9has54vps10f5iv831cb29vqvbvx0m2djv9pacqp17")))) (arguments (list #:tests? #t From fdad266577939725676910aa4508828e495d3693 Mon Sep 17 00:00:00 2001 From: Hilton Chain via Guix-patches via Date: Fri, 25 Nov 2022 09:16:09 +0800 Subject: [PATCH 810/824] gnu: emacs-ebuku: Update to commit 0c6cf404a49b. * gnu/packages/emacs-xyz.scm (emacs-ebuku): Update to commit 0c6cf404a49b. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1a2819e22a..3c9c3ef60d 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -13429,8 +13429,8 @@ news items, openrc and runscripts.") (define-public emacs-ebuku ;; Upstream has no tagged release. - (let ((revision "0") - (commit "5b8bf34b8ea5d05f0b8dfc12bfea825f9cffbeda")) + (let ((revision "1") + (commit "0c6cf404a49bd68800221446df186fffa0139325")) (package (name "emacs-ebuku") (version (git-version "0" revision commit)) @@ -13442,7 +13442,7 @@ news items, openrc and runscripts.") (file-name (git-file-name name version)) (sha256 (base32 - "04733lqa6z3kmdjcgdi58q3wrqan2qib43rvjw51qc739fwmwb5y")))) + "09fkzmcvzdbdjaa167wiybj0kir7y12pcq2varjywshvq2l7niz4")))) (build-system emacs-build-system) (home-page "https://github.com/flexibeast/ebuku") (synopsis "Emacs interface to the buku Web bookmark manager") From 920e80931212c37db926f4aa0b9aeac918fc3fc8 Mon Sep 17 00:00:00 2001 From: Hilton Chain via Guix-patches via Date: Fri, 25 Nov 2022 09:16:32 +0800 Subject: [PATCH 811/824] gnu: emacs-straight-el: Update to commit f21103d97d18. * gnu/packages/emacs-xyz.scm (emacs-straight-el): Update to commit f21103d97d18. Signed-off-by: Nicolas Goaziou --- gnu/packages/emacs-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 3c9c3ef60d..8eb4dab077 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -33664,8 +33664,8 @@ headlines, keywords, tables and source blocks.") (license license:gpl3+)))) ; License is in pyimport.el (define-public emacs-straight-el - (let ((commit "fed215348076ba9182f634e0770a175220474b5a") - (revision "0")) + (let ((commit "f21103d97d180fba0b6e2e86ebb0b6269219ef2c") + (revision "1")) (package (name "emacs-straight-el") (version (git-version "0" revision commit)) @@ -33678,7 +33678,7 @@ headlines, keywords, tables and source blocks.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0z0j670s18mp1bhrsnng0mybcbnlywarhlz7zmrf9399rr513z1x")))) + (base32 "1dqhb7kx4hr3cm4gj6qdk9aav05vc016y4nks2dj1sy88wia6wsv")))) (build-system emacs-build-system) (arguments (list From c91712aebca332102dd23713e31dc609108e7fe2 Mon Sep 17 00:00:00 2001 From: Zhu Zihao Date: Wed, 23 Nov 2022 18:42:09 +0800 Subject: [PATCH 812/824] gnu: Add mogan. * gnu/packages/text-editors.scm (mogan): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/text-editors.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index ed77113726..57341cd198 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -49,6 +49,7 @@ #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system meson) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages aspell) @@ -59,6 +60,7 @@ #:use-module (gnu packages code) #:use-module (gnu packages cpp) #:use-module (gnu packages crates-io) + #:use-module (gnu packages curl) #:use-module (gnu packages datastructures) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) @@ -895,6 +897,39 @@ Octave. TeXmacs is completely extensible via Guile.") (license license:gpl3+) (home-page "https://www.texmacs.org/tmweb/home/welcome.en.html"))) +(define-public mogan + (package + (inherit texmacs) + (name "mogan") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/XmacsLabs/mogan") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04wz6xmimjv2l6baxgzm8vyq5grg102m3l4wq8i6bglv529yp4ff")))) + (build-system qt-build-system) + (inputs + (modify-inputs (package-inputs texmacs) + ;; Replaced