From 8d9bb5408a5088304ec8662bb53b9c3ded9ca725 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 9 Sep 2023 11:00:42 +0200 Subject: [PATCH 001/440] gnu: linux-libre: Fix cross-compilation. Fix generic aarch64 kernel cross-compilation by providing the missing hexdump binary. * gnu/packages/linux.scm (linux-libre)[native-inputs]: Add util-linux. --- gnu/packages/linux.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 36354b4d82..bc1fedaad5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1071,6 +1071,7 @@ ARCH and optionally VARIANT, or #f if there is no such configuration." elfutils ;needed to enable CONFIG_STACK_VALIDATION flex bison + util-linux ;needed for hexdump ;; These are needed to compile the GCC plugins. gmp mpfr From f85c6ee26a5e693aaaebdab33b156938e10fb060 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 9 Sep 2023 11:24:27 +0200 Subject: [PATCH 002/440] gnu: qgis: Fix build. * gnu/packages/geo.scm (qgis)[arguments]: Add test_core_authconfig to disabled tests in 'check' phase. --- gnu/packages/geo.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 0a823353fa..d702046865 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -2775,6 +2775,7 @@ growing set of geoscientific methods.") "ProcessingGrass7AlgorithmsRasterTestPt1" "ProcessingGrass7AlgorithmsRasterTestPt2" "ProcessingGrass7AlgorithmsVectorTest" + "test_core_authconfig" "test_core_authmanager" "test_core_compositionconverter" "test_core_expression" From 9f6fa3a9580a43d7406ac5b61c2fba0878a67edf Mon Sep 17 00:00:00 2001 From: Cayetano Santos Date: Sun, 30 Jul 2023 17:52:58 +0200 Subject: [PATCH 003/440] gnu: Add emacs-chatgpt-shell. * gnu/packages/emacs-xyz.scm (emacs-chatgpt-shell): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index baa67eefbb..1cce55bce9 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -493,6 +493,25 @@ just one-off queries and multiple independent sessions. It requires an OpenAI API key.") (license license:gpl3+))) +(define-public emacs-chatgpt-shell + (package + (name "emacs-chatgpt-shell") + (version "0.74.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/xenodium/chatgpt-shell") + (commit "1de7bfa6a34f20cca813006282d9a8f2ef291f95"))) + (sha256 + (base32 + "1rabpp70qlmc47lmp2v7ckvfjhy6wkk881fxpbv2dchzhn77qk5r")))) + (build-system emacs-build-system) + (home-page "https://github.com/xenodium/chatgpt-shell") + (synopsis "ChatGPT and DALL-E Emacs shells + Org Babel") + (description + "chatgpt-shell is a comint-based ChatGPT shell for Emacs.") + (license license:gpl3+))) + (define-public emacs-geiser-guile (package (name "emacs-geiser-guile") From 5e72bb5c67943fecf690190bdccbda2bf16d12b0 Mon Sep 17 00:00:00 2001 From: Reily Siegel Date: Mon, 28 Aug 2023 11:11:23 -0400 Subject: [PATCH 004/440] services: vpn: Fix broken format string for wireguard dns. * gnu/services/vpn.scm (wireguard-configuration-file): Fix broken format string. Signed-off-by: Liliana Marie Prikler --- gnu/services/vpn.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/vpn.scm b/gnu/services/vpn.scm index 9c8243d131..7fb4775757 100644 --- a/gnu/services/vpn.scm +++ b/gnu/services/vpn.scm @@ -820,7 +820,7 @@ strongSwan."))) (format #f "~@[ListenPort = ~a~]" #$port) #$@(if (null? dns) '() - (list (format #f "~{DNS = ~{~a~^, ~}" dns))))) + (list (format #f "DNS = ~{~a~^, ~}" dns))))) (mkdir #$output) (chdir #$output) From cab7ae94ec5e6e2c49946c82847d27499facc09a Mon Sep 17 00:00:00 2001 From: Mekeor Melire Date: Sun, 18 Jun 2023 23:17:18 +0000 Subject: [PATCH 005/440] gnu: Add emacs-jinx. * gnu/packages/emacs-xyz.scm (emacs-jinx): New variable. Signed-off-by: Liliana Marie Prikler --- gnu/packages/emacs-xyz.scm | 61 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 1cce55bce9..e971edb676 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -181,6 +181,7 @@ #:use-module (gnu packages djvu) #:use-module (gnu packages ebook) #:use-module (gnu packages emacs) + #:use-module (gnu packages enchant) #:use-module (gnu packages fonts) #:use-module (gnu packages freedesktop) #:use-module (gnu packages games) @@ -10349,6 +10350,66 @@ insertion mode. When enabled all keys are implicitly prefixed with sgml/html integration, and indentation (working with sgml).") (license license:gpl3+))) +(define-public emacs-jinx + (package + (name "emacs-jinx") + (version "0.8") + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/minad/jinx") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1y097rnf9zg26jf4vh74a0laddfp4x6pp1fjqs3xqgwc0cmdq59w")))) + (build-system emacs-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'expand-load-path 'build-jinx-mod + (lambda* _ + (invoke + "emacs" "--batch" "-L" "." + "-l" "jinx.el" + "-f" "jinx--load-module"))) + (add-after 'expand-load-path 'build-info + (lambda _ + (invoke "emacs" "--batch" + "--eval=(require 'ox-texinfo)" + "--eval=(find-file \"README.org\")" + "--eval=(org-texinfo-export-to-info)"))) + (add-after 'build-jinx-mod 'patch-path-to-jinx-mod + (lambda _ + (let ((file "jinx.el")) + (make-file-writable file) + (emacs-substitute-sexps file + ("\"Compile and load dynamic module.\"" + `(module-load + ,(string-append #$output + "/lib/emacs/jinx-mod.so"))))))) + (add-after 'install 'install-jinx-mod + (lambda _ + (install-file "jinx-mod.so" + (string-append #$output "/lib/emacs")))) + (add-after 'install 'install-info + (lambda _ + (install-file "jinx.info" + (string-append #$output "/share/info"))))))) + (inputs (list enchant)) + (propagated-inputs (list emacs-compat)) + (native-inputs (list emacs-compat enchant pkg-config texinfo)) + (home-page "https://github.com/minad/jinx") + (synopsis "Emacs Enchanted Spell Checker") + (description "Jinx is a just-in-time spell-checker for Emacs +based on the enchant library. It lazily highlights misspelled words in the +text of the visible portion of the buffer by honouring window boundaries as +well as text folding, if any.") + (license license:gpl3+))) + (define-public emacs-jit-spell (package (name "emacs-jit-spell") From 859928fc99015c64202eef6231c721e026925aec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 8 Sep 2023 22:10:36 +0200 Subject: [PATCH 006/440] gnu: cuirass: Update to 6131880. * gnu/packages/ci.scm (cuirass): Update to 6131880. --- gnu/packages/ci.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index 25566bc0fa..f38dd4383d 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -58,8 +58,8 @@ #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR))) (define-public cuirass - (let ((commit "7416bb916315730cd1ea74e7914f7532a1aba193") - (revision "17")) + (let ((commit "613188072c468fe2ffa4e8f83b48aefeb2488a2c") + (revision "18")) (package (name "cuirass") (version (git-version "1.1.0" revision commit)) @@ -72,7 +72,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1wc39c7aqva5sp3gpdxq2kqa17ywy21yn5w8r66qgxjinvj21a68")))) + "13ai3xmf62kx9ijc5imapcjwyvkhj2kxnh36chh3vbh3sxbbanzz")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) From 4cf4bd1ebe1c4b206ffd686058acd69261672536 Mon Sep 17 00:00:00 2001 From: Thomas Albers Date: Tue, 8 Aug 2023 18:37:10 +0200 Subject: [PATCH 007/440] =?UTF-8?q?services:=20cgit:=20Allow=20file-like?= =?UTF-8?q?=20objects=20for=20=E2=80=98root-readme=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/cgit.scm (cgit-configuration)[root-readme]: Accept 'file-object' instead of only 'string' Signed-off-by: Ludovic Courtès --- gnu/services/cgit.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/cgit.scm b/gnu/services/cgit.scm index e33cb9e7db..684ab73f76 100644 --- a/gnu/services/cgit.scm +++ b/gnu/services/cgit.scm @@ -581,7 +581,7 @@ removed for the URL and name.") (string "a fast webinterface for the git dscm") "Text printed below the heading on the repository index page.") (root-readme - (string "") + (file-object "") "The content of the file specified with this option will be included verbatim below the \"about\" link on the repository index page.") (root-title From 58fe4574a97046ffb3b015034a50119ffc04792d Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:13 -0500 Subject: [PATCH 008/440] gnu: Add rust-notify-5-pre.13. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-notify-5-pre.13): New variable. This pinned version is required by `rust-analyzer` version `2022-01-10`. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 77a41a5116..b6e2ac4507 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -41724,6 +41724,19 @@ with all line endings.") notification library.") (license (list license:cc0 license:artistic2.0)))) +(define-public rust-notify-5-pre.13 + (package + (inherit rust-notify-5) + (name "rust-notify") + (version "5.0.0-pre.13") + (source (origin + (method url-fetch) + (uri (crate-uri "notify" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0za8mpacxkr62fii5h7ny4h396y0m8myd3hf08njqdg2h21kap94")))))) + (define-public rust-notify-4 (package (inherit rust-notify-5) From a4514556df4e3138544def7286c6ecf640634a57 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:14 -0500 Subject: [PATCH 009/440] gnu: rust-analyzer: Fix build of version 2022-01-10. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/rust-apps.scm (rust-analyzer): Update dependency rust-notify-5-pre.13. This fixes the build of `rust-analyzer@2022-01-10`, which required a pinned version of `rust-notify` (`rust-notify-5-pre.13`) to compile and rust >= 1.64. Signed-off-by: Ludovic Courtès --- gnu/packages/rust-apps.scm | 22 +++++++++++++++------- gnu/packages/rust.scm | 6 +++--- 2 files changed, 18 insertions(+), 10 deletions(-) diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index a291282325..8c7d8006cc 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -1780,9 +1780,10 @@ background agent taking care of maintaining the necessary state.") "1ci85bp8xwqrk8nqr8sh6yj8njgd98nhgnhaks2g00c77wwyra41")))) (build-system cargo-build-system) (arguments - `(#:install-source? #f ; virtual manifest + `(#:rust ,rust-1.64 + #:install-source? #f ; virtual manifest #:cargo-test-flags - '("--release" "--" + '("--release" "--lib" "--tests" "--" "--skip=tests::test_version_check" ;it need rustc's version ;; FIXME: Guix's rust does not install source in ;; %out/lib/rustlib/src/rust so "can't load standard library from @@ -1793,12 +1794,19 @@ background agent taking care of maintaining the necessary state.") "--skip=tests::sourcegen::sourcegen_assists_docs" ;need rustfmt "--skip=tests::sourcegen_ast::sourcegen_ast" ;same - "--skip=tidy::cargo_files_are_tidy" ;not needed "--skip=tidy::check_licenses" ;it runs cargo metadata "--skip=tidy::check_merge_commits" ;it runs git rev-list "--skip=tidy::check_code_formatting" ;need rustfmt as cargo fmt - "--skip=tidy::generate_grammar" ;same - "--skip=tidy::generate_assists_tests") ;same + + ;; These tests require rust <= 1.60 and too many packages + ;; has as dependency rust-serde-json-1 that use indexmap2 + ;; and it need rust >= 1.64 + "--skip=tests::list_test_macros" + "--skip=tests::test_derive_empty" + "--skip=tests::test_attr_macro" + "--skip=tests::test_fn_like_macro" + "--skip=tests::test_fn_like_macro2" + "--skip=tests::test_derive_error") #:cargo-development-inputs (("rust-arbitrary" ,rust-arbitrary-1) ("rust-derive-arbitrary" ,rust-derive-arbitrary-1) @@ -1845,7 +1853,7 @@ background agent taking care of maintaining the necessary state.") ("rust-memmap2" ,rust-memmap2-0.5) ("rust-mimalloc" ,rust-mimalloc-0.1) ("rust-miow" ,rust-miow-0.4) - ("rust-notify" ,rust-notify-5) + ("rust-notify" ,rust-notify-5-pre.13) ("rust-object" ,rust-object-0.28) ("rust-once-cell" ,rust-once-cell-1) ("rust-parking-lot" ,rust-parking-lot-0.11) @@ -1927,7 +1935,7 @@ exec -a \"$0\" \"~a\" \"$@\"" (chdir "../..") (install-file "LICENSE-MIT" doc) (install-file "LICENSE-APACHE" doc))))))) - (native-inputs (list rust-src)) + (native-inputs (list rust-src-1.64)) (home-page "https://rust-analyzer.github.io/") (synopsis "Experimental Rust compiler front-end for IDEs") (description "Rust-analyzer is a modular compiler frontend for the Rust diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index 4ee5ded5de..5cfdeffa81 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -652,7 +652,7 @@ safety and thread safety guarantees.") (rust-bootstrapped-package rust-1.62 "1.63.0" "1l4rrbzhxv88pnfq94nbyb9m6lfnjwixma3mwjkmvvs2aqlq158z")) -(define rust-1.64 +(define-public rust-1.64 (let ((base-rust (rust-bootstrapped-package rust-1.63 "1.64.0" "018j720b2n12slp4xk64jc6shkncd46d621qdyzh2a8s3r49zkdk"))) @@ -891,10 +891,10 @@ safety and thread safety guarantees.") `("procps" ,procps) (package-native-inputs base-rust)))))) -(define-public rust-src +(define-public rust-src-1.64 (hidden-package (package - (inherit rust) + (inherit rust-1.64) (name "rust-src") (build-system copy-build-system) (native-inputs '()) From 26c10ac9bf373475f08442d52e2162ec2504f265 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:15 -0500 Subject: [PATCH 010/440] gnu: Add rust-either-1.6.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-either-1.6.0): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index b6e2ac4507..6a0f4e187d 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -21557,6 +21557,24 @@ signing, and verification in pure Rust.") @code{Right} is a general purpose sum type with two cases.") (license (list license:expat license:asl2.0)))) +(define-public rust-either-1.6.0 + (package + (inherit rust-either-1) + (name "rust-either") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "either" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0mwl9vngqf5jvrhmhn9x60kr5hivxyjxbmby2pybncxfqhf4z3g7")))) + (arguments + `(#:cargo-inputs (("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs (("rust-serde-json" ,rust-serde-json-1.0.73)))))) + (define-public rust-elf-0.0.10 (package (name "rust-elf") From 63eddbb920e847129affce3ea17880fd699dd06f Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:16 -0500 Subject: [PATCH 011/440] gnu: Add rust-proc-macro2-1.0.34. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-proc-macro2-1.0.34): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 6a0f4e187d..70918d16d0 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -49419,6 +49419,27 @@ in your code.") in terms of the upstream unstable API.") (license (list license:asl2.0 license:expat)))) +(define-public rust-proc-macro2-1.0.34 + (package + (inherit rust-proc-macro2-1) + (name "rust-proc-macro2") + (version "1.0.34") + (source + (origin + (method url-fetch) + (uri (crate-uri "proc-macro2" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1c93jhwl8lv3hiqqvdhd2d2xhjryh5bqb9w5icr5i7bw1wnfk11g")))) + (arguments + `(#:cargo-test-flags '("--lib") + #:cargo-inputs + (("rust-unicode-ident" ,rust-unicode-ident-1)) + #:cargo-development-inputs + (("rust-quote" ,rust-quote-1.0.10) + ("rust-rustversion" ,rust-rustversion-1)))))) + (define-public rust-proc-macro2-0.4 (package (inherit rust-proc-macro2-1) From e32ae2fbf6f3c52d849036026ecc09a94d57fbb7 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:17 -0500 Subject: [PATCH 012/440] gnu: Add rust-quote-1.0.10. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-quote-1.0.10): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 70918d16d0..d245b32959 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -51640,6 +51640,25 @@ transport protocol in Rust.") (description "Quasi-quoting macro quote!(...)") (license (list license:asl2.0 license:expat)))) +(define-public rust-quote-1.0.10 + (package + (inherit rust-quote-1) + (name "rust-quote") + (version "1.0.10") + (source (origin + (method url-fetch) + (uri (crate-uri "quote" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01ff7a76f871ggnby57iagw6499vci4bihcr11g6bqzjlp38rg1q")))) + (arguments + `(#:cargo-inputs + (("rust-proc-macro2" ,rust-proc-macro2-1.0.34)) + #:cargo-development-inputs + (("rust-rustversion" ,rust-rustversion-1) + ("rust-trybuild" ,rust-trybuild-1.0.19)))))) + (define-public rust-quote-0.6 (package (inherit rust-quote-1) From 590d408c56bd63a429d51e8a47862e08e8862fb1 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:18 -0500 Subject: [PATCH 013/440] gnu: Add rust-serde-json-1.0.73. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-serde-json-1.0.73): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index d245b32959..a89db5ba46 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -59866,6 +59866,32 @@ data. This crate provides a wrapper that works with any existing Serde "This package provides a JSON serialization file format.") (license (list license:expat license:asl2.0)))) +(define-public rust-serde-json-1.0.73 + (package + (inherit rust-serde-json-1) + (name "rust-serde-json") + (version "1.0.73") + (source + (origin + (method url-fetch) + (uri (crate-uri "serde-json" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1xbwmzc5j6r1nz62a20w6l9bkwbhzd11vwbdqmzbqcv5pi207gdw")))) + (arguments + `(#:cargo-inputs + (("rust-indexmap" ,rust-indexmap-1.7) + ("rust-itoa" ,rust-itoa-1) + ("rust-ryu" ,rust-ryu-1) + ("rust-serde" ,rust-serde-1)) + #:cargo-development-inputs + (("rust-automod" ,rust-automod-1) + ("rust-rustversion" ,rust-rustversion-1) + ("rust-serde-bytes" ,rust-serde-bytes-0.11) + ("rust-serde-derive" ,rust-serde-derive-1) + ("rust-serde-stacker" ,rust-serde-stacker-0.1) + ("rust-trybuild" ,rust-trybuild-1)))))) + (define-public rust-serde-json-0.9 (package (inherit rust-serde-json-1) From bf7fcedbdfb2695f0f9197cfa812ce74033f36ae Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:19 -0500 Subject: [PATCH 014/440] gnu: Add rust-trybuild-1.0.19. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crates-io.scm (rust-trybuild-1.0.19): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a89db5ba46..019afc010a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -73245,6 +73245,29 @@ the Trust-DNS client to use rustls for TLS.") "Test harness for ui tests of compiler diagnostics.") (license (list license:expat license:asl2.0)))) +(define-public rust-trybuild-1.0.19 + (package + (inherit rust-trybuild-1) + (name "rust-trybuild") + (version "1.0.19") + (source + (origin + (method url-fetch) + (uri (crate-uri "trybuild" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0ab7ahdx563n6kbm14pm3qnxq4fp06pz42nh5ii4acvlzycnwdh4")))) + (arguments + `(#:cargo-inputs + (("rust-toml" ,rust-toml-0.5) + ("rust-dissimilar" ,rust-dissimilar-1) + ("rust-glob" ,rust-glob-0.3) + ("rust-lazy-static" ,rust-lazy-static-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1.0.73) + ("rust-termcolor" ,rust-termcolor-1)) + #:cargo-development-inputs (("rust-automod" ,rust-automod-1)))))) + (define-public rust-trybuild2-1 (package (name "rust-trybuild2") From 6fa720831f3337e729fdd50ef6ed44cd152cc698 Mon Sep 17 00:00:00 2001 From: Distopico Date: Wed, 30 Aug 2023 14:58:20 -0500 Subject: [PATCH 015/440] gnu: rust-analyzer: Update required dependencies version. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use pinned versions of different dependencies required by rust-analyzer@2022-01-10. * gnu/packages/crates-io.scm (rust-salsa-0.17): Require RUST-INDEXMAP-1.7. (rust-serde-path-to-error-0.1): Require RUST-SERDE-JSON-1.0.73. (rust-serde-repr-0.1): Require RUST-QUOTE-1.0.10, RUST-PROC-MACRO2-1.0.34, RUST-SERDE-JSON-1.0.73, RUST-TRYBUILD-1.0.19. * gnu/packages/rust-apps.scm (rust-analyzer): Adjust versions similarly. Signed-off-by: Ludovic Courtès --- gnu/packages/crates-io.scm | 12 ++++++------ gnu/packages/rust-apps.scm | 12 +++++------- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 019afc010a..3c83563c45 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -57560,7 +57560,7 @@ in pure Rust.") #:cargo-inputs (("rust-crossbeam-utils" ,rust-crossbeam-utils-0.8) - ("rust-indexmap" ,rust-indexmap-1) + ("rust-indexmap" ,rust-indexmap-1.7) ("rust-lock-api" ,rust-lock-api-0.4) ("rust-log" ,rust-log-0.4) ("rust-oorandom" ,rust-oorandom-11.1) @@ -59960,7 +59960,7 @@ programs in rust.") (("rust-serde" ,rust-serde-1)) #:cargo-development-inputs (("rust-serde-derive" ,rust-serde-derive-1) - ("rust-serde-json" ,rust-serde-json-1)))) + ("rust-serde-json" ,rust-serde-json-1.0.73)))) (home-page "https://github.com/dtolnay/path-to-error") (synopsis @@ -60018,14 +60018,14 @@ commonly used by Ruby on Rails via Rack.") (build-system cargo-build-system) (arguments `(#:cargo-inputs - (("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quote" ,rust-quote-1) + (("rust-proc-macro2" ,rust-proc-macro2-1.0.34) + ("rust-quote" ,rust-quote-1.0.10) ("rust-syn" ,rust-syn-1)) #:cargo-development-inputs (("rust-rustversion" ,rust-rustversion-1) ("rust-serde" ,rust-serde-1) - ("rust-serde-json" ,rust-serde-json-1) - ("rust-trybuild" ,rust-trybuild-1)))) + ("rust-serde-json" ,rust-serde-json-1.0.73) + ("rust-trybuild" ,rust-trybuild-1.0.19)))) (home-page "https://github.com/dtolnay/serde-repr") (synopsis "Serialize and deserialize C-like enum as underlying repr") (description diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 8c7d8006cc..76d48e55f1 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -1812,7 +1812,7 @@ background agent taking care of maintaining the necessary state.") ("rust-derive-arbitrary" ,rust-derive-arbitrary-1) ("rust-expect-test" ,rust-expect-test-1) ("rust-oorandom" ,rust-oorandom-11.1) - ("rust-quote" ,rust-quote-1) + ("rust-quote" ,rust-quote-1.0.10) ("rust-rayon" ,rust-rayon-1) ("rust-tracing" ,rust-tracing-0.1) ("rust-tracing-subscriber" ,rust-tracing-subscriber-0.3) @@ -1823,7 +1823,6 @@ background agent taking care of maintaining the necessary state.") ("rust-anyhow" ,rust-anyhow-1) ("rust-anymap" ,rust-anymap-0.12) ("rust-arrayvec" ,rust-arrayvec-0.7) - ("rust-backtrace" ,rust-backtrace-0.3) ("rust-cargo-metadata" ,rust-cargo-metadata-0.14) ("rust-cfg-if" ,rust-cfg-if-1) ("rust-chalk-ir" ,rust-chalk-ir-0.75) @@ -1832,17 +1831,16 @@ background agent taking care of maintaining the necessary state.") ("rust-countme" ,rust-countme-3) ("rust-cov-mark" ,rust-cov-mark-2) ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5) - ("rust-dashmap" ,rust-dashmap-4) ("rust-dissimilar" ,rust-dissimilar-1) ("rust-dot" ,rust-dot-0.1) ("rust-drop-bomb" ,rust-drop-bomb-0.1) - ("rust-either" ,rust-either-1) + ("rust-either" ,rust-either-1.6.0) ("rust-ena" ,rust-ena-0.14) ("rust-env-logger" ,rust-env-logger-0.8) ("rust-flate2" ,rust-flate2-1) ("rust-fst" ,rust-fst-0.4) ("rust-home" ,rust-home-0.5) - ("rust-indexmap" ,rust-indexmap-1) + ("rust-indexmap" ,rust-indexmap-1.7) ("rust-itertools" ,rust-itertools-0.10) ("rust-jod-thread" ,rust-jod-thread-0.1) ("rust-libc" ,rust-libc-0.2) @@ -1858,7 +1856,7 @@ background agent taking care of maintaining the necessary state.") ("rust-once-cell" ,rust-once-cell-1) ("rust-parking-lot" ,rust-parking-lot-0.11) ("rust-perf-event" ,rust-perf-event-0.4) - ("rust-proc-macro2" ,rust-proc-macro2-1) + ("rust-proc-macro2" ,rust-proc-macro2-1.0.34) ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.8) ("rust-pulldown-cmark-to-cmark" ,rust-pulldown-cmark-to-cmark-7) ("rust-rowan" ,rust-rowan-0.15) @@ -1867,7 +1865,7 @@ background agent taking care of maintaining the necessary state.") ("rust-salsa" ,rust-salsa-0.17) ("rust-scoped-tls" ,rust-scoped-tls-1) ("rust-serde" ,rust-serde-1) - ("rust-serde-json" ,rust-serde-json-1) + ("rust-serde-json" ,rust-serde-json-1.0.73) ("rust-serde-path-to-error" ,rust-serde-path-to-error-0.1) ("rust-typed-arena" ,rust-typed-arena-2) ("rust-smallvec" ,rust-smallvec-1) From 9aed82fe05b41ae37737bf741c85d030cf20d345 Mon Sep 17 00:00:00 2001 From: Yovan Naumovski Date: Sun, 27 Aug 2023 13:10:59 +0300 Subject: [PATCH 016/440] gnu: vcmi: Update to 1.3.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (vcmi): Update to 1.3.1. Signed-off-by: Ludovic Courtès --- 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 760234b031..4d5b85248a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -11059,7 +11059,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.") (define-public vcmi (package (name "vcmi") - (version "1.2.1") + (version "1.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -11068,7 +11068,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.") (file-name (git-file-name name version)) (sha256 (base32 - "0f3fk1fc2wb7f2j4pxz89dzr8zjnrdh435mijia483a3bq59w7pk")) + "0jq84i6lxp96xkzq9mq8n2bbmincjzi39vijj9ws8i59c7xvjw5f")) (patches (search-patches "vcmi-disable-privacy-breach.patch")))) (build-system cmake-build-system) (arguments From cd469932758bf2bec1ff9c82aeb373e18730d0c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B6ren=20Tempel?= Date: Sat, 26 Aug 2023 09:00:37 +0200 Subject: [PATCH 017/440] daemon: Fix build with GCC 13. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The sqlite.hh file uses fixed-width integer types from stdint.h. As such, it needs to include . Without this include, the file doesn't compile successfully with GCC13. See: https://gcc.gnu.org/gcc-13/porting_to.html#header-dep-changes * nix/libstore/sqlite.hh: include Signed-off-by: Sören Tempel Signed-off-by: Ludovic Courtès --- nix/libstore/sqlite.hh | 1 + 1 file changed, 1 insertion(+) diff --git a/nix/libstore/sqlite.hh b/nix/libstore/sqlite.hh index 326e4a4855..6cadba6849 100644 --- a/nix/libstore/sqlite.hh +++ b/nix/libstore/sqlite.hh @@ -2,6 +2,7 @@ #include #include +#include #include "types.hh" From d4bd5bc799e2face0b30bdb3a6ec3c347c0d1e22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 9 Sep 2023 19:33:11 +0200 Subject: [PATCH 018/440] time-travel-manifest: Add 1.4.0. * etc/time-travel-manifest.scm (%release-commits): Add 1.4.0. --- etc/time-travel-manifest.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/etc/time-travel-manifest.scm b/etc/time-travel-manifest.scm index ab890dd903..43d6708a0a 100644 --- a/etc/time-travel-manifest.scm +++ b/etc/time-travel-manifest.scm @@ -66,7 +66,8 @@ (define %release-commits ;; Release commits: the list of version/commit pairs. - '(("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") + '(("1.4.0" . "8e2f32cee982d42a79e53fc1e9aa7b8ff0514714") + ("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") From a4c35c607cfd7d6b0bad90cfcc46188d489e1754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 9 Sep 2023 19:36:05 +0200 Subject: [PATCH 019/440] time-travel-manifest: Comment out versions older than 1.3.0 for now. * etc/time-travel-manifest.scm (%release-commits): Comment out revisions older than 1.3.0. --- etc/time-travel-manifest.scm | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/etc/time-travel-manifest.scm b/etc/time-travel-manifest.scm index 43d6708a0a..80c4c7c346 100644 --- a/etc/time-travel-manifest.scm +++ b/etc/time-travel-manifest.scm @@ -68,11 +68,19 @@ ;; Release commits: the list of version/commit pairs. '(("1.4.0" . "8e2f32cee982d42a79e53fc1e9aa7b8ff0514714") ("1.3.0" . "a0178d34f582b50e9bdbb0403943129ae5b560ff") - ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") - ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") - ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") - ("1.0.0" . "6298c3ffd9654d3231a6f25390b056483e8f407c") - ("0.16.0" . "4a0b87f0ec5b6c2dcf82b372dd20ca7ea6acdd9c"))) + + ;; FIXME: To merely compute the derivation of these revisions, we need to + ;; be able to build their dependencies. However, pre-built binaries are + ;; currently missing and some of these no longer build from source due to + ;; time bombs like . Thus, comment + ;; them output until we have substitutes for these old things. + + ;; ("1.2.0" . "a099685659b4bfa6b3218f84953cbb7ff9e88063") + ;; ("1.1.0" . "d62c9b2671be55ae0305bebfda17b595f33797f2") + ;; ("1.0.1" . "d68de958b60426798ed62797ff7c96c327a672ac") + ;; ("1.0.0" . "6298c3ffd9654d3231a6f25390b056483e8f407c") + ;; ("0.16.0" . "4a0b87f0ec5b6c2dcf82b372dd20ca7ea6acdd9c") + )) (manifest (map (match-lambda From 62ea0a0d3a921a25593b2a8db97d744fd2c53c08 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 9 Sep 2023 21:23:30 +0300 Subject: [PATCH 020/440] gnu: global: Fix ctags creation using pygments. * gnu/packages/code.scm (global)[arguments]: Adjust configure-flags to use a specific python interpreter. --- gnu/packages/code.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 9cdda2b751..1c21ad475b 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -200,6 +200,10 @@ highlighting your own code that seemed comprehensible when you wrote it.") (string-append "--with-universal-ctags=" #$(this-package-input "universal-ctags") "/bin/ctags") + ;; Otherwise this gets overridden in the 'configure phase. + (string-append "--with-python-interpreter=" + #$(this-package-input "python-wrapper") + "/bin/python") (string-append "--sysconfdir=" #$output "/share/gtags") "--localstatedir=/var" ; This needs to be a writable location. From 1bc09757868c26f14c119e3ce9842b86cb446f92 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:03 -0400 Subject: [PATCH 021/440] gnu: linux-libre: Update to 6.4.15. * gnu/packages/linux.scm (linux-libre-6.4-version): Update to 6.4.15. (linux-libre-6.4-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 bc1fedaad5..a347b8e8d2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -490,7 +490,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.4-version "6.4.14") +(define-public linux-libre-6.4-version "6.4.15") (define-public linux-libre-6.4-gnu-revision "gnu") (define deblob-scripts-6.4 (linux-libre-deblob-scripts @@ -500,7 +500,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1rwm09anyn4py1g877f9vh6ya86y2hfvlqx51bpa53dci5k0b0ds"))) (define-public linux-libre-6.4-pristine-source (let ((version linux-libre-6.4-version) - (hash (base32 "1rjh0jrn5qvxwzmyg478n08vckkld8r52nkc102ppqvsfhiy7skm"))) + (hash (base32 "1phlx375ln5pslw5vjqm029cdv6pzf4ang10xlrf90x5sb4fgy93"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.4))) From ea8a92701102a31d0c6923693834575192e7caa3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:17 -0400 Subject: [PATCH 022/440] gnu: linux-libre 6.1: Update to 6.1.52. * gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.52. (linux-libre-6.1-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 a347b8e8d2..04bcdd94d0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-6.1-version "6.1.51") +(define-public linux-libre-6.1-version "6.1.52") (define-public linux-libre-6.1-gnu-revision "gnu") (define deblob-scripts-6.1 (linux-libre-deblob-scripts @@ -518,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11"))) (define-public linux-libre-6.1-pristine-source (let ((version linux-libre-6.1-version) - (hash (base32 "0fqhmb6v28rssd44z7jw57mwvvskpl4kabjylck0pg54irnl9c2q"))) + (hash (base32 "0lis73mxnl7hxz8lyja6sfgmbym944l3k1h7dab6b4mw1nckfxsn"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.1))) From 5db78e7c1b06d1b4892bdb3e153b95b21577271e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 6 Sep 2023 23:39:43 -0400 Subject: [PATCH 023/440] gnu: linux-libre 5.15: Update to 5.15.131. * gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.131. (linux-libre-5.15-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 04bcdd94d0..67edc98013 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -523,7 +523,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (%upstream-linux-source version hash) deblob-scripts-6.1))) -(define-public linux-libre-5.15-version "5.15.130") +(define-public linux-libre-5.15-version "5.15.131") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -533,7 +533,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1c3lm0j401lv2lk39dmr4mlf5ic173snm7cc0cckl6czyvxr5ysy"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "0qix62jsn3z9yccakac7fvqnip19zi05qn0w5wkgb7rj0x0lwimb"))) + (hash (base32 "0sacnbw48lblnqaj56nybh588sq4k84gwf0r5zinzyrryj8k6z4r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) From 610752ac1ae8cef027c0c0afcef3e73b7747ef49 Mon Sep 17 00:00:00 2001 From: Olivier Dion Date: Thu, 7 Sep 2023 11:20:52 -0400 Subject: [PATCH 024/440] gnu: multipath-tools: Update to 0.9.6. * gnu/packages/linux.scm (multipath-tools): Update to 0.9.6. [#:make-flags]: Set systemd_prefix to output and remove SYSTEMDPATH. [#:phases]: Add phase 'no-fortfify-3 before 'build. [inputs]: Add util-linux "lib" output for libmount. Signed-off-by: Maxim Cournoyer --- gnu/packages/linux.scm | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 67edc98013..b1bcda5e70 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -5548,7 +5548,7 @@ arrays when needed.") (define-public multipath-tools (package (name "multipath-tools") - (version "0.9.3") + (version "0.9.6") (home-page "https://github.com/opensvc/multipath-tools") (source (origin (method git-fetch) @@ -5556,7 +5556,7 @@ arrays when needed.") (file-name (git-file-name name version)) (sha256 (base32 - "0zcnr1135znizbnfqhqv3by9i2qwn5vg6kgmj6ma3yy1x1krx0d4")) + "1933iqh9r54pdl95yck0n4bw7jiiblymc964vlc1787qd4q012sz")) (modules '((guix build utils))) (snippet '(begin @@ -5574,7 +5574,7 @@ arrays when needed.") (string-append "prefix=" #$output) ;; Install Udev rules below this directory, relative ;; to the prefix. - "SYSTEMDPATH=lib") + (string-append "systemd_prefix=" #$output)) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-source @@ -5606,6 +5606,16 @@ arrays when needed.") (("CFLAGS \\+= " match) (string-append match "-Wno-error=unused-function "))))) (delete 'configure) ;no configure script + (add-before 'build 'no-fortify-3 + (lambda _ + ;; NOTE: The check made seems to wrongly assume the + ;; FORTIFY_SOURCE=3 is valid. However, when compiling, warnings + ;; are emitted from glibc, resulting in failed build. Fix this + ;; by forcing the usage of FORTIFY_SOURCE=2. + (substitute* "create-config.mk" + (("FORTIFY_SOURCE=3") + "FORTIFY_SOURCE=2")) + )) (add-before 'build 'set-LDFLAGS (lambda _ ;; Note: this cannot be passed as a make flag because that will @@ -5623,7 +5633,9 @@ arrays when needed.") liburcu lvm2 readline - eudev)) + eudev + ;; For libmount. + `(,util-linux "lib"))) (synopsis "Access block devices through multiple paths") (description "This package provides the following binaries to drive the From ff3eb851171f20654b8d6462c6b01ff3198a60e5 Mon Sep 17 00:00:00 2001 From: Olivier Dion Date: Thu, 7 Sep 2023 11:20:53 -0400 Subject: [PATCH 025/440] gnu: liburcu: Update to 0.14.0. * gnu/packages/datastructures.scm (liburcu): Update to 0.14.0. Signed-off-by: Maxim Cournoyer --- gnu/packages/datastructures.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm index bd4f099d94..0689ef4259 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -213,14 +213,14 @@ allows multiple concurrent reader and writer threads.") (define-public liburcu (package (name "liburcu") - (version "0.13.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (string-append "https://www.lttng.org/files/urcu/" "userspace-rcu-" version ".tar.bz2")) (sha256 (base32 - "10rh6v9j13622cjlzx31cfpghjy0kqkvn6pb42whwwcg5cyz64rj")))) + "0kwx4fi3gn4p4sdxqkz2zh4z0fv06q449bnz43zjqfad3lkbyhya")))) (build-system gnu-build-system) (native-inputs (list perl)) ; for tests From 2eb6df537c36da8bf8e81ff698421f6fb1bfd1ab Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 10 Sep 2023 09:19:18 -0400 Subject: [PATCH 026/440] gnu: Remove extraneous imports. * gnu/packages/perl.scm: Remove (gnu packages hurd) import. * gnu/packages/boost.scm: Likewise. Remove (srfi srfi-1). --- gnu/packages/boost.scm | 4 +--- gnu/packages/perl.scm | 1 - 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index d2b676cc73..98dccf7f16 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -45,14 +45,12 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages compression) - #:use-module (gnu packages hurd) #:use-module (gnu packages icu4c) #:use-module (gnu packages llvm) #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages shells) - #:use-module (gnu packages mpi) - #:use-module (srfi srfi-1)) + #:use-module (gnu packages mpi)) (define (version-with-underscores version) (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 6175a38365..8b82c272fc 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -76,7 +76,6 @@ #:use-module (gnu packages gd) #:use-module (gnu packages gl) #:use-module (gnu packages gtk) - #:use-module (gnu packages hurd) #:use-module (gnu packages image) #:use-module (gnu packages language) #:use-module (gnu packages less) From ab971e9c1922ae6eeec47401cb589ae15f29e15f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 11 Sep 2023 10:56:03 +0300 Subject: [PATCH 027/440] system: vm-image: Remove duplicate packages. * gnu/system/examples/vm-image.tmpl (use-package-modules): Remove unneeded modules. (operating-system)[packages]: Remove nvi, wget. --- gnu/system/examples/vm-image.tmpl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/system/examples/vm-image.tmpl b/gnu/system/examples/vm-image.tmpl index 343287eaf6..b68183a023 100644 --- a/gnu/system/examples/vm-image.tmpl +++ b/gnu/system/examples/vm-image.tmpl @@ -7,8 +7,8 @@ (use-modules (gnu) (guix) (srfi srfi-1)) (use-service-modules desktop mcron networking spice ssh xorg sddm) -(use-package-modules bootloaders certs fonts nvi - package-management wget xorg) +(use-package-modules bootloaders certs fonts + package-management xorg) (define vm-image-motd (plain-file "motd" " \x1b[1;37mThis is the GNU system. Welcome!\x1b[0m @@ -77,7 +77,7 @@ accounts.\x1b[0m root ALL=(ALL) ALL %wheel ALL=NOPASSWD: ALL\n")) - (packages (append (list font-bitstream-vera nss-certs nvi wget) + (packages (append (list font-bitstream-vera nss-certs) %base-packages)) (services From 3f76970fda82057f12429f81c41a47d8d8c3b954 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 2 Sep 2023 23:18:48 +0200 Subject: [PATCH 028/440] gnu: yelp: Provide dependencies to display "man:" URIs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Previously a command like the following one would fail to display the expected man page: guix shell yelp coreutils -C \ --expose=/tmp/.X11-unix --expose=/run/user \ --expose=/var/run/dbus --expose=/etc/machine-id -E ^DISPLAY -- \ /bin/sh -c \ 'export MANPATH=$GUIX_ENVIRONMENT/share/man; echo $MANPATH; yelp man:ls' * gnu/packages/gnome.scm (yelp)[arguments]: New field. [inputs]: Add ‘man-db’ and ‘groff-minimal’. Reported-by: Luis Felipe --- gnu/packages/gnome.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 3b80692e90..36fe1a80a1 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -142,6 +142,7 @@ #:use-module (gnu packages geo) #:use-module (gnu packages gperf) #:use-module (gnu packages graphviz) + #:use-module (gnu packages groff) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -7336,6 +7337,28 @@ jQuery.Syntax JavaScript libraries.") (base32 "0h9vf4fx056imjf8ibmn03wg1c3hniipy1nsm2jqi62lp1m19c95")))) (build-system glib-or-gtk-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-man-file-name + (lambda* (#:key inputs #:allow-other-keys) + ;; Invoke 'man' directly instead of searching $PATH. + (substitute* '("libyelp/yelp-man-parser.c" + "libyelp/yelp-uri.c") + (("\"man\"") + (string-append "\"" + (search-input-file inputs "bin/man") + "\"")) + (("G_SPAWN_SEARCH_PATH") + "0")))) + (add-after 'install 'help-man-find-its-dependencies + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; XXX: Currently 'man' looks for 'groff' in $PATH in one + ;; case. This should be fixed in 'man-db' proper. + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/yelp") + `("PATH" ":" prefix + (,(dirname (search-input-file inputs "bin/groff")))))))))) (native-inputs (list `(,glib "bin") ; for glib-genmarshal, etc. intltool @@ -7347,6 +7370,8 @@ jQuery.Syntax JavaScript libraries.") (list gsettings-desktop-schemas libhandy libxslt + man-db ;for URIs like "man:ls" + groff-minimal ;ditto sqlite webkitgtk yelp-xsl)) From d514b7b4adf9aef198e5aedecffaf6f7014c0044 Mon Sep 17 00:00:00 2001 From: Thanos Apollo Date: Mon, 14 Aug 2023 12:38:19 +0300 Subject: [PATCH 029/440] gnu: Add emacs-yeetube. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-yeetube): New variable. Signed-off-by: Ludovic Courtès --- 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 e971edb676..355afbf8fb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -134,6 +134,7 @@ ;;; Copyright © 2023 Ahmad Draidi ;;; Copyright © 2023 Sergiu Ivanov ;;; Copyright © 2023 Camilo Q.S. (Distopico) +;;; Copyright © 2023 Thanos Apollo ;;; ;;; This file is part of GNU Guix. ;;; @@ -27896,6 +27897,33 @@ as playing them in some video player, or downloading them.") and comments.") (license license:gpl3+)))) +(define-public emacs-yeetube + (package + (name "emacs-yeetube") + (version "1.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~thanosapollo/yeetube.el") + (commit version))) + (sha256 + (base32 + "0vfap6sri6qnswrjsp6qvmrp98bvrfh58gwdqbjiakq1fzvcrm03")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (inputs + (list mpv yt-dlp)) + (home-page "https://sr.ht/~thanosapollo/yeetube.el") + (synopsis "Youtube & Invidious front-end for Emacs") + (description + "This package offers an Emacs interface that allows you to search YouTube +or an Invidious instance for a specific query. The search results are shown as +links in an org-mode buffer. The videos can be opened to a user-defined video +player(by default mpv) or downloaded using yt-dlp. This package also includes +a yt-dlp front-end.") + (license license:gpl3+))) + (define-public emacs-org-web-tools (package (name "emacs-org-web-tools") From 251bf55f507860d9775b520585c0fdd7ede7d534 Mon Sep 17 00:00:00 2001 From: Fabio Natali Date: Sun, 13 Aug 2023 16:16:15 +0100 Subject: [PATCH 030/440] gnu: Add emacs-notmuch-indicator. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-notmuch-indicator): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 355afbf8fb..4a4aa85dbc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -30302,6 +30302,27 @@ displays as you type thanks to Helm, though @command{notmuch-search} does the real search.") (license license:gpl3+))) +(define-public emacs-notmuch-indicator + (package + (name "emacs-notmuch-indicator") + (version "1.0.1") + (home-page "https://git.sr.ht/~protesilaos/notmuch-indicator") + (source (origin + (method url-fetch) + (uri (string-append + "https://elpa.gnu.org/packages/notmuch-indicator-" version + ".tar")) + (sha256 + (base32 + "1n5k2ikk93mdwqqysf6l7gd8i6iazk8yvbqpf8xnz5zny248cc2x")))) + (build-system emacs-build-system) + (synopsis "Display a mode line indicator with @code{notmuch-count} output") + (description "This package renders an indicator with an email count of the +@code{notmuch} index on the Emacs mode line. The underlying mechanism is that of +@code{notmuch-count}, which is used to find the number of items that match the +given search terms.") + (license license:gpl3+))) + (define-public emacs-notmuch-maildir (package (name "emacs-notmuch-maildir") From 1cca04d7cff75fc1fe8913b23096109a17d43a97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 11 Sep 2023 23:35:28 +0200 Subject: [PATCH 031/440] gnu: emacs-php-mode: Update URL. * gnu/packages/emacs-xyz.scm (emacs-php-mode)[source, home-page]: Update URL and factorize it. Co-authored-by: Piotr Kwiecinski --- 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 4a4aa85dbc..a380abc4ed 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -18304,11 +18304,12 @@ in Emacs.") (package (name "emacs-php-mode") (version "1.25.0") + (home-page "https://github.com/emacs-php/php-mode") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ejmr/php-mode") + (url home-page) (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -18331,7 +18332,6 @@ in Emacs.") (lambda _ (chdir "lisp")))))) (propagated-inputs (list emacs-projectile)) - (home-page "https://github.com/ejmr/php-mode") (synopsis "Major mode for editing PHP code") (description "PHP mode is a major mode for editing PHP source code. It's an extension From a35bfb61168ee706a94556a5bf834d27c022d2bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Pastor=20P=C3=A9rez?= Date: Sun, 10 Sep 2023 17:42:05 +0200 Subject: [PATCH 032/440] gnu: Add mini. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/image.scm (mini): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/image.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 75f9e3c691..b41c1eac73 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1931,6 +1931,45 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI (home-page "https://niftilib.sourceforge.net") (license license:public-domain))) +(define-public mini + (package + (name "mini") + (version "0.9.14") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pulzed/mINI") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01wn7h9rjz9h6cr11dd62jsb3315d1h6c33pdmwi2l7d8a4n3h8d")))) + (build-system gnu-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (delete 'build) + (delete 'configure) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "tests" + (for-each (lambda (test) + (let ((test-name (basename test + ".cpp"))) + (invoke "./build.sh" test-name) + (invoke "./run.sh" test-name))) + (find-files "." ".cpp")))))) + (replace 'install + (lambda _ + (install-file "src/mini/ini.h" + (string-append #$output "/include/mini"))))))) + (home-page "https://github.com/pulzed/mINI") + (synopsis "INI file reader and writer header library") + (description + "This is a tiny, header-only C++ library for manipulating INI files.") + (license license:expat))) + (define-public gpick (package (name "gpick") From 3235bfa25a82c1dbe6a8a0ec83ae98f840d1deb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Pastor=20P=C3=A9rez?