by S7 scheme + ;; TODO: Maybe unbundle S7 + (delete "guile") + (prepend curl))) + (arguments + (substitute-keyword-arguments (package-arguments texmacs) + ((#:phases orig) + #~(modify-phases #$orig + ;; The non-deterministic compression issue is solved in Mogan. + (delete 'gzip-flags))))) + (home-page "https://github.com/XmacsLabs/mogan") + (synopsis "Scientific structural text editor") + (description + "Mogan is a scientific structural text editor, a fork of GNU TeXmacs.") + (license license:gpl3+))) + (define-public textpieces (package (name "textpieces") From adf3eecedade19ce88d3df4325acef4559d05e8f Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 26 Nov 2022 12:10:10 +0100 Subject: [PATCH 813/824] gnu: lagrange: Update to 1.14.0. * gnu/packages/web-browsers.scm (lagrange): Update to 1.14.0. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 31885fcbe0..51c0f68680 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -705,7 +705,7 @@ is fully configurable and extensible in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.13.8") + (version "1.14.0") (source (origin (method url-fetch) @@ -713,7 +713,7 @@ is fully configurable and extensible in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "1l6cfvmmw2g30qsxmn5jma17kxgmfknlgji4pbdj1flv8p73bvza")) + (base32 "08qb8f0j3sdbrkr4zsy5pcpqz2cy520q6vb8vq7ilkbz0yfxmgf2")) (modules '((guix build utils))) (snippet '(begin From 2f0f12933f3b48e7f04371d507a460faf873f22b Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 26 Nov 2022 13:21:39 +0100 Subject: [PATCH 814/824] gnu: emacs-rec-mode: Use modern package style * gnu/packages/databases.scm (emacs-rec-mode)[source]: Use G-Expression. [arguments]: Convert to list of G-Expressions. [native-inputs]: Drop gratuitous newline. --- gnu/packages/databases.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index e4dde1b22b..de30145ec5 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1628,17 +1628,17 @@ types are supported, as is encryption.") (sha256 (base32 "1w1q6kh567fd8xismq9i6wr1y893lypd30l452yvydi1qjiq1n6x")) - (snippet '(begin (delete-file "rec-mode.info"))))) + (snippet #~(begin (delete-file "rec-mode.info"))))) (build-system emacs-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (add-before 'install 'make-info - (lambda _ - (invoke "makeinfo" "--no-split" - "-o" "rec-mode.info" "rec-mode.texi")))))) - (native-inputs - (list texinfo)) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'make-info + (lambda _ + (invoke "makeinfo" "--no-split" + "-o" "rec-mode.info" "rec-mode.texi")))))) + (native-inputs (list texinfo)) (home-page "https://www.gnu.org/software/recutils/") (synopsis "Emacs mode for working with recutils database files") (description "This package provides an Emacs major mode @code{rec-mode} From 6c6cc42f0ac095ecc6d2f20cd399d77d86080b66 Mon Sep 17 00:00:00 2001 From: "(" Date: Sat, 26 Nov 2022 10:09:05 +0000 Subject: [PATCH 815/824] gnu: emacs-rec-mode: Patch executable paths. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/databases.scm (emacs-rec-mode)[#:phases]: Add ‘patch-program-paths’. [inputs]: Add recutils. Signed-off-by: Liliana Marie Prikler --- gnu/packages/databases.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index de30145ec5..862d8bfd62 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1634,10 +1634,17 @@ types are supported, as is encryption.") (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'patch-program-paths + (lambda* (#:key inputs #:allow-other-keys) + (emacs-substitute-variables "rec-mode.el" + ("rec-recfix" (search-input-file inputs "bin/recfix")) + ("rec-recinf" (search-input-file inputs "bin/recinf")) + ("rec-recsel" (search-input-file inputs "bin/recsel"))))) (add-before 'install 'make-info (lambda _ (invoke "makeinfo" "--no-split" "-o" "rec-mode.info" "rec-mode.texi")))))) + (inputs (list recutils)) (native-inputs (list texinfo)) (home-page "https://www.gnu.org/software/recutils/") (synopsis "Emacs mode for working with recutils database files") From e1f8802dc1f2e4fb7f58958925af15a1191d4789 Mon Sep 17 00:00:00 2001 From: aecepoglu Date: Sat, 26 Nov 2022 13:35:07 +0100 Subject: [PATCH 816/824] gnu: bqn-sources: Update to commit 71ce3614... * gnu/packages/bqn.scm (bqn-sources): Update to commit 71ce36141aaacfa714edca2e408ca522a3bc5554. Signed-off-by: Liliana Marie Prikler --- gnu/packages/bqn.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bqn.scm b/gnu/packages/bqn.scm index 984dfbe53e..58e27b875f 100644 --- a/gnu/packages/bqn.scm +++ b/gnu/packages/bqn.scm @@ -113,7 +113,7 @@ the same author.") ;; Aside from dbqn above, the main bqn repository is used by other ;; implementations as a "known good" set of sources. CBQN uses dbqn to ;; generate an intermediate bytecode for its own compilation. - (let ((commit "e219af48401473a7bac49bdd8b89d69082cf5dd8")) + (let ((commit "71ce36141aaacfa714edca2e408ca522a3bc5554")) (origin (method git-fetch) (uri (git-reference @@ -121,7 +121,7 @@ the same author.") (commit commit))) (file-name (git-file-name "bqn-sources" commit)) (sha256 - (base32 "0r6pa9lscl2395g4xlvmg90vpdsjzhin4f1r0s7brymmpvmns2yc"))))) + (base32 "060a3r5m7hynzxj4iz1av2kj5jf8w3j8yswzzx9wkx31rdrsiv2c"))))) (define cbqn-bootstrap (let* ((revision "1") From 5ccb5837ccfb39af4e3e6399a0124997a187beb1 Mon Sep 17 00:00:00 2001 From: aecepoglu Date: Sat, 26 Nov 2022 13:37:08 +0100 Subject: [PATCH 817/824] gnu: cbqn-bootstrap: Update to 0-2.66584ce. * gnu/packages/bqn.scm (cbqn-bootstrap): Update to 0-2.66584ce. Signed-off-by: Liliana Marie Prikler --- gnu/packages/bqn.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bqn.scm b/gnu/packages/bqn.scm index 58e27b875f..d295019489 100644 --- a/gnu/packages/bqn.scm +++ b/gnu/packages/bqn.scm @@ -124,8 +124,8 @@ the same author.") (base32 "060a3r5m7hynzxj4iz1av2kj5jf8w3j8yswzzx9wkx31rdrsiv2c"))))) (define cbqn-bootstrap - (let* ((revision "1") - (commit "9c1cbdc99863b1da0116df61cd832137b196dc5c")) + (let* ((revision "2") + (commit "66584ce1491d300746963b8ed17170348b2a03e6")) (package (name "cbqn-bootstrap") (version (git-version "0" revision commit)) @@ -137,7 +137,7 @@ the same author.") (file-name (git-file-name name version)) (sha256 (base32 - "0w38fhwf20drkyijy6nfnhmc5g5gw0zmzgmy1q605x57znlj85a2")))) + "13gg96aa56b8k08bjvv8i0f5nxrah2sij7g6pg7i21fdv08rd9iv")))) (build-system gnu-build-system) (arguments (list From ca98b3ab26b0a6f8024e35a7a9c23b896fd26b8c Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 25 Oct 2022 11:49:38 +0100 Subject: [PATCH 818/824] gnu: gst-plugins-bad: Skip elements/camerabin test on some systems. It seems to frequently fail on i686-linux and aarch64-linux. * gnu/packages/gstreamer.scm (gst-plugins-bad)[arguments]: Skip the elements/camerabin test on i686-linux and aarch64-linux. Signed-off-by: Liliana Marie Prikler --- gnu/packages/gstreamer.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index a92588a9e2..e46bf7b741 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -791,6 +791,14 @@ model to base your own plug-in on, here it is.") ;; FIXME: Why is this failing. ((".*elements/dash_mpd\\.c.*") "") + ;; This test is flaky on at least some architectures. + ;; https://gitlab.freedesktop.org/gstreamer/gstreamer/-/issues/1244 + #$@(if (member (%current-system) + '("i686-linux" "aarch64-linux")) + `((("'elements/camerabin\\.c'\\]\\],") + "'elements/camerabin.c'], true, ],")) + '()) + ;; These tests are flaky and occasionally time out: ;; https://gitlab.freedesktop.org/gstreamer/gst-plugins-bad/-/issues/932 ((".