= Date: Sun, 10 Sep 2023 17:42:06 +0200 Subject: [PATCH 033/440] gnu: Add picket. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/image.scm (picket): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/image.scm | 46 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index b41c1eac73..403409975a 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1970,6 +1970,52 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI "This is a tiny, header-only C++ library for manipulating INI files.") (license license:expat))) +(define-public picket + (package + (name "picket") + (version "1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rajter/picket") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1zhpynyakjx9nc51b1j80b4y3138p3l380kp1cqmmjx2n9430144")) + (snippet '(begin + ;; bundled mINI header library. + (delete-file "src/cfg/ini.h"))))) + (native-inputs (list pkg-config)) + (inputs (list gtkmm-3 mini)) + (arguments + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-mini-includes + (lambda _ + (substitute* '("src/cfg/config.h" + "src/cfg/config.cpp") + (("#include \"ini.h\"") + "#include \"mini/ini.h\"")) + (substitute* "src/main.cpp" + (("/usr") + #$output)))) + (add-after 'unpack 'fix-cmake-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("src/cfg/ini.h") + (search-input-file inputs + "/include/mini/ini.h")) + (("/usr/") + #$output))))))) + (build-system cmake-build-system) + (home-page "https://github.com/rajter/picket") + (synopsis "Screen color picker with custom format output") + (description + "Picket is a screen color picker that includes a magnifier and supports +custom formats for representing color values..") + (license license:gpl3+))) + (define-public gpick (package (name "gpick") From 5ff9afb5fdc6e34936683524907343859976a805 Mon Sep 17 00:00:00 2001 From: Cayetano Santos Date: Mon, 21 Aug 2023 09:46:34 +0200 Subject: [PATCH 034/440] gnu: emacs-mastodon: Update to 1.0.0-1.20dec88. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs-xyz.scm (emacs-mastodon): Update to 1.0.0-1.20dec88. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs-xyz.scm | 63 ++++++++++++++++++++------------------ 1 file changed, 33 insertions(+), 30 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a380abc4ed..6063dc8958 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -32794,37 +32794,40 @@ time.") (license license:gpl3+))) (define-public emacs-mastodon - (package - (name "emacs-mastodon") - (version "1.0.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://codeberg.org/martianh/mastodon.el") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "13swcbvwhjl8ksrgzvmfafkgd3iz8znk49bs1n48w3g9qvh097w7")))) - (build-system emacs-build-system) - (arguments - (list #:phases - #~(modify-phases %standard-phases - ;; Move the source files to the top level, which is included in - ;; the EMACSLOADPATH. - (add-after 'unpack 'move-source-files - (lambda _ - (let ((el-files (find-files "./lisp" ".*\\.el$"))) - (for-each (lambda (f) - (rename-file f (basename f))) - el-files))))))) - (propagated-inputs - (list emacs-request)) - (home-page "https://codeberg.org/martianh/mastodon.el") - (synopsis "Emacs client for Mastodon") - (description "@code{mastodon.el} is an Emacs client for Mastodon, the + ;; No release in ~1 year, hence this snapshot. + (let ((commit "20dec8871c9bb5f5e418bfc197e7533b5e3065e3") + (revision "1")) + (package + (name "emacs-mastodon") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://codeberg.org/martianh/mastodon.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15cfjny99yw5frdp8nlyazlwgscvfvbinsj0fbdfprxf50k2zjs6")))) + (build-system emacs-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; Move the source files to the top level, which is included in + ;; the EMACSLOADPATH. + (add-after 'unpack 'move-source-files + (lambda _ + (let ((el-files (find-files "./lisp" ".*\\.el$"))) + (for-each (lambda (f) + (rename-file f (basename f))) + el-files))))))) + (propagated-inputs + (list emacs-request emacs-ts emacs-persist)) + (home-page "https://codeberg.org/martianh/mastodon.el") + (synopsis "Emacs client for Mastodon") + (description "@code{mastodon.el} is an Emacs client for Mastodon, the federated microblogging social network.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-ebdb (package From a5b5df7f7fbbb98487b2e7a59941efee6492bc7f Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 15:46:47 -0400 Subject: [PATCH 035/440] gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. Fixes . * guix/gnu-maintenance.scm (import-html-updatable-release): Update doc. : New nested procedure. Apply it to the origin URI. Reported-by: kiasoc5 --- guix/gnu-maintenance.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 5a84fcb117..302243559d 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,17 +975,24 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE. Do that by crawling the HTML page of -the directory containing its source tarball. Optionally include a VERSION -string to fetch a specific version." - (let* ((uri (string->uri - (match (origin-uri (package-source package)) - ((and (? string?) - (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) url) - ((url _ ...) url)))) + "Return the latest release of PACKAGE else #f. Do that by crawling the HTML +page of the directory containing its source tarball. Optionally include a +VERSION string to fetch a specific version." + + (define (expand-uri uri) + (string->uri + (match uri + ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) + url) + ((url _ ...) + ;; This case is for when the URI is a list of possibly mirror URLs as + ;; well as HTTP URLs. + (expand-uri url))))) + + (let* ((uri (expand-uri (origin-uri (package-source package)))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From a9d5d1d9dd186ab21ee44ccf9b5c777e79f83c5b Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:30:43 -0400 Subject: [PATCH 036/440] Revert "gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs." This reverts commit a5b5df7f7fbbb98487b2e7a59941efee6492bc7f. Pushed too early. --- guix/gnu-maintenance.scm | 29 +++++++++++------------------ 1 file changed, 11 insertions(+), 18 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 302243559d..5a84fcb117 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,24 +975,17 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE else #f. Do that by crawling the HTML -page of the directory containing its source tarball. Optionally include a -VERSION string to fetch a specific version." - - (define (expand-uri uri) - (string->uri - (match uri - ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) - url) - ((url _ ...) - ;; This case is for when the URI is a list of possibly mirror URLs as - ;; well as HTTP URLs. - (expand-uri url))))) - - (let* ((uri (expand-uri (origin-uri (package-source package)))) + "Return the latest release of PACKAGE. Do that by crawling the HTML page of +the directory containing its source tarball. Optionally include a VERSION +string to fetch a specific version." + (let* ((uri (string->uri + (match (origin-uri (package-source package)) + ((and (? string?) + (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) url) + ((url _ ...) url)))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From 2a7f031ca9d6d16fe0264023d8beca02b3ac0050 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:37:34 -0400 Subject: [PATCH 037/440] gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. This reinstate commit a5b5df7f7fbbb98487b2e7a59941efee6492bc7f with a fix to the inner expand-uri procedure. --- guix/gnu-maintenance.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/guix/gnu-maintenance.scm b/guix/gnu-maintenance.scm index 5a84fcb117..881e941fbf 100644 --- a/guix/gnu-maintenance.scm +++ b/guix/gnu-maintenance.scm @@ -975,17 +975,24 @@ updater." ((url-predicate http-url?) package))) (define* (import-html-updatable-release package #:key (version #f)) - "Return the latest release of PACKAGE. Do that by crawling the HTML page of -the directory containing its source tarball. Optionally include a VERSION -string to fetch a specific version." - (let* ((uri (string->uri - (match (origin-uri (package-source package)) - ((and (? string?) - (? (cut string-prefix? "mirror://" <>) url)) - ;; Retrieve the authoritative HTTP URL from a mirror. - (http-url? url)) - ((? string? url) url) - ((url _ ...) url)))) + "Return the latest release of PACKAGE else #f. Do that by crawling the HTML +page of the directory containing its source tarball. Optionally include a +VERSION string to fetch a specific version." + + (define (expand-uri uri) + (match uri + ((and (? string?) (? (cut string-prefix? "mirror://" <>) url)) + ;; Retrieve the authoritative HTTP URL from a mirror. + (http-url? url)) + ((? string? url) + url) + ((url _ ...) + ;; This case is for when the URI is a list of possibly + ;; mirror URLs as well as HTTP URLs. + (expand-uri url)))) + + (let* ((uri (string->uri + (expand-uri (origin-uri (package-source package))))) (custom (assoc-ref (package-properties package) 'release-monitoring-url)) (base (or custom From daeeaa221605726d8853b00261619ba039bd6db7 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 23:48:19 -0400 Subject: [PATCH 038/440] gnu: emacs-magit: Update to 3.3.0-6.7a1d503. * gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.3.0-6.7a1d503. --- gnu/packages/emacs-xyz.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6063dc8958..a4c6f45feb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -1464,10 +1464,10 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (license license:gpl2+)))) (define-public emacs-magit - ;; Use this unreleased commit to benefit from a recent change needed to - ;; add Reviewed-by: tags for any contributor in commit messages. - (let ((commit "186414ae418a07a46c413f05c68413a76256a05e") - (revision "5")) + ;; Use this unreleased commit to benefit from a recent improvements with + ;; regard to adding git trailers such as "Reviewed-by". + (let ((commit "7a1d50347086678217cf90a32dda277b76ea3081") + (revision "6")) (package (name "emacs-magit") (version (git-version "3.3.0" revision commit)) @@ -1479,7 +1479,7 @@ libgit2 bindings for Emacs, intended to boost the performance of Magit.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0rhsbcjfjw0z3vy2ix30y4h55c0cx4lyvz6mbijwbbjryln71kpj")))) + (base32 "1yn3v24w0sx6r8jqw8blfvyjdjfz5xa7c3x8p6xw1lj7b81l8i0l")))) (build-system emacs-build-system) (arguments (list From 288799d3e8fa995a8bdc1f460378484124a30248 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:10 +0100 Subject: [PATCH 039/440] gnu: musl-cross: Remove i586-gnu from supported-systems. As I don't think musl supports the Hurd. * gnu/packages/heads.scm (musl-cross)[supported-systems]: Remove i586-gnu. --- gnu/packages/heads.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/heads.scm b/gnu/packages/heads.scm index 212849f2a9..268d4d0198 100644 --- a/gnu/packages/heads.scm +++ b/gnu/packages/heads.scm @@ -158,6 +158,7 @@ done (uri "http://www.musl-libc.org/releases/musl-1.1.24.tar.gz") (sha256 (base32 "18r2a00k82hz0mqdvgm7crzc7305l36109c0j9yjmkxj2alcjw0k")))))) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://github.com/osresearch/heads") (synopsis "Musl-cross gcc 5 toolchain") (description "Musl-cross toolchain: binutils, gcc 5 and musl.") From 0e08ad7f19d5b29a4883468552b5d213a7bdb66e Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:11 +0100 Subject: [PATCH 040/440] gnu: linux-libre-headers: Remove i586-gnu from supported-systems. As I don't think attempting to build for the Hurd is useful. * gnu/packages/heads.scm (make-linux-libre-headers*): Remove i586-gnu from supported-systems. --- gnu/packages/linux.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b1bcda5e70..91109c41d9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -739,6 +739,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (format p "~a-default~%" ,version))))))) #:allowed-references () #:tests? #f)) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://www.gnu.org/software/linux-libre/") (synopsis "GNU Linux-Libre kernel headers") (description "Headers of the Linux-Libre kernel.") From 53f510dad6cc1b55b4abdbbfd55e507a9463a80f Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 5 Sep 2023 12:35:12 +0100 Subject: [PATCH 041/440] gnu: skalibs: Remove i586-gnu from %supported-systems. * gnu/packages/skarnet.scm (skalibs)[supported-systems]: Remove i586-gnu. --- gnu/packages/skarnet.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm index 2c7b0f9c23..6781e2eb58 100644 --- a/gnu/packages/skarnet.scm +++ b/gnu/packages/skarnet.scm @@ -49,6 +49,7 @@ (substitute* "Makefile" (("\\$\\(wildcard src/lib\\*/\\*.c\\)") "$(sort $(wildcard src/lib*/*.c))"))))))) + (supported-systems (delete "i586-gnu" %supported-systems)) (home-page "https://skarnet.org/software/skalibs/") (synopsis "Platform abstraction libraries for skarnet.org software") (description From 93cb2880d6c45f113c3b18d3732049115ef08070 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 12 Sep 2023 08:15:07 +0100 Subject: [PATCH 042/440] gnu: nar-herder: Use guile-next. As this provides suspendable soft/custom ports, which I'd like to use. * gnu/packages/package-management.scm (nar-herder)[native-inputs,inputs]: Use guile-next. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index aa24798071..51a5d52131 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1771,7 +1771,7 @@ in an isolated environment, in separate namespaces.") guile-gnutls ;; Guile libraries are needed here for cross-compilation. - (car (assoc-ref (package-native-inputs guix) "guile")) + guile-next guile-json-4 guile-gcrypt guix @@ -1783,7 +1783,7 @@ in an isolated environment, in separate namespaces.") guile-sqlite3)) (inputs (list bash-minimal - (car (assoc-ref (package-native-inputs guix) "guile")))) + guile-next)) (propagated-inputs (list guile-json-4 guile-gcrypt From 3acd355455a74a6e08bdcecc72e314c27e7c56b3 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Thu, 7 Sep 2023 18:27:09 +0800 Subject: [PATCH 043/440] gnu: svt-av1: Update to 1.7.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/video.scm (svt-av1): Update to 1.7.0. Signed-off-by: 宋文武 Signed-off-by: Christopher Baines --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 153fe354d5..e8cee27382 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -5255,7 +5255,7 @@ transcode or reformat the videos in any way, producing perfect backups.") (define-public svt-av1 (package (name "svt-av1") - (version "1.3.0") + (version "1.7.0") (source (origin (method git-fetch) @@ -5264,7 +5264,7 @@ transcode or reformat the videos in any way, producing perfect backups.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0blnla32yz665bx0xyx8lrjs2wqd2xhpbqwwpz72mq7zf341j8vv")))) + (base32 "1308g0nqxq65h76a7h91999cbglkwihgrpid64kdn0r9vh6399sq")))) (build-system cmake-build-system) (arguments ;; The test suite tries to download test data and git clone a 3rd-party From 8d51e31f862181c835dc75b74033be325d85d967 Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Tue, 12 Sep 2023 08:29:24 +0100 Subject: [PATCH 044/440] gnu: sqlite-next: Update to 3.42.0. * gnu/packages/sqlite.scm (sqlite-next): Update to 3.42.0. Signed-off-by: Christopher Baines --- gnu/packages/sqlite.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/sqlite.scm b/gnu/packages/sqlite.scm index 2e727bd933..a4db47270d 100644 --- a/gnu/packages/sqlite.scm +++ b/gnu/packages/sqlite.scm @@ -115,10 +115,10 @@ is in the public domain.") (define-public sqlite-next (package (inherit sqlite) - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (sqlite-uri version 2022)) (sha256 (base32 - "1rw0i63822pdkb3a16sqj4jdcp5zg0ffjmi26mshqw6jfqh5acq3")))))) + "19lc11fwl7jfv94hnjih0gr41jakz38ra23cbk5449vf3hbgvg3s")))))) From d6ad06cd6c9d96735aea5fe98c7dbf27adec25db Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Thu, 27 Jul 2023 22:37:14 +0800 Subject: [PATCH 045/440] gnu: python-apsw: Update to 3.42.0.1. * gnu/packages/databases.scm (python-apsw): Update to 3.42.0.1. Signed-off-by: Christopher Baines --- gnu/packages/databases.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 3d41649f4d..8d87f238b5 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3706,7 +3706,7 @@ PickleShare.") (define-public python-apsw (package (name "python-apsw") - (version "3.40.0.0") + (version "3.42.0.1") ;; The compressed release has fetching functionality disabled. (source (origin @@ -3716,11 +3716,11 @@ PickleShare.") version "/apsw-" version ".zip")) (sha256 (base32 - "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad")))) + "0dr7zymn45x2793cilr709rnwn9g1c4n4vzln57y2lhj7420ykic")))) (build-system pyproject-build-system) (native-inputs (list python-cython unzip)) - (inputs (list sqlite-next)) ;SQLite 3.40 required. + (inputs (list sqlite-next)) ;SQLite 3.42 required. (arguments (list #:phases From 8294f45dfc849f3006ea362ce754d04c5ecf89db Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Thu, 27 Jul 2023 22:43:07 +0800 Subject: [PATCH 046/440] gnu: python-cgatcore: Update to 0.6.15. * gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15. Signed-off-by: Christopher Baines --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8968325e83..9500751a96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19134,7 +19134,7 @@ coordinates between different assemblies.") (define-public python-cgatcore (package (name "python-cgatcore") - (version "0.6.14") + (version "0.6.15") ;; The version of pypi does not include test data. (source (origin (method git-fetch) @@ -19144,7 +19144,7 @@ coordinates between different assemblies.") (file-name (git-file-name name version)) (sha256 (base32 - "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p")))) + "103hpdnkqr3a34blbicshk56j36g652s0g1zi9isppc5dngn0s18")))) (build-system pyproject-build-system) (arguments (list From cdddc6bc28e2026b78800533069688e510df42f2 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Thu, 24 Aug 2023 09:05:04 +0300 Subject: [PATCH 047/440] gnu: guile-png: Update to 0.7.1 * gnu/packages/guile-xyz.scm (guile-png): Update to 0.7.1. [arguments]: Update style and delete "strip" phase. [description]: Update. Signed-off-by: Christopher Baines --- gnu/packages/guile-xyz.scm | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index b40079c383..01dbe9b3ad 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -3856,7 +3856,7 @@ debugging code.") (define-public guile-png (package (name "guile-png") - (version "0.7.0") + (version "0.7.1") (source (origin (method git-fetch) (uri (git-reference @@ -3865,10 +3865,13 @@ debugging code.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0nkim662lb48y8n5hik8rrj76600v2inwaxwnfpdny7h2j0yq1wm")))) + "0y65795s9bs69msqvdbq8h34n00bkfs5v1d44wz21nwdffvq6557")))) (build-system gnu-build-system) (arguments - `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings + (list + #:make-flags #~(list "GUILE_AUTO_COMPILE=0") ;to prevent guild warnings + #:phases #~(modify-phases %standard-phases + (delete 'strip)))) (native-inputs (list autoconf automake pkg-config @@ -3884,9 +3887,9 @@ debugging code.") (synopsis "PNG file parsing library for Guile") (description "@code{guile-png} is a GNU Guile library for working with the -@url{https://en.wikipedia.org/wiki/PNG, PNG format}. This library provides -API for reading and writing PNG data, as well as some basic image processing -filters.") +@url{https://en.wikipedia.org/wiki/PNG, PNG format}. This library provides API for +reading and writing PNG data, as well as some graphic primitives and basic image +processing filters.") (license license:gpl3+))) (define-public nomad From e2a7c227dea5b361e2ebdbba24b923d1922a79d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sat, 2 Sep 2023 11:50:29 +0800 Subject: [PATCH 048/440] gnu: xfce4-terminal: Update to 1.1.0. * gnu/packages/xfce.scm (xfce4-terminal): Update to 1.1.0. 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 3292db4f58..cb2121f338 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -1082,7 +1082,7 @@ features playback of local media files, DVD/CD and live streams.") (define-public xfce4-terminal (package (name "xfce4-terminal") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" name "/" @@ -1090,7 +1090,7 @@ features playback of local media files, DVD/CD and live streams.") name "-" version ".tar.bz2")) (sha256 (base32 - "1x5saijxykxmn2hksf4qvaj965b6i0wy62z9hgrc2vvwmxbmkrbq")))) + "18yl792x617qa90g6caw4cy1arfl847majjxkxs0k6rb4ivk70j0")))) (build-system gnu-build-system) (arguments (list From 30ec6f2fb5bdac917df16d1efa122fad81518a0e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 12:26:41 +0200 Subject: [PATCH 049/440] gnu: macs: Update to 2.2.9.1. * gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase. [native-inputs]: Move python-cython from here... [inputs]: ...and python-numpy from here... [propagated-inputs]: ...to here. --- gnu/packages/bioinformatics.scm | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9500751a96..0df5bbfad5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7023,7 +7023,7 @@ experiments.") (define-public macs (package (name "macs") - (version "2.2.7.1") + (version "2.2.9.1") (source (origin ;; The PyPi tarball does not contain tests. (method git-fetch) @@ -7033,7 +7033,7 @@ experiments.") (file-name (git-file-name name version)) (sha256 (base32 - "08zsgh65xbpv1md2s3wqmrk9g2mz6izmn59ryw5lbac54120p291")) + "10vwc09fq4nvbd39hax1949mvq2wvkgz0k3p2zqmqwq8hv9r5l0j")) (modules '((guix build utils))) ;; Remove files generated by Cython (snippet @@ -7048,21 +7048,17 @@ experiments.") ;; Python 3.10 is in fact more recent than 3.6. (substitute* "setup.py" (("float\\(sys.version\\[:3\\]\\)<3.6") "False")))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'build 'set-HOME - (lambda _ (setenv "HOME" "/tmp"))) - (replace 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "-v"))))))) - (inputs - (list python-numpy)) + (lambda _ (setenv "HOME" "/tmp")))))) + ;; Propagate these for use of macs as a library. + (propagated-inputs + (list python-cython python-numpy)) (native-inputs - (list python-cython python-pytest)) + (list python-pytest)) (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description From 9996896dc252a02ba3b17473a685ce8957237546 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 12:28:08 +0200 Subject: [PATCH 050/440] gnu: Add python-peaks2utr. * gnu/packages/bioinformatics.scm (python-peaks2utr): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0df5bbfad5..e24d70e569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1945,6 +1945,42 @@ matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.") (license license:expat))) +(define-public python-peaks2utr + (package + (name "python-peaks2utr") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "peaks2utr" version)) + (sha256 + (base32 + "1idp9cgwqxvryf4qqrc1xjsamfqn3jmr56kmjp2h1ysmckwmhw4v")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; These two tests fail because file names are not URLs. + '(list "-k" "not test_annotation.py"))) + (propagated-inputs + (list python-asgiref + python-gffutils + python-importlib-resources + macs + python-numpy + python-psutil + python-pybedtools + python-pysam + python-requests + python-tqdm + python-typing-extensions + python-zipp)) + (home-page "https://github.com/haessar/peaks2utr") + (synopsis "Python CLI for annotating three prime UTR") + (description + "This package provides a robust, parallelized Python CLI for annotating +three prime UTR.") + (license license:gpl3+))) + (define-public python-pegasusio (package (name "python-pegasusio") From 076b3384dfa29ae118d0375d516376a7fe98a197 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 09:29:22 -0400 Subject: [PATCH 051/440] gnu: qemu: Reinstate the iothreads-commit-active test. * gnu/packages/virtualization.scm (qemu) [arguments]: Add set-SOCK_DIR phase. (qemu-minimal) [arguments]: Delete the disable-extra-tests phase. --- gnu/packages/virtualization.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 5c5225b694..f5bdedd45e 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -385,6 +385,14 @@ (cut string-suffix? "-linux-user" <>)))))))) + (add-before 'check 'set-SOCK_DIR + (lambda _ + ;; The default value for SOCK_DIR is TMPDIR, which can be long + ;; in the build chroot (e.g.: + ;; /tmp/guix-build-qemu-minimal-drv-0); set it to SOCK_DIR to + ;; avoid using more than 109 characters for socket files (the + ;; limit when using the kernel Linux). + (setenv "SOCK_DIR" "/tmp"))) (add-after 'install 'delete-firmwares (lambda _ ;; Delete firmares that are accessible on --firmwarepath. @@ -542,14 +550,7 @@ server and embedded PowerPC, and S390 guests.") #~(modify-phases #$phases (delete 'configure-user-static) (delete 'build-user-static) - (delete 'install-user-static) - (add-after 'disable-unusable-tests 'disable-extra-tests - (lambda _ - ;; Interesting, the iothreads-commit-active test only fails in - ;; qemu-minimal, not the complete variant (see: - ;; https://gitlab.com/qemu-project/qemu/-/issues/1855). - (delete-file - "tests/qemu-iotests/tests/iothreads-commit-active"))))))) + (delete 'install-user-static))))) ;; Remove dependencies on optional libraries, notably GUI libraries. (native-inputs (filter (lambda (input) From f0e05411bdcb36f5adba493555c360799307f641 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 10:03:44 -0400 Subject: [PATCH 052/440] search-paths: Add $TZDIR. * guix/search-paths.scm ($TZDIR): New search path. --- guix/search-paths.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/guix/search-paths.scm b/guix/search-paths.scm index fcbe7b7953..8dc81861c9 100644 --- a/guix/search-paths.scm +++ b/guix/search-paths.scm @@ -37,6 +37,7 @@ $PKG_CONFIG_PATH $SSL_CERT_DIR $SSL_CERT_FILE + $TZDIR search-path-specification->sexp sexp->search-path-specification @@ -104,16 +105,22 @@ (define $SSL_CERT_DIR (search-path-specification (variable "SSL_CERT_DIR") - (separator #f) ;single entry + (separator #f) ;single entry (files '("etc/ssl/certs")))) (define $SSL_CERT_FILE (search-path-specification (variable "SSL_CERT_FILE") (file-type 'regular) - (separator #f) ;single entry + (separator #f) ;single entry (files '("etc/ssl/certs/ca-certificates.crt")))) +(define $TZDIR + (search-path-specification + (variable "TZDIR") + (files '("share/zoneinfo")) + (separator #f))) ;single entry + (define (search-path-specification->sexp spec) "Return an sexp representing SPEC, a . The sexp corresponds to the arguments expected by `set-path-environment-variable'." From 4cb2e08b8eb1acc824b72ec17b483d7d85b5af68 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Tue, 12 Sep 2023 10:05:00 -0400 Subject: [PATCH 053/440] gnu: python-django-4.0: Use $TZDIR. * gnu/packages/django.scm (python-django-4.0) [native-search-paths]: Use $TZDIR. --- gnu/packages/django.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index b089954b6b..577789e988 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -34,6 +34,7 @@ #:use-module (guix gexp) #:use-module (guix build-system python) #:use-module (guix deprecation) + #:use-module (guix search-paths) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages compression) @@ -126,9 +127,7 @@ ;; Set TZDIR when 'tzdata' is available so that timezone functionality ;; works (mostly) out of the box in containerized environments. ;; Note: This search path actually belongs to 'glibc'. - (list (search-path-specification - (variable "TZDIR") - (files '("share/zoneinfo"))))) + (list $TZDIR)) (home-page "https://www.djangoproject.com/") (synopsis "High-level Python Web framework") (description From 07d43c66d5c11fef61f9846fefb97fa18e4764f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 12 Sep 2023 23:28:40 +0200 Subject: [PATCH 054/440] gnu: Add swineherd. * gnu/packages/admin.scm (swineherd): New variable. --- gnu/packages/admin.scm | 40 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 5d586e6f36..2492890ee5 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2016, 2017, 2020 Leo Famulari ;;; Copyright © 2016 Pjotr Prins -;;; Copyright © 2016, 2017 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2023 Ricardo Wurmus ;;; Copyright © 2016-2023 Efraim Flashner ;;; Copyright © 2016 Peter Feigl ;;; Copyright © 2016 John J. Foerch @@ -153,6 +153,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages networking) #:use-module (gnu packages openldap) + #:use-module (gnu packages package-management) #:use-module (gnu packages patchutils) #:use-module (gnu packages pciutils) #:use-module (gnu packages pcre) @@ -407,6 +408,43 @@ interface and is based on GNU Guile.") (native-inputs (list pkg-config guile-2.2)) (inputs (list guile-2.2 guile2.2-fibers)))) +(define-public swineherd + (package + (name "swineherd") + (version "0.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BIMSBbioinfo/swineherd") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18nk0sy5s0dm2rhxnrrn8g0m098b110mxnnxa2vnl1dnvfdzszw8")))) + (build-system gnu-build-system) + (arguments + '(#:configure-flags '("--localstatedir=/var") + #:make-flags '("GUILE_AUTO_COMPILE=0"))) + (native-inputs + (list autoconf automake guile-3.0 pkg-config texinfo)) + (inputs + (list btrfs-progs + guile-config + guile-fibers-1.3 + guile-netlink + guile-3.0 + guix + shepherd-0.10)) + (home-page "https://github.com/BIMSBbioinfo/swineherd") + (synopsis "System container manager") + (description + "This project aims to provide an extension to the Shepherd, retraining it +as a swineherd, a manager of crude system containers. It does this by +providing a Shepherd service @code{swineherd} that talks to the Shepherd +process to create Guix System containers as Shepherd services. It also comes +with an optional HTTP API server.") + (license license:gpl3+))) + (define-public cfm (package (name "cfm") From 10bc07671e2a3a699d4f56e405f50d766323319a Mon Sep 17 00:00:00 2001 From: Valter Nazianzeno Date: Thu, 24 Aug 2023 08:08:25 -0300 Subject: [PATCH 055/440] gnu: emilua: Update to 0.4.3. * gnu/packages/lua.scm (emilua): Update to 0.4.3. [source]: Remove recursive? and replace with inputs. [arguments]: Update style, add patch phase, enable tests and enable some more features. [native-inputs]: Add gperf, gawk and xdd. [inputs]: Add emilua-http and trial-protocol as origin is no longer recursive, also add serd, sord, libcap and liburing. Signed-off-by: Christopher Baines --- gnu/packages/lua.scm | 151 +++++++++++++++++++++++++++---------------- 1 file changed, 97 insertions(+), 54 deletions(-) diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 405f8511cb..3b58952911 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2022 Luis Henrique Gomes Higino ;;; Copyright © 2022 Leo Nikkilä ;;; Copyright © 2023 Yovan Naumovski +;;; Copyright © 2023 Valter Nazianzeno ;;; ;;; This file is part of GNU Guix. ;;; @@ -50,14 +51,18 @@ #:use-module (gnu packages bash) #:use-module (gnu packages boost) #:use-module (gnu packages build-tools) + #:use-module (gnu packages gcc) #:use-module (gnu packages glib) + #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) + #:use-module (gnu packages linux) #:use-module (gnu packages m4) #:use-module (gnu packages ncurses) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) + #:use-module (gnu packages rdf) #:use-module (gnu packages re2c) #:use-module (gnu packages readline) #:use-module (gnu packages tls) @@ -1129,63 +1134,101 @@ shell command executions.") (define-public emilua (package - (name "emilua") - (version "0.3.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/emilua/emilua.git") - (commit (string-append "v" version)) - ;; Current version requires Trial.Protocol and the HTTP lib - ;; developed as part of GSoC 2014 for Boost, and these are - ;; dependencies unlikely to be "unbundled" in future releases. - (recursive? #t))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1999bgrh52124a5g4qizav3x257ff2brjr855srpm1jv1nxzbygv")))) - (build-system meson-build-system) - (arguments - `(;; Tests are disabled for now due to an issue that affecs guix: - ;; + (name "emilua") + (version "0.4.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/emilua/emilua.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dwag2pyqc0g86rris4w4fzafmz9a6kiqd47vdq7hl3a1lyi74mx")))) + (build-system meson-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/emilua_gperf.awk" + (("/usr/bin/env") (which "env"))) + (substitute* "src/system.cpp" + (("P_PIDFD") "P_PID")) + + (copy-recursively + (assoc-ref inputs "emilua-http") + "emilua-http") + (copy-recursively + (assoc-ref inputs "trial-protocol") + "trial-protocol") + + (with-directory-excursion "subprojects" + (symlink "../emilua-http" "emilua-http") + (copy-file "packagefiles/emilua-http/meson.build" + "emilua-http/meson.build") + (symlink "../trial-protocol" "trial-protocol") + (copy-file "packagefiles/trial.protocol/meson.build" + "trial-protocol/meson.build"))))) #:configure-flags - (list "-Denable_http=true" - "-Denable_tests=false" - "-Denable_manpages=false" - "-Dversion_suffix=-guix1"))) - (native-inputs - (list luajit-lua52-openresty - pkg-config - re2c - xxd)) - (inputs - (list boost - boost-static - fmt-7 - ;; LuaJIT has a 2GiB addressing limit[1] that has been fixed on OpenResty - ;; fork. Emilua is severely affected by this limit, so the upstream package - ;; is avoided. Emilua also depends on the -DLUAJIT_ENABLE_LUA52COMPAT - ;; configure flag[2] for some features to work (e.g. __pairs on HTTP - ;; headers). - ;; - ;; [1] - ;; [2] - luajit-lua52-openresty - ncurses - openssl)) - (native-search-paths - (list - (search-path-specification - (variable "EMILUA_PATH") - (files - (list (string-append "lib/emilua-" (version-major+minor version))))))) - (home-page "https://gitlab.com/emilua/emilua") - (synopsis "Lua execution engine") - (description - "Emilua is a LuaJIT-based Lua execution engine that supports async IO, + #~(list "-Denable_http=true" + "-Denable_file_io=true" + "-Denable_io_uring=true" + ;; TODO: Linux namespaces are disabled for now due to conflict + ;; with some packages in guix. + "-Denable_linux_namespaces=false" + "-Denable_manpages=false" + "-Dversion_suffix=-guix1"))) + (native-inputs + (list luajit-lua52-openresty + re2c + gperf + xxd + pkg-config)) + (inputs + `(("emilua-http" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BoostGSoC14/boost.http") + (commit "93ae527c89ffc517862e1f5f54c8a257278f1195"))) + (sha256 + (base32 + "0jm7fw0cjd3s9zkkvyh6mcj6z32hcy7l9bszv74l92qk15ivvp9h")))) + ("trial-protocol" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/breese/trial.protocol") + (commit "79149f604a49b8dfec57857ca28aaf508069b669"))) + (sha256 + (base32 + "0k42i5b4v3zz5x0r3dssiymgmn2x8zg4fzdksya9aggxgigippsx")))) + ("boost" ,boost) + ("boost-static" ,boost-static) + ("fmt" ,fmt-8) + ("gcc" ,gcc-12) + ("luajit-lua52-openresty" ,luajit-lua52-openresty) + ("ncurses" ,ncurses) + ("serd" ,serd) + ("sord" ,sord) + ("libcap" ,libcap) + ("liburing" ,liburing) + ("openssl" ,openssl))) + (native-search-paths + (list + (search-path-specification + (variable "EMILUA_PATH") + (files + (list (string-append "lib/emilua-" (version-major+minor version))))))) + (home-page "https://gitlab.com/emilua/emilua") + (synopsis "Lua execution engine") + (description + "Emilua is a LuaJIT-based Lua execution engine that supports async IO, fibers and actor-inspired threading. The experimental builtin HTTP module is enabled.") - (license license:boost1.0))) + (license license:boost1.0))) (define-public fennel (package From de2ee9cae67079daf380f09c095f2a4b37be40e6 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 5 Sep 2023 23:24:29 +0100 Subject: [PATCH 056/440] gnu: python-libsass: Update to 0.22.0. * gnu/packages/python-xyz.scm (python-libsass): Update to 0.22.0. [phases]: Add new phase 'silent-failing-tests and disable 2 failing tests to complete build. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 304258b811..5ba51ca654 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14314,7 +14314,7 @@ specification.") (define-public python-libsass (package (name "python-libsass") - (version "0.20.1") + (version "0.22.0") (source (origin ;; PyPI tarball is missing some test files. @@ -14324,7 +14324,7 @@ specification.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1r0kgl7i6nnhgjl44sjw57k08gh2qr7l8slqih550dyxbf1akbxh")))) + (base32 "0j6c7jb1bnpmz76gs5za41qwgrs7v1yd1jkgvsy5ql6dg2ph9vp4")))) (build-system python-build-system) (arguments '(#:phases @@ -14332,6 +14332,17 @@ specification.") ;; Use Guix package of libsass instead of compiling from a checkout. (add-before 'build 'set-libsass (lambda _ (setenv "SYSTEM_SASS" "indeed"))) + ;; XXX: Silent 2 failing tests, reported to upstream (closed), see + ;; https://github.com/sass/libsass-python/issues/440. It passed with + ;; libsass@3.6.5 which requires rebuild the world (1200+ packages), + ;; remove when v3.6.5 is available. + (add-before 'check 'silent-failing-tests + (lambda _ + (substitute* "sasstests.py" + (("def test_build_one") + "def __off_test_build_one") + (("def test_stack_trace_formatting") + "def __off_test_stack_trace_formatting")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From 7f150a18957daddb53caf11e23eb12122198d65c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Tue, 5 Sep 2023 23:24:30 +0100 Subject: [PATCH 057/440] gnu: python-qtsass: Update to 0.4.0. This also fixes test failures preventing the package from building. * gnu/packages/python-xyz.scm (python-qtsass): Update to 0.4.0, fix build. [native-inputs]: Add python-flaky. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5ba51ca654..dd43fb3cd1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -29978,7 +29978,7 @@ applications and daemons.") (define-public python-qtsass (package (name "python-qtsass") - (version "0.3.0") + (version "0.4.0") (source (origin ;; There are no tests in the PyPI tarball. @@ -29988,7 +29988,7 @@ applications and daemons.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "09s04aa14d8jqbh71clrb5y7vcmkxlp94mwmvzrkxahry3bk03cb")))) + (base32 "1skdihfby2f41zxgwa5zv44vdxjrw301rh88rjmzj4xbdlix6cig")))) (build-system python-build-system) (arguments `(#:test-target "pytest" @@ -30000,7 +30000,7 @@ applications and daemons.") (for-each make-file-writable (find-files ".")) #t))))) (native-inputs - (list python-pytest python-pytest-cov python-pytest-runner)) + (list python-flaky python-pytest python-pytest-cov python-pytest-runner)) (propagated-inputs (list python-libsass)) (home-page "https://github.com/spyder-ide/qtsass") From 901eaca92becd99d297a09a4480f7095278b22b5 Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Mon, 4 Sep 2023 19:09:12 -0400 Subject: [PATCH 058/440] gnu: tennix: Update to 1.3.4. * gnu/packages/games.scm (tennix): Update to 1.3.4. [arguments]<#:phases>: Update style and remove fix-include phase. [inputs]: Remove labels, update to SDL2, add SDL2_gfx dependency. [license]: Remove LGPL license, as SDL_rotozoom is no longer included. Signed-off-by: Christopher Baines --- gnu/packages/games.scm | 96 +++++++++++++++++++----------------------- 1 file changed, 44 insertions(+), 52 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 4d5b85248a..78063fa625 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5571,65 +5571,57 @@ fullscreen, use F5 or Alt+Enter.") (define-public tennix (package (name "tennix") - (version "1.3.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://repo.or.cz/tennix.git") - (commit (string-append "tennix-" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "02cj4lrdrisal5s9pnbf2smx7qz9czczjzndfkhfx0qy67b957sk")) - ;; Remove non-free images. - (modules '((guix build utils))) - (snippet - '(begin - (for-each delete-file - '("data/loc_training_camp.png" - "data/loc_austrian_open.png" - "data/loc_olympic_green_tennis.png")) - #t)))) + (version "1.3.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://repo.or.cz/tennix.git") + (commit (string-append "tennix-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fmg0vw8c2spyxy4k64nwky80jsw9mc3vnlch49q6cagjsg9y8dj")) + ;; Remove non-free images. + (modules '((guix build utils))) + (snippet '(begin + (for-each delete-file + '("data/loc_training_camp.png" + "data/loc_austrian_open.png" + "data/loc_olympic_green_tennis.png")) #t)))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;no test - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-include - (lambda _ - (substitute* '("src/graphics.h" "src/sound.h") - (("#include \"(SDL_(image|ttf|mixer)\\.h)\"" _ header) - (string-append "#include \"SDL/" header "\""))) - (substitute* '("src/tennix.h" "src/network.h" "src/SDL_rotozoom.h") - (("#include ") "#include ") - (("#include ") "#include ")) - #t)) - (add-after 'unpack 'locate-install - ;; Build process cannot expand "$(INSTALL)" in Makefile. - (lambda _ - (substitute* "makefile" - (("^CONFIGURE_OUTPUT :=.*" all) - (string-append "INSTALL := install -c\n" all))) - #t)) - (replace 'configure - ;; The "configure" script is picky about the arguments it - ;; gets. Call it ourselves. - (lambda _ - (invoke "./configure" "--prefix" (assoc-ref %outputs "out"))))))) - (native-inputs - (list which)) - (inputs - `(("python" ,python-wrapper) - ("sdl" ,(sdl-union (list sdl sdl-image sdl-mixer sdl-ttf sdl-net))))) + (list + #:tests? #f ;no tests + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'locate-install + ;; Build process cannot expand "$(INSTALL)" in Makefile. + (lambda _ + (substitute* "makefile" + (("^CONFIGURE_OUTPUT :=.*" all) + (string-append "INSTALL := install -c\n" all))) #t)) + (replace 'configure + ;; The "configure" script is picky about the arguments it + ;; gets. Call it ourselves. + (lambda _ + (invoke "./configure" "--prefix" + (assoc-ref %outputs "out"))))))) + (native-inputs (list which)) + (inputs (list python + (sdl-union (list sdl2 + sdl2-image + sdl2-mixer + sdl2-ttf + sdl2-net + sdl2-gfx)))) (home-page "https://icculus.org/tennix/") (synopsis "Play tennis against the computer or a friend") - (description "Tennix is a 2D tennis game. You can play against the + (description + "Tennix is a 2D tennis game. You can play against the computer or against another player using the keyboard. The game runs in-window at 640x480 resolution or fullscreen.") ;; Project is licensed under GPL2+ terms. It includes images - ;; released under Public Domain terms, and SDL_rotozoom, released - ;; under LGPL2.1 terms. - (license (list license:gpl2+ license:public-domain license:lgpl2.1)))) + ;; released under Public Domain terms. + (license (list license:gpl2+ license:public-domain)))) (define-public warzone2100 (package From 8d5304b143eee34e1998fca8f0c9f2fad7599d1a Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 16:55:39 +0800 Subject: [PATCH 059/440] gnu: libvterm: Update to 0.3.3. * gnu/packages/terminals.scm (libvterm): Update to 0.3.3. [source]: Use launchpad.net url. [arguments]: Use CC-FOR-TARGET. Signed-off-by: Christopher Baines --- gnu/packages/terminals.scm | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 43aeac9fd7..1f72393593 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -35,6 +35,7 @@ ;;; Copyright © 2022 jgart ;;; Copyright © 2023 Aaron Covrig ;;; Copyright © 2023 Foundation Devices, Inc. +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -629,19 +630,25 @@ should be thread-safe.") (define-public libvterm (package (name "libvterm") - (version "0.3.1") + (version "0.3.3") (source (origin (method url-fetch) - (uri (string-append "https://www.leonerd.org.uk/code/libvterm/" - "libvterm-" version ".tar.gz")) + (uri (string-append + "https://launchpad.net/libvterm/trunk/v" + (version-major+minor version) + "/+download/libvterm-" version ".tar.gz")) (sha256 - (base32 "15y3y23kfpcda7n79ym3gp1abzn8mshxrad8s3gnhls82nfava15")))) + (base32 "1q16fbznm54p24hqvw8c9v3347apk86ybsxyghsbsa11vm1ny589")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list "CC=gcc" - (string-append "PREFIX=" (assoc-ref %outputs "out"))) + (list + ;; FIXME: cross build fails. + ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format + ;; collect2: error: ld returned 1 exit status + (string-append "CC=" ,(cc-for-target)) + (string-append "PREFIX=" (assoc-ref %outputs "out"))) #:test-target "test" #:phases (modify-phases %standard-phases From 79988ab742fdb8b13ab61269ed11c0144593f320 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 16:55:40 +0800 Subject: [PATCH 060/440] gnu: libvterm: Update arguments style. * gnu/packages/terminals.scm (libvterm)[arguments]: Update arguments style. Signed-off-by: Christopher Baines --- gnu/packages/terminals.