*elements/curlhttpsrc\\.c.*") "") From fc061ce2979be0ff20423a6cd6dfb085581d7531 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 15 Oct 2022 16:45:33 +0200 Subject: [PATCH 819/824] gnu: Add aiger. * gnu/packages/maths.scm (aiger): New variable. --- gnu/packages/maths.scm | 54 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ebb3a8fbd1..d819df2343 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -55,6 +55,7 @@ ;;; Copyright © 2022 Philip McGrath ;;; Copyright © 2022 Marek Felšöci ;;; Copyright © 2022 vicvbcun +;;; Copyright © 2022 Liliana Marie Prikler ;;; ;;; This file is part of GNU Guix. ;;; @@ -7362,6 +7363,59 @@ back to C with improved data structures, better scheduling of inprocessing and optimized algorithms and implementation.") (license license:expat))) +(define-public aiger + (package + (name "aiger") + (version "1.9.9") + (source (origin + (method url-fetch) + (uri (string-append "http://fmv.jku.at/aiger/aiger-" + version ".tar.gz")) + (sha256 + (base32 + "1ish0dw0nf9gyghxsdhpy1jjiy5wp54c993swp85xp7m6vdx6l0y")))) + (outputs (list "out" "static")) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ; no check target + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "aiger.c" + (("\"(gzip|gunzip)" all cmd) + (string-append + "\"" + (search-input-file inputs (string-append "bin/" cmd))))))) + (add-after 'unpack 'patch-build-files + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "makefile.in" + (("test -d .*") "true") + (("/usr/local") (assoc-ref outputs "out"))))) + (replace 'configure + (lambda* (#:key configure-flags #:allow-other-keys) + (apply invoke "./configure.sh" configure-flags))) + (add-after 'install 'install-static + (lambda* (#:key outputs #:allow-other-keys) + (apply invoke #$(ar-for-target) "rcs" "libaiger.a" + (find-files "." "\\.o$")) + (let* ((static (assoc-ref outputs "static")) + (lib (string-append static "/lib")) + (incl (string-append static "/include/aiger"))) + (mkdir-p lib) + (mkdir-p incl) + (install-file "libaiger.a" lib) + (for-each (lambda (f) (install-file f incl)) + (find-files "." "\\.h$")))))))) + (inputs (list gzip)) + (home-page "http://fmv.jku.at/aiger") + (synopsis "Utilities for And-Inverter Graphs") + (description "AIGER is a format, library and set of utilities for +@acronym{AIG, And-Inverter Graphs}s. The focus is on conversion utilities and a +generic reader and writer API.") + (license (list license:expat + license:bsd-3)))) ; blif2aig + (define-public libqalculate (package (name "libqalculate") From 58c24ec748f9f01d6c56a737a81a22e60ff88d55 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 15 Oct 2022 16:45:44 +0200 Subject: [PATCH 820/824] gnu: Add lingeling. * gnu/packages/maths.scm (lingeling): New variable. --- gnu/packages/maths.scm | 82 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d819df2343..fedee36c55 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -7416,6 +7416,88 @@ generic reader and writer API.") (license (list license:expat license:bsd-3)))) ; blif2aig +(define-public lingeling + (let ((commit "72d2b13eea5fbd95557a3d0d199cd98dfbdc76ee") + (revision "1")) + (package + (name "lingeling") + (version (git-version "sc2022" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arminbiere/lingeling") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16s30x8s2cw6icchwm65zj56ph4qwz6i07g3hwkknvajisvjq85c")))) + (build-system gnu-build-system) + (arguments + (list #:test-target "test" + #:modules `((ice-9 match) + ,@%gnu-build-system-modules) + #:configure-flags #~(list "--aiger=.") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-aiger + (lambda* (#:key inputs #:allow-other-keys) + (invoke #$(ar-for-target) "x" + (search-input-file inputs "lib/libaiger.a") + "aiger.o") + (copy-file + (search-input-file inputs "include/aiger/aiger.h") + "aiger.h"))) + (add-after 'unpack 'hard-code-commit + (lambda _ + (substitute* "mkconfig.sh" + (("`\\./getgitid`") #$commit)))) + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* (list "treengeling.c" "lgldimacs.c") + (("\"(gunzip|xz|bzcat|7z)" all cmd) + (string-append + "\"" + (search-input-file inputs (string-append "bin/" cmd))))))) + (replace 'configure + (lambda* (#:key configure-flags #:allow-other-keys) + (apply invoke "./configure.sh" configure-flags))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (for-each + (lambda (file) + (install-file file bin)) + '("blimc" "ilingeling" "lglddtrace" "lglmbt" + "lgluntrace" "lingeling" "plingeling" + "treengeling"))))) + (add-after 'install 'wrap-path + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion (string-append + (assoc-ref outputs "out") + "/bin") + (for-each + (lambda (file) + (wrap-program + file + '("PATH" suffix + #$(map (lambda (input) + (file-append (this-package-input input) "/bin")) + '("gzip" "bzip2" "xz" "p7zip"))))) + ;; These programs use sprintf on buffers with magic + ;; values to construct commands (yes, eww), so we + ;; can't easily substitute* them. + '("lglddtrace" "lgluntrace" "lingeling" "plingeling")))))))) + (inputs (list `(,aiger "static") gzip bzip2 xz p7zip)) + (home-page "http://fmv.jku.at/lingeling") + (synopsis "SAT solver") + (description "This package provides a range of SAT solvers, including +the sequential @command{lingeling} and its parallel variants +@command{plingeling} and @command{treengeling}. A bounded model checker is +also included.") + (license license:expat)))) + (define-public libqalculate (package (name "libqalculate") From d3ce4a2619784e58876ae81cef0cf099e9206be4 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 15 Oct 2022 16:46:40 +0200 Subject: [PATCH 821/824] gnu: Add louvain-community. * gnu/packages/maths.scm (louvain-community): New variable. --- gnu/packages/maths.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index fedee36c55..5fc93fa4d8 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -7498,6 +7498,37 @@ the sequential @command{lingeling} and its parallel variants also included.") (license license:expat)))) +(define-public louvain-community + (let ((commit "8cc5382d4844af127b1c1257373740d7e6b76f1e") + (revision "1")) + (package + (name "louvain-community") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/meelgroup/louvain-community") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ss00hkdvr9bdkd355hxf8zd7xycb3nm8qpy7s75gjjf6yng0bfj")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f ; tests appear to require missing files + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'encode-git-hash + (lambda _ + (substitute* "CMakeLists.txt" + (("GIT-hash-notfound") #$commit))))))) + (native-inputs (list python)) + (home-page "https://github.com/meelgroup/louvain-communities") + (synopsis "Multi-criteria community detection") + (description "This package provides a C++ implementation of the Louvain +community detection algorithm.") + (license license:lgpl3+)))) + (define-public libqalculate (package (name "libqalculate") From 2404afea8b51b5ddf3f29d1f050d6a5a93aeb0b1 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Sat, 15 Oct 2022 16:47:03 +0200 Subject: [PATCH 822/824] gnu: Add cryptominisat. * gnu/packages/maths.scm (cryptominisat): New variable. Co-authored-by: Maximilian Heisinger --- gnu/packages/maths.scm | 51 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5fc93fa4d8..531e3f0324 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -56,6 +56,7 @@ ;;; Copyright © 2022 Marek Felšöci ;;; Copyright © 2022 vicvbcun ;;; Copyright © 2022 Liliana Marie Prikler +;;; Copyright © 2022 Maximilian Heisinger ;;; ;;; This file is part of GNU Guix. ;;; @@ -159,6 +160,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) + #:use-module (gnu packages sqlite) #:use-module (gnu packages swig) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) @@ -7529,6 +7531,55 @@ also included.") community detection algorithm.") (license license:lgpl3+)))) +(define-public cryptominisat + (package + (name "cryptominisat") + (version "5.11.