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 1f72393593..a67ec97859 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -642,17 +642,17 @@ should be thread-safe.") (base32 "1q16fbznm54p24hqvw8c9v3347apk86ybsxyghsbsa11vm1ny589")))) (build-system gnu-build-system) (arguments - `(#:make-flags - (list - ;; FIXME: cross build fails. - ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format - ;; collect2: error: ld returned 1 exit status - (string-append "CC=" ,(cc-for-target)) - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (list #:make-flags + #~(list + ;; FIXME: cross build fails. + ;; ld: src/.libs/encoding.o: error adding symbols: file in wrong format + ;; collect2: error: ld returned 1 exit status + (string-append "CC=" #$(cc-for-target)) + (string-append "PREFIX=" #$output)) + #:test-target "test" + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) (native-inputs (list libtool perl)) (home-page "https://www.leonerd.org.uk/code/libvterm/") From c30c9df5e9eb2d28e1b593128f05a0aae1919826 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Wed, 6 Sep 2023 14:12:10 +0300 Subject: [PATCH 061/440] gnu: yoyo-migrations: Update to 8.2.0. * gnu/packages/databases.scm (yoyo-migrations): Update to 8.2.0. [propagated-inputs]: Add python-importlib-metadata. Signed-off-by: Christopher Baines --- gnu/packages/databases.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 8d87f238b5..d0f8ce2001 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -59,7 +59,8 @@ ;;; Copyright © 2022 muradm ;;; Copyright © 2022 Thomas Albers Raviola ;;; Copyright © 2021, 2022 jgart -;;; Copyright © 2023 Felix Gruber +;;; Copyright © 2023 Felix Gruber ;;; ;;; This file is part of GNU Guix. ;;; @@ -3963,7 +3964,7 @@ database).") (define-public yoyo-migrations (package (name "yoyo-migrations") - (version "7.2.0") + (version "8.2.0") (source (origin ;; We use the upstream repository, as the tests are not included in the @@ -3974,14 +3975,14 @@ database).") (changeset (string-append "v" version "-release")))) (file-name (string-append name "-" version "-checkout")) (sha256 - (base32 "0q2z9bgdj3wyix7yvqsayfs21grp5av8ilh411lgmjhigszkvhcq")))) + (base32 "1al030ix0w63hr4s3mqry6s0mlqdj8p242pdqks06br7c25nx3yj")))) (build-system python-build-system) (arguments ;; XXX: Tests require a connection to some pgsql database and psycopg ;; fails to connect to it. '(#:tests? #f)) (propagated-inputs - (list python-sqlparse python-tabulate)) + (list python-sqlparse python-tabulate python-importlib-metadata)) (home-page "https://ollycope.com/software/yoyo/latest/") (synopsis "Database migrations with SQL") (description From 6a01c1142b0099bc5ccff6550c2dd24b90ec6aad Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 21 Aug 2023 22:12:28 +0200 Subject: [PATCH 062/440] gnu: hdf4, hdf4-alt: Update to 4.2.16-2. * gnu/packages/maths.scm (hdf4)[source]: Update to 4.2.16-2. Drop patches that do not apply any more. [arguments]: Drop configure flag related to libtirpc. Add configure flag to build xdr library and drop unneeded substitutions. * gnu/packages/patches/hdf4-architectures.patch, gnu/packages/patches/hdf4-tirpc.patch: Remove files. * gnu/local.mk (dist_patch_DATA): Unregister patches. --- gnu/local.mk | 2 - gnu/packages/maths.scm | 28 +- gnu/packages/patches/hdf4-architectures.patch | 632 ------------------ gnu/packages/patches/hdf4-tirpc.patch | 33 - 4 files changed, 8 insertions(+), 687 deletions(-) delete mode 100644 gnu/packages/patches/hdf4-architectures.patch delete mode 100644 gnu/packages/patches/hdf4-tirpc.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4f8637418a..924d497057 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1372,10 +1372,8 @@ dist_patch_DATA = \ %D%/packages/patches/gtksourceview-2-add-default-directory.patch \ %D%/packages/patches/gzdoom-search-in-installed-share.patch \ %D%/packages/patches/gzdoom-find-system-libgme.patch \ - %D%/packages/patches/hdf4-architectures.patch \ %D%/packages/patches/hdf4-reproducibility.patch \ %D%/packages/patches/hdf4-shared-fortran.patch \ - %D%/packages/patches/hdf4-tirpc.patch \ %D%/packages/patches/hdf5-config-date.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 38e71e18f8..e3cd0762be 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge +;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020, 2023 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington ;;; Copyright © 2014-2022 Eric Bavier @@ -1321,18 +1321,16 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.14") + (version "4.2.16-2") (source (origin (method url-fetch) (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" version "/src/hdf-" version ".tar.bz2")) (sha256 - (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l")) - (patches (search-patches "hdf4-architectures.patch" - "hdf4-reproducibility.patch" - "hdf4-shared-fortran.patch" - "hdf4-tirpc.patch")))) + (base32 "0b395czhqr43mmbiifmg2mhb488wnd4zccj45vpql98ja15j7hy5")) + (patches (search-patches "hdf4-reproducibility.patch" + "hdf4-shared-fortran.patch")))) (build-system gnu-build-system) (native-inputs (list gfortran bison flex)) @@ -1345,9 +1343,7 @@ computations.") #:configure-flags (list "--enable-shared" "FCFLAGS=-fallow-argument-mismatch" "FFLAGS=-fallow-argument-mismatch" - (string-append "CPPFLAGS=-I" - (assoc-ref %build-inputs "libtirpc") - "/include/tirpc")) + "--enable-hdf4-xdr") #:phases (modify-phases %standard-phases ;; This is inspired by two of Debian's patches. @@ -1362,14 +1358,7 @@ computations.") (substitute* '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in") (("/bin/rm") "rm") - (("/bin/mkdir") "mkdir")) - (substitute* (find-files "." "^Makefile\\.in$") - (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \ --R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "") - (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ --R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ --R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) - #t)) + (("/bin/mkdir") "mkdir")))) (add-after 'configure 'patch-settings (lambda _ ;; libhdf4.settings contains the full path of the @@ -1389,8 +1378,7 @@ computations.") ;; files. Fix it manually to avoid having to propagate it. (substitute* (find-files (string-append out "/lib") "\\.la$") (("-ljpeg") - (string-append "-L" libjpeg "/lib -ljpeg"))) - #t)))))) + (string-append "-L" libjpeg "/lib -ljpeg"))))))))) (home-page "https://www.hdfgroup.org/products/hdf4/") (synopsis "Library and multi-object file format for storing and managing data") diff --git a/gnu/packages/patches/hdf4-architectures.patch b/gnu/packages/patches/hdf4-architectures.patch deleted file mode 100644 index aa71d5a383..0000000000 --- a/gnu/packages/patches/hdf4-architectures.patch +++ /dev/null @@ -1,632 +0,0 @@ -Copied from Debian. - -Description: Support additional architectures. -Author: Francesco Paolo Lovergine - ---- a/hdf/src/hdfi.h -+++ b/hdf/src/hdfi.h -@@ -48,6 +48,7 @@ - /* 8 - Cray IEEE */ - /* (i.e. Big-Endian, all 64-bit architecture w/IEEE Floats) */ - /*--------------------------------------------------------------------------*/ -+#define DFMT_S390 0x1111 - #define DFMT_SUN 0x1111 - #define DFMT_SUN_INTEL 0x4441 - #define DFMT_ALLIANT 0x1111 -@@ -62,6 +63,7 @@ - #define DFMT_CTSS 0x3331 - #define DFMT_VAX 0x2221 - #define DFMT_MIPSEL 0x4441 -+#define DFMT_MIPSEB 0x1111 - #define DFMT_PC 0x4441 - #define DFMT_APPLE 0x1111 - #define DFMT_APPLE_INTEL 0x4441 -@@ -75,6 +77,13 @@ - #define DFMT_IA64 0x4441 - #define DFMT_LINUX64 0x4441 - #define DFMT_POWERPC64 0x1111 -+#define DFMT_POWERPC64LE 0x4441 -+#define DFMT_ARMV4L 0x4441 -+#define DFMT_AARCH64 0x4441 -+#define DFMT_X86_64 0x4441 -+#define DFMT_SH 0x4441 -+#define DFMT_SHEB 0x1111 -+#define DFMT_RISCV64 0x4441 - - /* I/O library constants */ - #define UNIXUNBUFIO 1 -@@ -288,7 +297,7 @@ typedef int hdf_pint_t; - - #endif /* IBM6000 */ - --#if defined(HP9000) || (!defined(__convexc__) && (defined(hpux) || defined(__hpux))) -+#if defined(HP9000) || (!defined(__convexc__) && (defined(hpux) || defined(__hpux) || defined(__hppa__))) - - #ifndef HP9000 - #define HP9000 -@@ -347,6 +356,10 @@ typedef int hdf_pint_t; - /* what each does */ - #define JMEMSYS MEM_ANSI - -+#ifdef __linux__ -+#define FNAME_POST_UNDERSCORE -+#endif -+ - #endif /* HP9000 */ - - -@@ -670,6 +683,462 @@ typedef int hdf_pint_t; - #endif /* !(defined(__APPLE__)) */ - - /*-----------------------------------------------------*/ -+#if defined (__linux__) && defined (__mc68000__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_MOTOROLA -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/m68k */ -+ -+#if defined (__linux__) && defined (__sparc__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_SUN -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+#ifdef _LP64 /* 64-bit environment */ -+typedef int int32; -+typedef unsigned int uint32; -+#else /* 32-bit environment */ -+typedef long int int32; -+typedef unsigned long int uint32; -+#endif -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+#ifdef _LP64 /* 64-bit environment */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#else /* 32-bit environment */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#endif -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/Sparc */ -+ -+#if defined (__linux__) && defined (__powerpc__) && !defined(__powerpc64__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_MOTOROLA -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/powerpc */ -+ -+#if defined (__linux__) && defined (__s390__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_S390 -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+#ifdef _LP64 /* 64-bit environment */ -+typedef int int32; -+typedef unsigned int uint32; -+#else /* 32-bit environment */ -+typedef long int int32; -+typedef unsigned long int uint32; -+#endif -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+#ifdef _LP64 /* 64-bit environment */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#else /* 32-bit environment */ -+typedef int hdf_pint_t; /* an integer the same size as a pointer */ -+#endif -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/s390 */ -+ -+#if defined (__linux__) && (defined (__MIPSEB__) || defined(__MIPSEL__)) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#if defined (__MIPSEB__) -+#define DF_MT DFMT_MIPSEB -+#elif defined(__MIPSEL__) -+#define DF_MT DFMT_MIPSEL -+#endif -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef long int hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/mips */ -+ -+#if defined (__linux__) && defined (__arm__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_ARMV4L -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/arm */ -+ -+#if defined (__linux__) && defined (__aarch64__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_AARCH64 -+ -+typedef void VOID; -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef int intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+#define FILELIB UNIXBUFIO -+ -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/aarch64 */ -+ -+#if defined (__linux__) && defined (__riscv) && (__riscv_xlen == 64) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#define DF_MT DFMT_RISCV64 -+ -+typedef void VOID; -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef int int32; -+typedef unsigned int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef int intf; /* size of INTEGERs in Fortran compiler */ -+typedef long hdf_pint_t; /* an integer the same size as a pointer */ -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+#define FILELIB UNIXBUFIO -+ -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/riscv64 */ -+ - #if defined(NEXT) || defined(NeXT) - - #ifndef NEXT -@@ -932,7 +1401,11 @@ Please check your Makefile. - - #include /* for unbuffered i/o stuff */ - #include --#define DF_MT DFMT_POWERPC64 -+#ifdef __LITTLE_ENDIAN__ -+#define DF_MT DFMT_POWERPC64LE -+#else -+#define DF_MT DFMT_POWERPC64 -+#endif - typedef void VOID; - typedef void *VOIDP; - typedef char *_fcd; -@@ -956,6 +1429,11 @@ typedef long hdf_pint_t; - #define _fcdtocp(desc) (desc) - #define FILELIB UNIXBUFIO - -+#ifndef BIG_LONGS -+#define BIG_LONGS -+#endif -+ -+ - /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ - - /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1101,6 +1579,8 @@ typedef long hdf_pint_t; - #define _fcdtocp(desc) (desc) - #define FILELIB UNIXBUFIO - -+#define BIG_LONGS -+ - /* JPEG #define's - Look in the JPEG docs before changing - (Q) */ - - /* Determine the memory manager we are going to use. Valid values are: */ -@@ -1115,6 +1595,66 @@ typedef long hdf_pint_t; - - #endif /* IA64 */ - -+/* Renesas SuperH SH3(little/big)/SH4(little/big) */ -+#if defined (__linux__) && defined(__sh__) -+ -+#ifdef GOT_MACHINE -+If you get an error on this line more than one machine type has been defined. -+Please check your Makefile. -+#endif -+#define GOT_MACHINE 1 -+ -+#include -+#include /* for unbuffered file I/O */ -+#include -+#include -+#include /* for character macros */ -+ -+#if defined (__LITTLE_ENDIAN__) -+#define DF_MT DFMT_SH -+#elif defined(__BIG_ENDIAN__) -+#define DF_MT DFMT_SHEB -+#endif -+ -+#ifndef VOID /* The stupid windows.h header file uses a #define instead of a typedef */ -+typedef void VOID; -+#endif /* end VOID */ -+ -+typedef void * VOIDP; -+typedef char * _fcd; -+typedef char char8; -+typedef unsigned char uchar8; -+typedef signed char int8; -+typedef unsigned char uint8; -+typedef short int int16; -+typedef unsigned short int uint16; -+typedef long int int32; -+typedef unsigned long int uint32; -+typedef int intn; -+typedef unsigned int uintn; -+typedef float float32; -+typedef double float64; -+typedef long intf; -+typedef int hdf_pint_t; -+#define FNAME_POST_UNDERSCORE -+#define _fcdtocp(desc) (desc) -+ -+#ifdef HAVE_FMPOOL -+#define FILELIB PAGEBUFIO /* enable page buffering */ -+#else -+#define FILELIB UNIXBUFIO -+#endif -+ -+/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ -+/* Determine the memory manager we are going to use. Valid values are: */ -+/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ -+/* what each does */ -+#define JMEMSYS MEM_ANSI -+#define HAVE_STDC -+#define INCLUDES_ARE_ANSI -+ -+#endif /* Linux/sh */ -+ - #ifndef GOT_MACHINE - No machine type has been defined. Your Makefile needs to have someing like - -DSUN or -DUNICOS in order for the HDF internal structures to be defined ---- a/hdf/src/hconv.h -+++ b/hdf/src/hconv.h -@@ -59,7 +59,7 @@ - /* CONSTANT DEFINITIONS */ - /*****************************************************************************/ - /* Generally Big-Endian machines */ --#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) -+#if !defined(INTEL86) && !defined(MIPSEL) && !defined(DEC_ALPHA) && !defined(I860) && !defined(SUN386) && !(defined(__ia64) && !(defined(hpux) || defined(__hpux))) && !defined(__x86_64__) && !(defined(__powerpc__) && defined(__LITTLE_ENDIAN__)) && !defined(__aarch64__) && !defined(__ARM_EABI__) && !defined(__riscv) - # define UI8_IN DFKnb1b /* Unsigned Integer, 8 bits */ - # define UI8_OUT DFKnb1b - # define SI16_IN DFKnb2b /* S = Signed */ diff --git a/gnu/packages/patches/hdf4-tirpc.patch b/gnu/packages/patches/hdf4-tirpc.patch deleted file mode 100644 index 3f436e3887..0000000000 --- a/gnu/packages/patches/hdf4-tirpc.patch +++ /dev/null @@ -1,33 +0,0 @@ -Build with libtirpc on all architectures because glibc no longer provides -SunRPC support. - -diff --git a/configure b/configure ---- a/configure -+++ b/configure -@@ -23635,10 +23635,13 @@ - *-pc-cygwin*) - LIBS="$LIBS -ltirpc" - CPPFLAGS="$CPPFLAGS -I/usr/include/tirpc" ;; -+ *-linux-gnu) -+ LIBS="$LIBS -ltirpc" -+ CPPFLAGS="$CPPFLAGS" ;; - *) ;; - esac - --if test "X$BUILD_XDR" != "Xyes"; then -+if test "X$BUILD_XDR" = "Xyes"; then - cat confdefs.h - <<_ACEOF >conftest.$ac_ext - /* end confdefs.h. */ - -@@ -23693,9 +23696,9 @@ - ## but we need to make sure that it is present on the system. Do that here, - ## The SunRPC of the glibc has been replaced by a TI-RPC (Transport Independent RPC) library for IPv6 support - case "$host" in -- *-pc-cygwin*) -+ *) - HAVE_RPC="yes" -- ac_fn_c_check_header_mongrel "$LINENO" "rpc.h" "ac_cv_header_rpc_h" "$ac_includes_default" -+ ac_fn_c_check_header_mongrel "$LINENO" "rpc/rpc.h" "ac_cv_header_rpc_h" "$ac_includes_default" - if test "x$ac_cv_header_rpc_h" = xyes; then : - : - else From cda20190bccf9bd55c264b1084eab8b6499c15cc Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Sat, 2 Sep 2023 21:56:44 +0000 Subject: [PATCH 063/440] gnu: Add r-interactivedisplay. * gnu/packages/bioconductor.scm (r-interactivedisplay): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 85 +++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c913232680..e5e9c80291 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages javascript) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -7734,6 +7735,90 @@ of other R packages who wish to make use of HTSlib.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplay + (package + (name "r-interactivedisplay") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplay" version)) + (sha256 + (base32 + "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl")) + (snippet + '(for-each delete-file + '("inst/www/js/jquery.js" + "inst/www/js/jquery.min.js" + "inst/www/js/jquery.dataTables.min.js"))))) + (properties `((upstream-name . "interactiveDisplay"))) + (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery-1.8.2") + "inst/www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + "inst/www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + "inst/www/js/jquery.dataTables.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets)))))))) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocmanager + r-category + r-dt + r-ggplot2 + r-gridsvg + r-interactivedisplaybase + r-plyr + r-rcolorbrewer + r-reshape2 + r-shiny + r-zlibbioc + r-xml)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-datatables" ,js-datatables) + ("js-jquery-1.8.2" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.8.2.js") + (sha256 + (base32 + "0nikk2clbnyi02k0brvhbd8m43lfh4l1zrya35jya9sy6wb9b9ng")))) + ("js-jquery-1.9.1" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.9.1.js") + (sha256 + (base32 + "0h4dk67yc9d0kadqxb6b33585f3x3559p6qmp70l00qwq030vn3v")))))) + (home-page "https://bioconductor.org/packages/interactiveDisplay") + (synopsis "Package for Shiny web displays of Bioconductor objects") + (description + "This package offers interactive Shiny displays for Bioconductor +objects. In addition, this package empowers users to develop engaging +visualizations and interfaces for working with Bioconductor data.") + (license license:artistic2.0))) + (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") From 3007f77596a19608e4216ada575bec374da63f6f Mon Sep 17 00:00:00 2001 From: Artyom Bologov Date: Wed, 13 Sep 2023 02:37:08 +0400 Subject: [PATCH 064/440] gnu: cl-njson: Update to 1.2.0. * gnu/packages/lisp-xyz.scm (sbcl-njson): Update to 1.2.0. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 69686dbed9..e43bda9c5f 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -26603,7 +26603,7 @@ instead of #'FOO. (define-public sbcl-njson (package (name "sbcl-njson") - (version "1.1.1") + (version "1.2.0") (source (origin (method git-fetch) (uri (git-reference @@ -26612,7 +26612,7 @@ instead of #'FOO. (file-name (git-file-name "cl-njson" version)) (sha256 (base32 - "0zdf6mlbpc2j95qm000ljf642af18sfz45yxh6rnxrbf8m4laxxa")))) + "1zsf7sm88wjrd4da5bvpxi8fvsx01cv51p8820fnj062x6hlhg38")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-cl-json sbcl-jzon)) (native-inputs (list sbcl-lisp-unit2)) From 828b08d58526cf242e121da3f0e3a3524aa507c8 Mon Sep 17 00:00:00 2001 From: "Andre A. Gomes" Date: Mon, 11 Sep 2023 17:44:38 +0300 Subject: [PATCH 065/440] gnu: cl-nasdf: Update to 0.1.8. * gnu/packages/lisp-xyz.scm (sbcl-nasdf): Update to 0.1.8. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index e43bda9c5f..1d88654962 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -25824,12 +25824,11 @@ change since last write. (inputs (cons (list "iolib" cl-iolib) (package-inputs sbcl-nfiles))))) - (define-public sbcl-nasdf - (let ((commit "dd9fb2df7174464b54561b2a2f3c3e00fdd5d4f7")) + (let ((commit "ab7a018f3a67a999c72710644b10b4545130c139")) (package (name "sbcl-nasdf") - (version "0.1.7") + (version "0.1.8") (source (origin (method git-fetch) @@ -25838,7 +25837,7 @@ change since last write. (commit commit))) (file-name (git-file-name "cl-ntemplate" version)) (sha256 - (base32 "1q8ky8hz8xrr37h7yyc6ysvrcwlsp1i6r2x44c060drspgjbqj70")))) + (base32 "15j7kqxvn0blr0i2xgk0il0ia91p28clfqxdh00vlp423v9a2wbx")))) (build-system asdf-build-system/sbcl) (arguments `(#:phases From 4f933f977dd8aa61ca3e50b194d3b56e298a3e30 Mon Sep 17 00:00:00 2001 From: "Andre A. Gomes" Date: Mon, 11 Sep 2023 17:44:45 +0300 Subject: [PATCH 066/440] gnu: nyxt: Update to 3.7.0. * gnu/packages/web-browsers.scm (nyxt): Update to 3.7.0. Signed-off-by: Guillaume Le Vaillant --- 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 5fb43d0ee9..a8ef7099f5 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -586,7 +586,7 @@ driven and does not detract you from your daily work.") (define-public nyxt (package (name "nyxt") - (version "3.6.1") + (version "3.7.0") (source (origin (method git-fetch) @@ -595,7 +595,7 @@ driven and does not detract you from your daily work.") (commit version))) (sha256 (base32 - "0gf4akrkp15c3z3v3i5c94ga282ygqxb0rqxwm9ivchby0xv9lmd")) + "0mar3y69b62jby4kfdsm2xsnb830v1d468zspa3frpnphwxv4a5y")) (file-name (git-file-name "nyxt" version)) (modules '((guix build utils))) (snippet From 67268d9a8109936d9e7e486394fcc021880c6a28 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Mon, 11 Sep 2023 01:15:37 -0700 Subject: [PATCH 067/440] gnu: octave-cli: Update to 8.3.0 * gnu/packages/maths.scm (octave-cli): Update to 8.3.0 Signed-off-by: Eric Bavier --- 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 e3cd0762be..6141c09886 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2779,7 +2779,7 @@ can solve two kinds of problems: (define-public octave-cli (package (name "octave-cli") - (version "8.2.0") + (version "8.3.0") (source (origin (method url-fetch) @@ -2787,7 +2787,7 @@ can solve two kinds of problems: version ".tar.xz")) (sha256 (base32 - "1pkh4vmq4hcrmyl2gybd54i3qamyvmcjmpgy1i2kkw2g03jxdfdp")))) + "1aav8i88y2yl11g5d44wpjngkpldvzk90ja7wghkb91cy2a9974i")))) (build-system gnu-build-system) (inputs (list alsa-lib From b6441f7bd0257783fffecfc6b6b3c6f2950204c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 14:06:19 +0200 Subject: [PATCH 068/440] upstream: Compare symbols to symbols. The UNCHANGED? comparison would always yield #FALSE, because we have been comparing lists of strings with lists of symbols. * guix/upstream.scm (update-package-inputs): Convert string labels to symbols before comparison. --- guix/upstream.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/upstream.scm b/guix/upstream.scm index 33248d645c..e28ae12f3f 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2010-2023 Ludovic Courtès ;;; Copyright © 2015 Alex Kost -;;; Copyright © 2019, 2022 Ricardo Wurmus +;;; Copyright © 2019, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021, 2022 Maxime Devos ;;; Copyright © 2022 Hartmut Goebel @@ -534,7 +534,8 @@ specified in SOURCE, an ." (define old (match (package-inputs package) (((labels (? package? packages)) ...) - labels) + labels + (map string->symbol labels)) (_ '()))) From dc172966ba88895096f2c71dcdc3c4083f412dff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:03:59 +0200 Subject: [PATCH 069/440] gnu: Add r-quickjsr. * gnu/packages/cran.scm (r-quickjsr): 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 b6a01a99b0..21eaa6fbea 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15583,6 +15583,27 @@ estimation problem.") ;; The CRAN page only says GPL-3. (license license:gpl3+))) +(define-public r-quickjsr + (package + (name "r-quickjsr") + (version "1.0.6") + (source (origin + (method url-fetch) + (uri (cran-uri "QuickJSR" version)) + (sha256 + (base32 + "1n09jivw1qvsniyap0ki5ablvkwgggh981hcs7k5wx3lp3qxxlnk")))) + (properties `((upstream-name . "QuickJSR"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite r-r6 r-rcpp)) + (home-page "https://cran.r-project.org/package=QuickJSR") + (synopsis "Interface for the QuickJS lightweight JavaScript engine") + (description + "This package provides an R interface to the @code{QuickJS} portable +@code{JavaScript} engine. The engine is bundled entirely within the package, +requiring no external system dependencies beyond a C compiler.") + (license license:expat))) + (define-public r-abundant (package (name "r-abundant") From 2c1d86e2e0b52ce9ff916d4e6fd0f37998c9e430 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Wed, 13 Sep 2023 15:39:18 +0200 Subject: [PATCH 070/440] gnu: python-hicmatrix: Remove syntax error in setup.py. * gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase remove-invalid-syntax. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e24d70e569..1ceb429169 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16229,6 +16229,10 @@ includes operations like compartment, insulation or peak calling.") (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'remove-invalid-syntax + (lambda _ + (substitute* "setup.py" + ((".\\*\"") "\"")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From 4e8ec5a16b8334218e588b0e23924b796378f598 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:20:09 +0200 Subject: [PATCH 071/440] gnu: r-dt: Update to 0.29. * gnu/packages/statistics.scm (r-dt): Update to 0.29. [propagated-inputs]: Add r-httpuv. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index db99f4c7f2..67837a8e62 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3837,13 +3837,13 @@ using the multicore functionality of the parallel package.") extensions))))) (package (name "r-dt") - (version "0.28") + (version "0.29") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "0khdl21kvgi9k7dlpfshk1xz9bkly5lq6p41plfh4g2jv1yxaxfr")) + "1b9qshrjv9xaak92rvg65vkak4pyci9js4j7nkfcg0p19ghnvlm8")) (modules '((guix build utils) (ice-9 match))) (snippet @@ -3917,6 +3917,7 @@ using the multicore functionality of the parallel package.") (list r-crosstalk r-htmltools r-htmlwidgets + r-httpuv r-jquerylib r-jsonlite r-magrittr From aaaaa2ea074526c5b036fa6aa77e1c519a6e4d6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:20:43 +0200 Subject: [PATCH 072/440] gnu: r-minqa: Update to 1.2.6. * gnu/packages/statistics.scm (r-minqa): Update to 1.2.6. [inputs]: Move gfortran from here... [native-inputs]: ...to here. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 67837a8e62..1f4d76af60 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5826,18 +5826,18 @@ showing the progress is useful e.g. bootstrap.") (define-public r-minqa (package (name "r-minqa") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "minqa" version)) (sha256 (base32 - "1gpli7f3piz3jqjj63a6bk9v1jlygjdaqqqvqsr083crj0imd0wv")))) + "0421b4ysslaqmdgwlz080abis8m4xkcvjq7lx1wywbsz1s2vi9si")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) - (inputs + (native-inputs (list gfortran)) (home-page "https://optimizer.r-forge.r-project.org") (synopsis "Derivative-free optimization algorithms by quadratic approximation") From 6739c534f8f0035dbfd18ecbec15a0173e409d03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:35:19 +0200 Subject: [PATCH 073/440] gnu: apache-arrow: Update to 13.0.0. * gnu/packages/databases.scm (apache-arrow): Update to 13.0.0. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index d0f8ce2001..2b8e80e1b0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -4305,7 +4305,7 @@ the SQL language using a syntax that reflects the resulting query.") (define-public apache-arrow (package (name "apache-arrow") - (version "12.0.1") + (version "13.0.0") (source (origin (method git-fetch) @@ -4315,7 +4315,7 @@ the SQL language using a syntax that reflects the resulting query.") (file-name (git-file-name name version)) (sha256 (base32 - "03flvb4xj6a7mfphx68ndrqr6g5jphmzb75m16fx7rnbzira2zpz")))) + "03ykynzz01ar2y4blhcxjh6xsi0gqv380h5m669dddfz2isplsf8")))) (build-system cmake-build-system) (arguments (list From 080d0880166aac172268c187a54aa843305430ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:35:50 +0200 Subject: [PATCH 074/440] gnu: r-arrow: Update to 13.0.0. * gnu/packages/cran.scm (r-arrow): Update to 13.0.0. --- 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 21eaa6fbea..2968742f99 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24338,14 +24338,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "12.0.1.1") + (version "13.0.0") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "18c864ingckbi3v2xhigaiv72sc2c4x3zps60z0v22slkpz5ba0s")))) + "0s29xw9r9hxyvcgdasw95qa7q8zvs79ffhfnlpnzsvb523d2cb6l")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs From bf982837412f271f74b148b22ff5ec4d107e045f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 15:47:15 +0200 Subject: [PATCH 075/440] gnu: r-radiant-data: Update to 1.6.1. * gnu/packages/cran.scm (r-radiant-data): Update to 1.6.1. [propagated-inputs]: Add r-arrow. --- gnu/packages/cran.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2968742f99..d79c70170c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10939,14 +10939,14 @@ local smoothers and many more.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.5.6") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "1dd18brwgcpkqbnxg6jqk4r7aw1i2d7lg9mnfw59q95n6jk86lr5")) + "00bjq3zpxhd6yjq3jwizgiyzp2qf557ms6mhlz74d0wcm0l3vd72")) (modules '((guix build utils))) (snippet '(begin @@ -10978,15 +10978,16 @@ local smoothers and many more.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - (list r-base64enc + (list r-arrow + r-base64enc r-broom r-bslib r-car r-curl r-dplyr r-dt - r-glue r-ggplot2 + r-glue r-import r-jsonlite r-knitr @@ -11006,8 +11007,8 @@ local smoothers and many more.") r-rstudioapi r-scales r-shiny - r-shinyfiles r-shinyace + r-shinyfiles r-stringi r-tibble r-tidyr From 9049506d8b11a4f77f207827cd8667e0dedeaeb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:19:23 +0200 Subject: [PATCH 076/440] gnu: python-hicmatrix: Remove custom 'check phase. * gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom 'check phase. --- gnu/packages/bioinformatics.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ceb429169..aa88692204 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16232,11 +16232,7 @@ includes operations like compartment, insulation or peak calling.") (add-after 'unpack 'remove-invalid-syntax (lambda _ (substitute* "setup.py" - ((".\\*\"") "\"")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "-m" "pytest" "-v"))))))) + ((".\\*\"") "\""))))))) (propagated-inputs (list python-cooler python-intervaltree From f2d690c6c54a6cbea49bf4ac997125f81074ae57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:41:25 +0200 Subject: [PATCH 077/440] gnu: r-leaflet: Update to 2.2.0. * gnu/packages/cran.scm (r-leaflet): Update to 2.2.0. [source]: Do not delete jquery.min.js, because it is no longer included. [arguments]: Adjust minification accordingly. [native-inputs]: Remove js-jquery. [propagated-inputs]: Remove r-base64enc and r-markdown; add r-jquerylib and r-xfun. --- gnu/packages/cran.scm | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d79c70170c..a3d70f2852 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9912,20 +9912,19 @@ information between package updates.") (define-public r-leaflet (package (name "r-leaflet") - (version "2.1.2") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "leaflet" version)) (sha256 - (base32 "0fa0f9fcrxbqhmcm45l0byws56d8gg0bi3vx4m65mn4rihg6gn16")) + (base32 "0k0zplbhmvld6q1id17s827z1230kvnz16c4hlvp6jn9g26yy0dq")) (snippet '(for-each delete-file (list "inst/htmlwidgets/lib/leaflet/leaflet.js" "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" - "inst/htmlwidgets/lib/jquery/jquery.min.js" "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" @@ -9956,8 +9955,6 @@ information between package updates.") "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js") (,(assoc-ref inputs "js-leaflet-omnivore") "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js") - (,(assoc-ref inputs "js-jquery") - "htmlwidgets/lib/jquery/jquery.min.js") ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js" "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js") (,(assoc-ref inputs "js-bootstrap3") @@ -9992,13 +9989,6 @@ information between package updates.") (sha256 (base32 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha")))) - ("js-jquery" - ,(origin - (method url-fetch) - (uri "https://code.jquery.com/jquery-1.12.4.js") - (sha256 - (base32 - "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) ("js-leaflet" ,(origin (method url-fetch) @@ -10061,19 +10051,19 @@ information between package updates.") (base32 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) (propagated-inputs - (list r-base64enc - r-crosstalk + (list r-crosstalk r-htmltools r-htmlwidgets + r-jquerylib r-leaflet-providers r-magrittr - r-markdown r-png r-raster r-rcolorbrewer r-scales r-sp - r-viridis)) + r-viridis + r-xfun)) (home-page "https://rstudio.github.io/leaflet/") (synopsis "Create interactive web maps with the JavaScript Leaflet library") (description From 455dadc41a706cdde336a01225c9846e67340dbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:51:14 +0200 Subject: [PATCH 078/440] gnu: r-iheatmapr: Update to 0.7.0. * gnu/packages/cran.scm (r-iheatmapr): Update to 0.7.0. [source]: Delete minified plotly JavaScript. [native-inputs]: Add esbuild and js-plotly. [arguments]: Add phase to minify plotly.js. --- gnu/packages/cran.scm | 29 ++++++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3d70f2852..a7f3b91207 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31098,16 +31098,29 @@ Haberman's interaction model when all items are dichotomously scored.") (define-public r-iheatmapr (package (name "r-iheatmapr") - (version "0.5.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "iheatmapr" version)) (sha256 (base32 - "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx")))) + "0ym796kf6d8cwd7nmgzy3ga7r8fyywddl3rr2hbn4cfmwhggv02l")) + (snippet + '(delete-file + "inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js")))) (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/plotlyjs/" + (invoke "esbuild" (assoc-ref inputs "js-plotly") + "--minify" + "--outfile=plotly-latest.min.js"))))))) (propagated-inputs (list r-fastcluster r-ggdendro @@ -31118,7 +31131,17 @@ Haberman's interaction model when all items are dichotomously scored.") r-rcolorbrewer r-scales)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-plotly" + ,(let ((version "2.10.1")) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v" + version "/dist/plotly.js")) + (sha256 + (base32 + "1cg2q681yjsrpjmm4nkfia7752wxnszi3c94nq9a91zpnfkm22yb"))))))) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description From ab1f8495f92641402e68de83f3f03630f6331d9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:57:03 +0200 Subject: [PATCH 079/440] gnu: r-rstan: Update to 2.26.23. * gnu/packages/cran.scm (r-rstan): Update to 2.26.23. [native-inputs]: Remove pandoc. [propagated-inputs]: Add r-quickjsr. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a7f3b91207..5d693f26c7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31391,14 +31391,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.8") + (version "2.26.23") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0xah8wl4lg8zh5982m20ipc6cjck1dsfi8lz1jbkg4212p1yvm5j")))) + "08hdwrpxbxp2wdnfk2jj2xsdgl7q9nbalz5wgwmy0m878swxxzci")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -31412,7 +31412,7 @@ techniques to average Bayesian predictive distributions.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list tzdata-for-tests pandoc r-knitr)) + (list r-knitr tzdata-for-tests)) (propagated-inputs (list r-bh r-ggplot2 @@ -31420,6 +31420,7 @@ techniques to average Bayesian predictive distributions.") r-inline r-loo r-pkgbuild + r-quickjsr r-rcpp r-rcppeigen r-rcppparallel From b3b369f9903222d4db426fcbe356a633a6a68224 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 22:58:18 +0200 Subject: [PATCH 080/440] gnu: r-hmisc: Update to 5.1-1. * gnu/packages/statistics.scm (r-hmisc): Update to 5.1-1. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1f4d76af60..c3444560fd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4876,13 +4876,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "5.1-0") + (version "5.1-1") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "0y10hnglid78gnaapmdy3ihjih4i2kvaycn2c60r2wr43nv7wl0q")))) + (base32 "0laan26ja6m9k3spkk1ymalwb181ramzjq6ii3b0404xv2kfywa9")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -4897,9 +4897,9 @@ package instead.") r-ggplot2 r-gridextra r-gtable - r-knitr r-htmltable r-htmltools + r-knitr r-nnet r-rmarkdown r-rpart From 4676f07f6d17df7d36dbcfaf76db24f7c8929e07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 23:02:37 +0200 Subject: [PATCH 081/440] gnu: r-glmnetutils: Update to 1.1.9. * gnu/packages/cran.scm (r-glmnetutils): Update to 1.1.9. --- gnu/packages/cran.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d693f26c7..679a37f9f3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5558,18 +5558,17 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (define-public r-glmnetutils (package (name "r-glmnetutils") - (version "1.1.8") + (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "glmnetUtils" version)) (sha256 (base32 - "1k8ivzjgpkm2a948qxx3wmkhlppbk31qc76spv2pscmp24x0lxyn")))) + "0rh07i9j6bxiqcl84d8jnn7dzqdwfdzak7w8bf4j4521r24mwm01")))) (properties `((upstream-name . "glmnetUtils"))) (build-system r-build-system) (propagated-inputs - (list r-glmnet - r-matrix)) + (list r-glmnet r-matrix)) (native-inputs (list r-knitr)) (home-page "https://github.com/hongooi73/glmnetUtils") (synopsis From 8f59ac151fc39a7dbad2c90a04d2c6c0fe5d3980 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Sep 2023 23:14:38 +0200 Subject: [PATCH 082/440] gnu: r-abn: Update to 3.0.0. * gnu/packages/bioconductor.scm (r-abn): Update to 3.0.0. [propagated-inputs]: Add r-mclogit and r-stringi. --- gnu/packages/bioconductor.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5e9c80291..68463f1f33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -21193,14 +21193,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-5") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "0ibznjhy7vmh2myarvmxy06rvddbpbarbp201px62mig2pb9aq4y")))) + "100nafmyddz0c1h01fbqw5q6pji7zhg2196rkyak88za6s5ms0s4")))) (build-system r-build-system) (inputs (list gsl)) @@ -21209,11 +21209,13 @@ on the plot.") r-foreach r-graph r-lme4 + r-mclogit r-nnet r-rcpp r-rcpparmadillo r-rgraphviz - r-rjags)) + r-rjags + r-stringi)) (native-inputs (list r-r-rsp)) (home-page "https://r-bayesian-networks.org/") From bf9cd9521a75eb928d70b39a30f7b19edb89089b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:05 +0200 Subject: [PATCH 083/440] gnu: r-htscluster: Update to 2.0.11. * gnu/packages/bioconductor.scm (r-htscluster): Update to 2.0.11. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68463f1f33..0b44257b16 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12649,14 +12649,14 @@ abnormal copy number.") (define-public r-htscluster (package (name "r-htscluster") - (version "2.0.10") + (version "2.0.11") (source (origin (method url-fetch) (uri (cran-uri "HTSCluster" version)) (sha256 (base32 - "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n")))) + "0x9shhyla9bldkkh367gfdmf0k72l1ppixb8gzsa6nf8jx8qdpbp")))) (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs From 34d08dc157b8ca611805720c2119e214fc3c8d31 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 084/440] gnu: r-ggfittext: Update to 0.10.1. * gnu/packages/cran.scm (r-ggfittext): Update to 0.10.1. --- 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 679a37f9f3..f55ce23af9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -782,13 +782,13 @@ text annotations.") (define-public r-ggfittext (package (name "r-ggfittext") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggfittext" version)) (sha256 (base32 - "06xfv552nhw13wc8dixyqhhmw5zh8hphrabw090nzb33cpfwzin8")))) + "1z06q55igv6nibc72hll93cpp80mfg3yqfqbi967832nfj7wll7a")))) (properties `((upstream-name . "ggfittext"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridtext r-shades r-stringi)) From 4e2c4c5d4d682b71567a26dcfce5d4a14afdc4cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 085/440] gnu: r-climaemet: Update to 1.2.0. * gnu/packages/cran.scm (r-climaemet): Update to 1.2.0. --- 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 f55ce23af9..af22783233 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1714,13 +1714,13 @@ size and can be easily tested locally before being sent to a remote.") (define-public r-climaemet (package (name "r-climaemet") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "climaemet" version)) (sha256 (base32 - "17g55shqsgpv9vpm41r5lc7ihqhfqj0phbsgv9ghpql9z1nxjy19")))) + "1276pxs3w610v6m8j5h206xxgwvm2wwma73jpvn7s3rcxycs32m5")))) (properties `((upstream-name . "climaemet"))) (build-system r-build-system) (propagated-inputs From 1af29b5f275604f975ffa662e73a303266afc289 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 086/440] gnu: r-mboost: Update to 2.9-8. * gnu/packages/cran.scm (r-mboost): Update to 2.9-8. --- 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 af22783233..d8e407b10c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3018,13 +3018,13 @@ objects.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-7") + (version "2.9-8") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2")))) + "1jyigxi5lzcaa6psc8lyvw2b6ylldqlnps3jlvjrl9zr6336nk6n")))) (build-system r-build-system) (propagated-inputs (list r-lattice From f5bc3727de04cc0398f500b4526cb4dd719943f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 087/440] gnu: r-askpass: Update to 1.2.0. * gnu/packages/cran.scm (r-askpass): Update to 1.2.0. --- 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 d8e407b10c..5952062fba 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3168,14 +3168,14 @@ large-scale hypothesis testing and false discovery rate estimation.") (define-public r-askpass (package (name "r-askpass") - (version "1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "askpass" version)) (sha256 (base32 - "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) + "1vrcb69gf5hc8rggc9m7wv19crz5mkl7f08cipy0ykckh6bkc8mr")))) (build-system r-build-system) (propagated-inputs (list r-sys)) (home-page "https://github.com/jeroen/askpass") From d0928fe95caaf4cc2ebc30646d4b9d9bd10a85d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 088/440] gnu: r-rcppnumerical: Update to 0.6-0. * gnu/packages/cran.scm (r-rcppnumerical): Update to 0.6-0. --- 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 5952062fba..41265e26d1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5938,13 +5938,13 @@ safely be interrupted from R.") (define-public r-rcppnumerical (package (name "r-rcppnumerical") - (version "0.5-0") + (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 - "15hb08vwdvjrhzq1pyalv3qv946jnlk0w77nn654zcmmsns2fqar")))) + "11nph9fz1bzb0pcvh6xx4cb94090ahwpj21zmbi06m4pibb1a1rg")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) From 273b193782f6e1e9afae81de83b2a90bfc7838af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 089/440] gnu: r-ctrdata: Update to 1.15.1. * gnu/packages/cran.scm (r-ctrdata): Update to 1.15.1. --- 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 41265e26d1..f4e9823a6c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6157,13 +6157,13 @@ graphics packages that comes with the base installation.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.15.0") + (version "1.15.1") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "16j44mzfllpp7il0kz3j4a6mi2k939yndgwxki01rqlmf8lrj15j")))) + "1yzn7cxsxbldnfhk83kw8p9qv0154lf2207qvlgjhpc6lzka4lic")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs From d530d51c395064e92983e67db8406c39b7e6a7f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 090/440] gnu: r-lambertw: Update to 0.6.8. * gnu/packages/cran.scm (r-lambertw): Update to 0.6.8. --- 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 f4e9823a6c..02d3cd1e81 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6680,13 +6680,13 @@ print, summary, etc.") (define-public r-lambertw (package (name "r-lambertw") - (version "0.6.7-1") + (version "0.6.8") (source (origin (method url-fetch) (uri (cran-uri "LambertW" version)) (sha256 (base32 - "0cdrq2nrvji8l5blswkffymm7cbjk5jzzx16js2a516cm3gjwxk4")))) + "10lqsz44ndm8pl8z75j35fzd1s313q09rs9bs3lkym8d43k50pha")))) (properties `((upstream-name . "LambertW"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 From 96841f9b22aac0ed66c8a14a5a7bb81f267a17d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:06 +0200 Subject: [PATCH 091/440] gnu: r-lpsolve: Update to 5.6.19. * gnu/packages/cran.scm (r-lpsolve): Update to 5.6.19. --- 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 02d3cd1e81..212b33578d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7144,14 +7144,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.18") + (version "5.6.19") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "04p71mcpksighyvl74ffvgxzc7iiv7nafphddhmqa6yqzhk1j7km")))) + "06sqjj69gp2ja2hgzfxii00js6pjbmhyp07a9jya5sy6cjgb9ma9")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") From ad05f415537ab0a34957d62e146e97dd0bbecd14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 092/440] gnu: r-prodlim: Update to 2023.08.28. * gnu/packages/cran.scm (r-prodlim): Update to 2023.08.28. --- gnu/packages/cran.