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/msoos/cryptominisat") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1izjn44phjp9670s7bxrdx4p0r59idqwv3bm6sr0qnlqlha5z4zc")))) + (build-system cmake-build-system) + (arguments + (list + #:build-type "Release" + #:test-target "test" + #:configure-flags #~(list "-DENABLE_TESTING=ON" "-DSTATS=ON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("add_subdirectory\\(utils/lingeling-ala\\)") "")) + ;; Transitively included in vendored gtest.h. Fixed in + ;; upstream: + ;; https://github.com/msoos/cryptominisat/pull/686 + (substitute* "tests/assump_test.cpp" + (("#include ") + "#include \n#include ")) + (substitute* "tests/CMakeLists.txt" + (("add_subdirectory\\(\\$\\{GTEST_PREFIX\\} gtest\\)") + "find_package(GTest REQUIRED)") + (("add_subdirectory\\(\\$\\{PROJECT_SOURCE_DIR\\}/utils/.*\\)") + ""))))))) + (inputs (list boost louvain-community python python-numpy sqlite zlib)) + (native-inputs (list googletest lingeling python python-wrapper python-lit)) + (synopsis "Incremental SAT solver") + (description + "CryptoMiniSat is an incremental SAT solver with both command line and +library (C++, C, Python) interfaces. The command-line interface takes a +@acronym{CNF, Conjunctive Normal Form} as an input in the DIMACS format with +the extension of XOR clauses. The library interfaces mimic this and also +allow incremental solving, including assumptions.") + (home-page "https://github.com/msoos/cryptominisat") + (license license:expat))) + (define-public libqalculate (package (name "libqalculate") From ac5b6006cfec2bf3b1c5eb53f3fbc1e223cc321d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 26 Nov 2022 12:08:02 +0100 Subject: [PATCH 823/824] gnu: varnish: Update to 7.2.1. * gnu/packages/web.scm (varnish): Update to 7.2.1. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d2c406915c..61e1d1f1bc 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5847,13 +5847,13 @@ deployments.") (package (name "varnish") (home-page "https://varnish-cache.org/") - (version "7.1.1") + (version "7.2.1") (source (origin (method url-fetch) (uri (string-append home-page "_downloads/varnish-" version ".tgz")) (sha256 (base32 - "14512fjjzwini3fics6sib9y83s45vlrpncamixqmmg7j0jvxbrc")))) + "0h590kr7rhp57a4kfx6apyvqk60w78qdjwpr6g2ikv5840bpv4sd")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath=" %output "/lib") From c457c715a83358fa1557f703b1e459435fb1a259 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 26 Nov 2022 15:37:30 +0100 Subject: [PATCH 824/824] gnu: cdogs-sdl: Update to 1.4.0. * gnu/packages/games.scm (cdogs-sdl): Update to 1.4.0. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 495fdf0f2d..d7af172d53 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -6239,7 +6239,7 @@ emerges from a sewer hole and pulls her below ground.") (define-public cdogs-sdl (package (name "cdogs-sdl") - (version "0.8.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -6248,7 +6248,7 @@ emerges from a sewer hole and pulls her below ground.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0vx37zb2iw7sfw5a2bs97ydlmb301nvy485ybdm8g46c5hn9s13c")))) + (base32 "1505z8rli59i1ych4rzwbf4dvhv72icdj22n1xarb8xfyz0wyp3b")))) (build-system cmake-build-system) (arguments `(#:configure-flags