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 212b33578d..3de5546a39 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7577,17 +7577,22 @@ regression using Kernel Ridge Regression.") (define-public r-prodlim (package (name "r-prodlim") - (version "2023.03.31") + (version "2023.08.28") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 - "003qg4apcayj5kr3730qcs8npibmv1vznzgjcrk9bjhihm7la42m")))) + "1s2xalxfq2q6a9ssz01vzpldpa98q3cl5icap0k2xr5v72gj40l0")))) (build-system r-build-system) (propagated-inputs - (list r-data-table r-diagram r-kernsmooth r-lava r-rcpp r-survival)) + (list r-data-table + r-diagram + r-kernsmooth + r-lava + r-rcpp + r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description From a8c112e212eee1fe3995d228e3c5098b676458d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 093/440] gnu: r-statsexpressions: Update to 1.5.2. * gnu/packages/cran.scm (r-statsexpressions): Update to 1.5.2. --- 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 3de5546a39..405a1d1209 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8249,13 +8249,13 @@ functions for: (define-public r-statsexpressions (package (name "r-statsexpressions") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "statsExpressions" version)) (sha256 (base32 - "1lq4h3a8yr7wnmjkg2rgr8524vdpfacr73pv4wxj44dbg9yh8l3x")))) + "1lqx6wcip0vzlrlhj8yg09009r1r12xg1wxkq93hrlkvya6wm66k")))) (properties `((upstream-name . "statsExpressions"))) (build-system r-build-system) (propagated-inputs (list r-afex From 4d0b8b39a7c7162a4a50b0b1ed619ef3717c35b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 094/440] gnu: r-rio: Update to 0.5.30. * gnu/packages/cran.scm (r-rio): Update to 0.5.30. --- 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 405a1d1209..98110625b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11663,14 +11663,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.29") + (version "0.5.30") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz")))) + "0ihpdwixzkpm3qqh7iy6xm9mmvka2hx50qdidhxnav72nx5b31w0")))) (build-system r-build-system) (propagated-inputs (list r-curl From 28d1e102b671f9642ded97d467946951284c0e87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 095/440] gnu: r-reticulate: Update to 1.32.0. * gnu/packages/cran.scm (r-reticulate): Update to 1.32.0. --- 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 98110625b8..f9f7060648 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -12357,14 +12357,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.31") + (version "1.32.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "19yrxn99xwv5pfn3rnp4ahnp4wfkavj0chqp3zkn223azsigz5cj")))) + "0r9rycwin4yv5k2n1lzybwblb8529yhw5xnl46if6yvxm3bcra9s")))) (build-system r-build-system) (arguments (list From e371d89fa466e07f71e24dda3b62185d73559d84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 096/440] gnu: r-insight: Update to 0.19.4. * gnu/packages/cran.scm (r-insight): Update to 0.19.4. --- 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 f9f7060648..ee512e7ba7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13254,14 +13254,14 @@ Decomposition in R (Beaton et al 2014) .") (define-public r-insight (package (name "r-insight") - (version "0.19.3") + (version "0.19.4") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0zl8in5mvqjq58kprn1slrgc5wfh8vv7wprfc3qp3xl4bsqkj7zz")))) + "1v9555c4rrq91gkpy995f4p6gzcmw7xir73pvi70jwy81agc99g1")))) (build-system r-build-system) (native-inputs (list r-knitr)) From 00a4e351ebdbc5fea36df0ddccdb681dd73ed589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 097/440] gnu: r-flextable: Update to 0.9.3. * gnu/packages/cran.scm (r-flextable): Update to 0.9.3. --- 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 ee512e7ba7..d3beb12a64 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -13413,14 +13413,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0gcjkw35dlhf71djkvmlz0rp62sy3zd45vm8qhk1v3z5ka8m7kdw")))) + "1jdikfiswxi63vj9xr9a24p8fv50h91pvhv3xllgwwfbs1wqyq4x")))) (build-system r-build-system) (propagated-inputs (list r-data-table From 52c69229f894a347502f7979ec68d2416d67e9b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:07 +0200 Subject: [PATCH 098/440] gnu: r-phyclust: Update to 0.1-34. * gnu/packages/cran.scm (r-phyclust): Update to 0.1-34. --- 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 d3beb12a64..9e71f33d8f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15090,13 +15090,13 @@ singular or ill-conditioned Jacobian.") (define-public r-phyclust (package (name "r-phyclust") - (version "0.1-33") + (version "0.1-34") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 - "04x4ymqnmc20pns89i4zs2yp75vchdgjszsinnpddjiv3446cy1q")))) + "1wzmd02ng7zphn97xdra3hgivrxqpizqcy5kpg45sk7jx4q7016j")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) From c4d627396f467b2e8d3fdc260663d4713f765b8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 099/440] gnu: r-tarchetypes: Update to 0.7.8. * gnu/packages/cran.scm (r-tarchetypes): Update to 0.7.8. --- 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 9e71f33d8f..de746ebcb5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15368,13 +15368,13 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.7.7") + (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "1vqyabk04kpskx1ny7c4knzg90ri99x17vfnwcb6syjbzpcfg444")))) + "1m43f2c2rrwnmsbhzfl97fvgjnfm4xwip09saia0dmp84lml26n1")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest From 73eec30f7cc3f1537d3206cb958a2522d27625f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 100/440] gnu: r-targets: Update to 1.3.0. * gnu/packages/cran.scm (r-targets): Update to 1.3.0. --- 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 de746ebcb5..0bc8c3c858 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15405,13 +15405,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "13znvv0qxdmad4rdxjm7zv1wayzj71m35vj8xxshf4fy55a1d59f")))) + "146ylh76sc5vzfgh2xp5mfpgdxvm3j9b2hzh0wqgih6d9d11n8pk")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url From b0a59e175c03c0a51ac61ebc4a392c4a4ea1c184 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 101/440] gnu: r-performance: Update to 0.10.5. * gnu/packages/cran.scm (r-performance): Update to 0.10.5. --- 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 0bc8c3c858..0194dd7f00 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16116,14 +16116,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.4") + (version "0.10.5") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0ddwfkrzwbj1bykvifzrb11hs5kh2a6ykr3ac1hi7cqpqikymfna")))) + "1bwcdz2iah6ya1p9ykbj5ybvzwlq9spv6mq3fn68cckymg0hs76r")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) From 2085788215c959fda22561aa017c4410b6d50052 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 102/440] gnu: r-ggeffects: Update to 1.3.1. * gnu/packages/cran.scm (r-ggeffects): Update to 1.3.1. --- 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 0194dd7f00..642c139cf8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16142,14 +16142,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "145lqfkbawfm9nb23znd80v80j4a5jj8fgyilxqf8pxbqdbwmqql")))) + "0cw9j08qqck1gbfqsfyl3nb4rgi5cwsydxazqw8ppfnjqzw3nwmp")))) (build-system r-build-system) (propagated-inputs (list r-insight)) From 27be02ef17c44763f5cd3d5559d2d498863b6718 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 103/440] gnu: r-credentials: Update to 2.0.1. * gnu/packages/cran.scm (r-credentials): Update to 2.0.1. --- 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 642c139cf8..89128ee0a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16405,14 +16405,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "1.3.2") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig")))) + "12rm7hjrbl3vfcbvdqc1hx3a6b91gf83xm455cn9myjapm2zqz1c")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments From d502c65bd4ee5ee27d5aa45861c96cce68c69ae0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 104/440] gnu: r-circular: Update to 0.5-0. * gnu/packages/cran.scm (r-circular): Update to 0.5-0. --- 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 89128ee0a5..7c2fbec0d1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17493,14 +17493,14 @@ University Press, 2007.") (define-public r-circular (package (name "r-circular") - (version "0.4-95") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "circular" version)) (sha256 (base32 - "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8")))) + "14kvkbmvdfzh8j4hgw93qkjkg86xlpw69sp7g8d5smcyw9fxmx2b")))) (build-system r-build-system) (propagated-inputs (list r-boot r-mvtnorm)) From b7b579dce4635d7db5d3ea0ad9f96c816b0558bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 105/440] gnu: r-fmri: Update to 1.9.12. * gnu/packages/cran.scm (r-fmri): Update to 1.9.12. --- 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 7c2fbec0d1..d506b01df7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17561,13 +17561,13 @@ for evolution along a phylogenetic tree.") (define-public r-fmri (package (name "r-fmri") - (version "1.9.11") + (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 - "07lk24jandnlxn6b8q8acnc4v6r2x2vsl734cpzhwxfjky119sz5")))) + "1cv5mxcdpyf05n5pcjdawl59j7f4k40386r4m38qf15vcy45zdfq")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) (propagated-inputs (list r-aws r-metafor r-nlme r-oro-nifti)) From d9b671a96ecff954238918321cd767551a5dd345 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:08 +0200 Subject: [PATCH 106/440] gnu: r-adimpro: Update to 0.9.6. * gnu/packages/cran.scm (r-adimpro): Update to 0.9.6. --- 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 d506b01df7..60883e4314 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17669,13 +17669,13 @@ Anderson-Darling Distribution\".") (define-public r-adimpro (package (name "r-adimpro") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 - "1w3zcazbxkn1vq37vm4zz4mcmmk1bhxy22gkmv1v9bkv63b46kzm")))) + "0d5viz9ayywpp1pas1yzmhllzn9rjrl8a3k7bj7h46f95l5x1586")))) (properties `((upstream-name . "adimpro"))) (build-system r-build-system) (propagated-inputs From 2dac269403ab6d0bf4bbf9e8c5170236f3683f43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 107/440] gnu: r-qmri: Update to 1.2.6. * gnu/packages/cran.scm (r-qmri): Update to 1.2.6. --- 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 60883e4314..5580331c46 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18278,13 +18278,13 @@ while other are highly specific for the special data format used for (define-public r-qmri (package (name "r-qmri") - (version "1.2") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "qMRI" version)) (sha256 (base32 - "10x59g8awxjib5j5mc1yd5wsibk3z6ki6zifxsg8azl0zblxbscf")))) + "1laslvp1h6xh73lbxvjysznazafcbl7bz0pw4h85n6mp3gsnlvcj")))) (properties `((upstream-name . "qMRI"))) (build-system r-build-system) (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti From 7dd9d99f717380b916b743ffe3995f35fd531974 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 108/440] gnu: r-nnls: Update to 1.5. * gnu/packages/cran.scm (r-nnls): Update to 1.5. --- 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 5580331c46..84d3913bc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18882,14 +18882,14 @@ inventor of the SOM.") (define-public r-nnls (package (name "r-nnls") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 - "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) + "0lilga63p7k5mkkfcf5p3swx76vwysl979jxszm6svzqhsrgww6d")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") From 982487c0fe4e6cbfdfdf12eea5ce1a8e9f3345af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 109/440] gnu: r-minpack-lm: Update to 1.2-4. * gnu/packages/cran.scm (r-minpack-lm): Update to 1.2-4. --- 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 84d3913bc9..224a2ebccf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21157,14 +21157,14 @@ user-defined patterns.") (define-public r-minpack-lm (package (name "r-minpack-lm") - (version "1.2-3") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 - "1w7f9zhqjzayppbd5r6wmlkzlv72nvg74cdjajd2qfq2kxkh59xz")))) + "0cg7arnmb7x6v5x487gkc2k4i5gchgdwblrrd0k0vw1w6pza83z3")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) From ebd91f1bb4d2c53b3f28e8d78ba367780f9f789e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 110/440] gnu: r-pbdzmq: Update to 0.3-10. * gnu/packages/cran.scm (r-pbdzmq): Update to 0.3-10. --- 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 224a2ebccf..528274c741 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21387,14 +21387,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-9") + (version "0.3-10") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "1dhg9sakfz4mivwvyfv5hnjrbi6gcd9cgis0dcgmh44q1a6j6cyh")))) + "14fi1bcvc77k5qjh0vb5r44p9rzlzrbzbw2c99psnzq2wic018ir")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs From d4dd9c352d7a4ac1fe1ae1a267c13c786bfe7578 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 111/440] gnu: r-classint: Update to 0.4-10. * gnu/packages/cran.scm (r-classint): Update to 0.4-10. --- 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 528274c741..400538ed24 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22011,14 +22011,14 @@ classes.") (define-public r-classint (package (name "r-classint") - (version "0.4-9") + (version "0.4-10") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 - "1hz1436apcnqvfyhmlv5f4127jviwfw6hz7f8xxkqygq11ysy4av")))) + "12rbwh7g0a6abvy423xjiv53gx1f9lg4y78r80lc0fj9pjpiwmn3")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs From c4084fb9d5a32969a7f41bf78c7e0f7652cf647f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 112/440] gnu: r-rms: Update to 6.7-1. * gnu/packages/cran.scm (r-rms): Update to 6.7-1. --- 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 400538ed24..bc5bca8ce5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22440,13 +22440,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.7-0") + (version "6.7-1") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zxv7njzaxh6ivrxcszcn128pfxqyh5ga1q8kx6v5brfgv218flb")))) + (base32 "199xb98zxsbd8wa9g33bgrvbcpq79glnfmq060ic8f9vjw96r0qz")))) (build-system r-build-system) (propagated-inputs (list r-cluster From 6589c5fab61f799edf9b98d9f12418d163375a02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 113/440] gnu: r-bqtl: Update to 1.0-35. * gnu/packages/cran.scm (r-bqtl): Update to 1.0-35. --- 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 bc5bca8ce5..5aed60dc1c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22554,14 +22554,14 @@ examples in the vignette.") (define-public r-bqtl (package (name "r-bqtl") - (version "1.0-34") + (version "1.0-35") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 - "1xlkgyhlgrwqfzph4sbhh49pjzfnw5zdr3y4786rsnr3faksnxns")))) + "107yq7mk4gdr1wm20i751682jlj172bzbdjgqwviwgjxzbd0c2xa")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") From d92372b3fad2a3eeaa6bbb6f24c734440736835f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:09 +0200 Subject: [PATCH 114/440] gnu: r-yulab-utils: Update to 0.0.9. * gnu/packages/cran.scm (r-yulab-utils): Update to 0.0.9. --- 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 5aed60dc1c..df0b9b05fe 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23248,14 +23248,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "1bb2rxpwisvb5a670n65k24rdd4aba2xx27dxb9wgj8swqc1rc6y")))) + "0y8594xmsg59p7pgz9bnjdc0bi50y6nmzvvzmjk8wyn4v5rz09ln")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs From 961a3a81ca4bccf60320c343f870b704cce1b294 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 115/440] gnu: r-ggcorrplot: Update to 0.1.4.1. * gnu/packages/cran.scm (r-ggcorrplot): Update to 0.1.4.1. --- 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 df0b9b05fe..7ab8c18857 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23901,14 +23901,14 @@ in-memory raw vectors.") (define-public r-ggcorrplot (package (name "r-ggcorrplot") - (version "0.1.4") + (version "0.1.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggcorrplot" version)) (sha256 (base32 - "186a0mpdpipp24fjbd52l1gdgpqm6vl83ff8069d8nngyqbrx0jr")))) + "0yd865lfs4144jqh9ilznqa69rj0183ashnhvmjmis87zw69a45q")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) From 6b25da59a10b4b3d41c17332ccd5cb3df93ac62e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 116/440] gnu: r-cyclocomp: Update to 1.1.1. * gnu/packages/cran.scm (r-cyclocomp): Update to 1.1.1. --- 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 7ab8c18857..8f749f9dae 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24566,14 +24566,14 @@ provided.") (define-public r-cyclocomp (package (name "r-cyclocomp") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "cyclocomp" version)) (sha256 (base32 - "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd")))) + "0kdinnn6cgkfc94japyyp5qr7imjxddajds3qqxf4q5higahdzws")))) (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs From ae07546906b23cf1a570e73456e372b0909588a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 117/440] gnu: r-styler: Update to 1.10.2. * gnu/packages/cran.scm (r-styler): Update to 1.10.2. --- 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 8f749f9dae..2a8316c81b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24724,14 +24724,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "0rswg2habyk38hcx0gn9hnvb200bq0dc4fy4k3gqhfhwjq9l7a1b")))) + "043v9xwm72jqrrzzmjgrkf34lncjnn69650ks72z7rjb1wqmbh56")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments From 99f4f47c8f5372bd08e5ff49a696a20d52d9ae5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 118/440] gnu: r-dqrng: Update to 0.3.1. * gnu/packages/cran.scm (r-dqrng): Update to 0.3.1. --- 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 2a8316c81b..4041e942be 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24907,14 +24907,14 @@ dimensional low-discrepancy sequence.") (define-public r-dqrng (package (name "r-dqrng") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 - "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) + "0vmrbnix05a9h1bc4b7d999qkzkk63i1arzyblyhmvydv4m8cc72")))) (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-sitmo)) From 331045a386a35f19824bd4f26b09cee8cc35b6bc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 119/440] gnu: r-leidenalg: Update to 1.1.2. * gnu/packages/cran.scm (r-leidenalg): Update to 1.1.2. --- 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 4041e942be..c43cdcd112 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -25672,13 +25672,13 @@ guaranteeing well-connected communities.\" .") (define-public r-leidenalg (package (name "r-leidenalg") - (version "1.1.0") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 - (base32 "1hn5fps5m5am4s82wvhr4fgfw49h0jar4i687czbkab3l9x1dr68")))) + (base32 "0wqay0rf28pgaf88bsvmrwgggzbma93rv9nqbydhjf1lc96ay1lz")))) (properties `((upstream-name . "leidenAlg") (updater-extra-inputs . ("gmp")))) From 53d902a9d4844475400b695ac00f52f8cdf2ec83 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 120/440] gnu: r-terra: Update to 1.7-46. * gnu/packages/cran.scm (r-terra): Update to 1.7-46. --- 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 c43cdcd112..cb3c0ee397 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26013,14 +26013,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-39") + (version "1.7-46") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "03kc2m89236qh50qfxl1101ys466ddhgjwp80x6hjpmd9fz5jf5l")))) + "0jpni25g9rhsqh71pgr2d3221r9xacsw3kz5qqnifj0jz5g3wyh1")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs From adb7d031270f9f5c0a70b32884e2ccc9afca8d67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:10 +0200 Subject: [PATCH 121/440] gnu: r-desolve: Update to 1.38. * gnu/packages/cran.scm (r-desolve): Update to 1.38. --- 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 cb3c0ee397..3824517b3c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26303,13 +26303,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.36") + (version "1.38") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "1ygijjvmi7igk3xmm2mzfnbw05kynjdqbwddifg798awk7mfffjw")))) + (base32 "0sc933g0jx25b7fm5bl6is95mn4fn1sf8cgb6qzhlmmf8rfgxd50")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs From aec1073ee7c44436c9b083cf778cfe57a30bac6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 122/440] gnu: r-gamlss: Update to 5.4-18. * gnu/packages/cran.scm (r-gamlss): Update to 5.4-18. --- 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 3824517b3c..7c71183105 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27506,14 +27506,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.4-12") + (version "5.4-18") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1w5630hzir49nacpvmx28hqc8hcc9acmba9dd8zwzhz5ywwi0ycz")))) + "1wj6hx6z48zpwkqz3w68dfsf2nfj8clhwqykq5ln94vrarqaim7g")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs From 39c45564506c8b387aa392abf7853843ba04ec3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 123/440] gnu: r-acopula: Update to 0.9.4. * gnu/packages/cran.scm (r-acopula): Update to 0.9.4. --- 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 7c71183105..233fe04f1c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27821,14 +27821,14 @@ and may be used to generate realistic data sets with known truth.") (define-public r-acopula (package (name "r-acopula") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "acopula" version)) (sha256 (base32 - "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) + "0asxfcjrsr9d7ab59pdajs0zvdjgwfswk9rdlpfdr51535wpjrfy")))) (properties `((upstream-name . "acopula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/acopula/") From cd57a3ec9fd9bd0d522191b24c11f1f38edfd21c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 124/440] gnu: r-emplik: Update to 1.3-1. * gnu/packages/cran.scm (r-emplik): Update to 1.3-1. --- 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 233fe04f1c..d6b19f95e7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -29788,14 +29788,14 @@ OpenMP.") (define-public r-emplik (package (name "r-emplik") - (version "1.3") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "emplik" version)) (sha256 (base32 - "14jgwwxvsglkbq7kwjl34lyax45qn4hkra4qmmv4ybnvvcmbcag1")))) + "1f6v0bg9sl8kn4y8bpgjyc1b18xkmfbs86gbbmbh198v335lgcrb")))) (properties `((upstream-name . "emplik"))) (build-system r-build-system) (propagated-inputs From 2b40d9b13afde321a3139502c622aa1ef5bb3a9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 125/440] gnu: r-forecast: Update to 8.21.1. * gnu/packages/cran.scm (r-forecast): Update to 8.21.1. --- 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 d6b19f95e7..4923efd05e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30047,14 +30047,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.21") + (version "8.21.1") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "1hn60p88jq9qprgwgh4ymb53fri71imad6kasycv6gwxb9wk3lgx")))) + "09w1vh96cf9wz071why5f4265cvvwqi2b3wb0khrjvkzgkiaq7l1")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs From 3c3dbf219660c8a1e3b29c2ee0681af8f130afaa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 126/440] gnu: r-stanheaders: Update to 2.26.28. * gnu/packages/cran.scm (r-stanheaders): Update to 2.26.28. --- 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 4923efd05e..d2c7cad995 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30637,14 +30637,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.27") + (version "2.26.28") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1cf9hc7z3d8b70jck37j3lc2ml040di91dylfb18yi6wx936bq3h")))) + "1s1xgvn5c1vjikm1dx9g0qm2k8m24clylgp7zssmfhx6sfb8v2lk")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) From b40994d97d893090f47c566aaa2e0855b778b3a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 127/440] gnu: r-packrat: Update to 0.9.2. * gnu/packages/cran.scm (r-packrat): Update to 0.9.2. --- 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 d2c7cad995..87a8644602 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31163,14 +31163,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "0i1kzmjzks6g673jkcqmra0nysviab0r915wkgk8aaad0k316h21")))) + "1mvj2s78n2r66nlqq5bjrvgdwlwbcqdj81yryc34sv3y4m1mkpv9")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") From d471fd760d8bd9eacd326719d56cdd759343713b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:11 +0200 Subject: [PATCH 128/440] gnu: r-rsconnect: Update to 1.1.0. * gnu/packages/cran.scm (r-rsconnect): Update to 1.1.0. --- 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 87a8644602..060eb2122b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31184,14 +31184,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "1cni5sc4qgvd3vvn2jy0saxsxz144yl2jahhbf0bhix35blgzlp1")))) + "1jpz9cx2fqj3cp69xd2vi9gc5wdfrs4rbpy81mm7hq1iaq5nd7pc")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs From f8fdfb731f1f2523852f445e094e13b5908447e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 129/440] gnu: r-directlabels: Update to 2023.8.25. * gnu/packages/cran.scm (r-directlabels): Update to 2023.8.25. --- 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 060eb2122b..eb4ad4195d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32664,14 +32664,14 @@ permuted copies (shadows).") (define-public r-directlabels (package (name "r-directlabels") - (version "2021.1.13") + (version "2023.8.25") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 - "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w")))) + "0p7as0yvvywbdqjpng70sdiy0xyczac4qbv534cwqxiqyx81vp8j")))) (build-system r-build-system) (propagated-inputs (list r-quadprog)) From 9cf2cf4c9a44726bd467e1b7bf10babbcf2f81a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 130/440] gnu: r-spatstat-explore: Update to 3.2-3. * gnu/packages/cran.scm (r-spatstat-explore): Update to 3.2-3. --- 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 eb4ad4195d..91d3d549e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33231,13 +33231,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.2-1") + (version "3.2-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "02n64bml361xakfbj71m7mgkb0p6szqc55lijjsnwa3z69pwwshb")))) + "18zhpspq07rcnpmnkc82hzjvjp39fsb06g73gin4x5bwzbi22kgr")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs From 1e6db67bc176b3d14f31f838529090511adf4819 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 131/440] gnu: r-spatstat-model: Update to 3.2-6. * gnu/packages/cran.scm (r-spatstat-model): Update to 3.2-6. --- 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 91d3d549e9..bfd989ef87 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33271,13 +33271,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.2-4") + (version "3.2-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "0vcxwwc4kjfmjd80sk7rbv8a9yg9v2m94brgww8fiibrm6m9psi6")))) + "1lvs6ns4hna7w6b0nvzsx2rw699ampdm8jmxdzlfpk4hla2lf7wq")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs From 3bf11b1eea2cfcd978df968b69ee96a8d1ed5fe7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 132/440] gnu: r-spatstat-geom: Update to 3.2-5. * gnu/packages/cran.scm (r-spatstat-geom): Update to 3.2-5. --- 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 bfd989ef87..5f9bba3ac2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33382,14 +33382,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.2-4") + (version "3.2-5") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "09x2z2jqgbmilqg2kx4sgzrz54hbkyfpv9hm759075i2hkaza796")))) + "13xlp88yfp61kl0c3vaqs7lrckkc4ixpp0mpf89h5ggmjyf57nxx")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs From 9de7344c48d2c1315a38c017fae7ad313a11325f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 133/440] gnu: r-spatstat-random: Update to 3.1-6. * gnu/packages/cran.scm (r-spatstat-random): Update to 3.1-6. --- 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 5f9bba3ac2..38513e0a4f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33468,13 +33468,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.1-5") + (version "3.1-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "128rm8k4b5rklddmnhbsv93jj6qym0fngir9nb65cawg3zb991m6")))) + (base32 "0vrx0mxzcd6yr6rzn9jk2wj5d2l7yn0ij1n58yb3hw2g7nasad06")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) From eb0ba6f4948cd5e224fa5f4650e1e54d3e8f955f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 134/440] gnu: r-config: Update to 0.3.2. * gnu/packages/cran.scm (r-config): Update to 0.3.2. --- 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 38513e0a4f..a6746b9efb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -34222,14 +34222,14 @@ coerce and verify the types and shapes of values for input checking.") (define-public r-config (package (name "r-config") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 - "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l")))) + "0r8hjg7jrhr9lncb82xmq2slygv3slacd2w8ds6shnvdp3122p3v")))) (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs From 09b6be49e82515d64c188f8946b9d6ab139979c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:12 +0200 Subject: [PATCH 135/440] gnu: r-infer: Update to 1.0.5. * gnu/packages/cran.scm (r-infer): Update to 1.0.5. [propagated-inputs]: Add r-vctrs. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a6746b9efb..bdb65b8497 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35088,14 +35088,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1s4q0nslykl0pb2w1i6ni6hkpp7awvp0wks79br3gk5wa1qkvs19")))) + "1zs1c22zc255m23in99cqp2chpdkski002rywmkdzwf6nd96mly7")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs @@ -35109,7 +35109,8 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") r-purrr r-rlang r-tibble - r-tidyr)) + r-tidyr + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/infer") From 8da144981873f8febaa9fa0fa0ff70606dc5ea6e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 136/440] gnu: r-seqminer: Update to 9.1. * gnu/packages/cran.scm (r-seqminer): Update to 9.1. --- 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 bdb65b8497..51ef53414d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35438,14 +35438,14 @@ designs. Broman et al. (2018) .") (define-public r-seqminer (package (name "r-seqminer") - (version "8.9") + (version "9.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "1cnsy1cjz4rcm32hzcvr1d43y4m7sdkzim1mwsn3490mf3xmi3i1")))) + "0vdprasxy4dc9p5k43xgcmi0q50iapgcam43qzbh1kr0vi6fgqkr")))) (build-system r-build-system) (inputs (list zlib)) From fe2a36ed5bb962420284500d562db59e5cc5a5f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 137/440] gnu: r-diversitree: Update to 0.9-20. * gnu/packages/cran.scm (r-diversitree): Update to 0.9-20. --- 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 51ef53414d..c522afa7fa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35820,14 +35820,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-19") + (version "0.9-20") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "1z3lzqphswb4r3rdh2jmi1pfagqs38dbccm9li02sc8aasdqk0if")))) + "0lm098ysk6np4dy1cifbhd85jd1f1iz4bqhgzlcx7x8qnhh3zc1c")))) (build-system r-build-system) (native-inputs (list gfortran)) From d8ac99ec8ee98ec8174337e56b20da9f9dade285 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 138/440] gnu: r-readods: Update to 2.1.0. * gnu/packages/cran.scm (r-readods): Update to 2.1.0. [propagated-inputs]: Remove r-xml2. --- gnu/packages/cran.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c522afa7fa..2af0435bdb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37190,14 +37190,14 @@ functionalities in strex.") (define-public r-readods (package (name "r-readods") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 - "09b0z5fbl09inygbmbgprj8v6cd8z8zw9r3j68rlmi7mivxzbqk4")))) + "1znp039wfbq8bbjj9pdkl8hwnhm9x5n8c7y5b53xmpnaqxx5agiz")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs @@ -37207,7 +37207,6 @@ functionalities in strex.") r-stringi r-tibble r-vctrs - r-xml2 r-zip)) (native-inputs (list r-knitr)) (home-page From 6287891b2ad77b3aa2c29c301f0d49570845574f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 139/440] gnu: r-pbdmpi: Update to 0.5-0. * gnu/packages/cran.scm (r-pbdmpi): Update to 0.5-0. [propagated-inputs]: Remove r-rlecuyer. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2af0435bdb..828f1cc149 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37260,13 +37260,13 @@ data you need the @code{pdftools} package.") (define-public r-pbdmpi (package (name "r-pbdmpi") - (version "0.4-6") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 - "0r6kbrvc0z4mb2dhrz1iqdyx0c03f682b5xfi1igp7z3rszd1va1")))) + "0wfx33jhdrwp97chsp9v8z2yf49shycvky8dwl9pgwqd9l69aw7x")))) (properties `((upstream-name . "pbdMPI"))) (build-system r-build-system) (arguments @@ -37275,7 +37275,7 @@ data you need the @code{pdftools} package.") (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs (list openmpi)) - (propagated-inputs (list r-float r-rlecuyer)) + (propagated-inputs (list r-float)) (native-inputs (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "Programming with Big Data -- Interface to MPI") From 1b2d3cf25d22aa7319c0ae006577ecda2887805d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:13 +0200 Subject: [PATCH 140/440] gnu: r-packcircles: Update to 0.3.6. * gnu/packages/cran.scm (r-packcircles): Update to 0.3.6. --- 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 828f1cc149..1202d009c1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37393,14 +37393,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-packcircles (package (name "r-packcircles") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 - "0m8ivgc5y1f9ramqw6sxb02ri6aqxz3av0l5csl32mdldrb126nc")))) + "0fjc575i1vxjp2v4niv2syqqk0d609wm86gkq9rvgmch841x40ps")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) From 6bf5162b1d0f8fa0fc981085af4fae9b435ecd73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 141/440] gnu: r-stars: Update to 0.6-4. * gnu/packages/cran.scm (r-stars): Update to 0.6-4. [propagated-inputs]: Remove r-lwgeom. --- gnu/packages/cran.scm | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1202d009c1..88aae7ee9b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -37443,23 +37443,18 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.6-3") + (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "08i5m46plkwkxwgzpy6srvn69jchp364vj3sg1isp2lj9pxhzfwc")))) + "0mqd2dfa8jhxjmfphvv3rkw2lri5sz49042asj5lyln3wkylqjj2")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs - (list r-abind - r-classint - r-lwgeom - r-rlang - r-sf - r-units)) + (list r-abind r-classint r-rlang r-sf r-units)) (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis From 0285844e14b6ef15e3f8afd01171c249fbb1f540 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 142/440] gnu: r-distributionutils: Update to 0.6-1. * gnu/packages/cran.scm (r-distributionutils): Update to 0.6-1. --- 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 88aae7ee9b..1a03e362c8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38491,14 +38491,14 @@ carrying out economic experiments.") (define-public r-distributionutils (package (name "r-distributionutils") - (version "0.6-0") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "DistributionUtils" version)) (sha256 (base32 - "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl")))) + "1mv3p7hm02q3mhrw5165gc2d77ighnykyfn6ibxvkc3ii2m9xrri")))) (properties `((upstream-name . "DistributionUtils"))) (build-system r-build-system) From a2afbbed24fe0aa35d6de31ceababd61e98d226e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 143/440] gnu: r-paws-common: Update to 0.6.0. * gnu/packages/cran.scm (r-paws-common): Update to 0.6.0. --- 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 1a03e362c8..b5cad45fb1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38709,14 +38709,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.8") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1vx74lxgzsl1yl4ak5zympkgwza023qbjwskp19nm2dvxhz75cfh")))) + "1451705w30lb33msi4qgzpfmw6xnwh2ffh30fwb9im8g47fqm2bw")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs From 067f519a4d2486d5dd91101acacdcb6f3e31bfe6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 144/440] gnu: r-paws-customer-engagement: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-customer-engagement): Update to 0.4.0. --- 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 b5cad45fb1..c487dc674b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38740,14 +38740,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "18gkr3272jj1pkksm6fy6qz5s5jn0yvb12pz29k204xrzmqwdwgm")))) + "0skfya3m9i36dd0jqvnnc72k1h3lb4s3fjkvg7na6aq6xgpjh4jv")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) From 6a6c29efb55fc30d3d061f5aaebf4b405078041d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 145/440] gnu: r-paws-cost-management: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-cost-management): Update to 0.4.0. --- 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 c487dc674b..faccc2d50b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38764,14 +38764,14 @@ service, and more.") (define-public r-paws-cost-management (package (name "r-paws-cost-management") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 - "0v0s8wwx2j3a6s0pl9vnvbpgdyhn3jlxri0b2fl3gc3zx6qh07dl")))) + "1j9zi73y9ng5m6wlws4crfv4j6b8qxk1m9g1hd286g4gg852g80y")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) From ab20ed6424435a131aa8aa93b79521fd0e0ea3cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 146/440] gnu: r-paws-developer-tools: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-developer-tools): Update to 0.4.0. --- 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 faccc2d50b..d0798be66a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38788,13 +38788,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "1b661gpg7rsdkgpriwczj4cvqg9rh1ajz9ma457bw4p3lv7n53x2")))) + (base32 "13i5yi23xsrks1dsw0k3cqzr2gqj8p23yajb3a7drim6d4rpsaxl")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs From 4052f7d113b17d917956f1bc86c5a37d19aa1726 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 147/440] gnu: r-paws-end-user-computing: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-end-user-computing): Update to 0.4.0. --- 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 d0798be66a..05c2e0cb1d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38810,13 +38810,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "0as9ix46rsa7sg8k96v6l3ibxqc95pf7swrij31ljmwfy82z2rq3")))) + (base32 "0v3ng20vrp5cvpbgipwwpvyhi995n2rp8jls0kklkrjax41x62cn")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs From 90aa4f2afe7833c7891dfba54fd8bc91c2f510d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:14 +0200 Subject: [PATCH 148/440] gnu: r-paws-application-integration: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-application-integration): Update to 0.4.0. --- 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 05c2e0cb1d..42dc5e057f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38832,14 +38832,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "19lz1vcvb1bn405saxx4zjsmm1q4zaw77z08iw4xbyny5xhkgyvi")))) + "0hilnczvamdv3bi1v6hdki05h8qqh0wlgvh5ilh09113005fpz98")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) From 6e8f6654d79e8ac9c7f026b21d9c645380155e4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 149/440] gnu: r-paws-security-identity: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-security-identity): Update to 0.4.0. --- 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 42dc5e057f..b8f8c111d4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38856,14 +38856,14 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "02k15skswd58icafydrbjrp7br5x8l93lwi5z1pwqak6xasi0vqh")))) + "081339201j19y8y28h0dhr876ii82zpfyqddc21lvmg27z53hj4x")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) From ba2fa58be01da4f6e4abee2e2831a55ac368aaff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 150/440] gnu: r-paws-analytics: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-analytics): Update to 0.4.0. --- 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 b8f8c111d4..f90803b949 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38881,14 +38881,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "0qjk1gn4p41l4ryqf9xppiphfakypl0xdjk23c9c8xdhqkbw0lcw")))) + "1x7ix8x0ks357b7gf2skixsd0najjbn8hnq7p6a354p5h7bz39b4")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) From 9497c4dbff01bbdbef9e6f235d92ca92f657e601 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 151/440] gnu: r-paws-machine-learning: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-machine-learning): Update to 0.4.0. --- 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 f90803b949..dfc5d31e88 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38905,14 +38905,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "092n5p5hjwaqkdnw4r7n71znabfazc2pg19raja69jgk6zh6csvy")))) + "0cwmriprwrz446q4d5ljkpvwdhmamnl98g1ks6p35vbjiv4imk21")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) From 98c8da964f680d4ad900a145987125f50b9bb90a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 152/440] gnu: r-paws-management: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-management): Update to 0.4.0. --- 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 dfc5d31e88..d78109c6af 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38929,14 +38929,14 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "0hdmc07i75hbk2fh580p7q7p3pk8ykr5m1jibnfk8azc4flikwv6")))) + "0lp8s4caxppwxsra6ijcz1dzkmnznwrrs92y87387vq53y3icc6m")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) From 2e8126e3baa07c370504f73af4a452b033a4defc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 153/440] gnu: r-paws-networking: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-networking): Update to 0.4.0. --- 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 d78109c6af..f8cb25fdfb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38953,14 +38953,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "0pf1vvwmgsz65bq5diabybnsgyxfbjq1f64srf3qk49ycfh2sc7h")))) + "1imq29nxy5hxz2vlijdj2jl0lllvm3plb3jwpvsx1wlcvhpz0in3")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) From 30bd163d01a271ec439fc9c9326562e10e551087 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 154/440] gnu: r-paws-database: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-database): Update to 0.4.0. --- 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 f8cb25fdfb..38f971d94a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -38977,14 +38977,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "08ak299kyr6dr8idcna7i433aab1bis2b9zqmwm1yma3m3xk4n8i")))) + "1rnjjdb4l7a943cawkkzfjkg8shy2vy5d9mcl2p5ms191lw056bn")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs From c165a1fa9b624a530399e8ea34cdb4bc45075226 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 155/440] gnu: r-paws-storage: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-storage): Update to 0.4.0. --- 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 38f971d94a..d047884fc7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39001,14 +39001,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "0z693wawgm975lw54xkbg9hwsf1lz69a4dsg85ywjpjcfvl1g1b7")))) + "0yr99328rwm6i95xhp4yds6dzfvrvbr7ys2hy17iqbyij958j0m4")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs From b2610240c4ec3c35abb988531523bcf0c8ce181a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:15 +0200 Subject: [PATCH 156/440] gnu: r-paws-compute: Update to 0.4.0. * gnu/packages/cran.scm (r-paws-compute): Update to 0.4.0. --- 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 d047884fc7..0b1185e4c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39023,14 +39023,14 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "17xzc1ngir4v043xclw6c1qs092aicj83qmn8sydn9apmlzcps1r")))) + "0q0xikrq7095l8fhii2jyjxfbihhnlm7nzzbspfqdh8xbr7g4kld")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs From 772f00b171f6ad3f497f4609defddf175cf6a773 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 157/440] gnu: r-mlearning: Update to 1.2.1. * gnu/packages/cran.scm (r-mlearning): Update to 1.2.1. [propagated-inputs]: Add r-rpart. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0b1185e4c6..9c93a5477b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39191,14 +39191,14 @@ large datasets.") (define-public r-mlearning (package (name "r-mlearning") - (version "1.1.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "mlearning" version)) (sha256 (base32 - "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3")))) + "0fh28i36smpybhzd2kni435m7wf20i3yib6h7jy173r1v5adzkba")))) (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs @@ -39207,7 +39207,8 @@ large datasets.") r-ipred r-mass r-nnet - r-randomforest)) + r-randomforest + r-rpart)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description From b832880b1e220148fc81a758e1439de400c35658 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 158/440] gnu: r-ggh4x: Update to 0.2.6. * gnu/packages/cran.scm (r-ggh4x): Update to 0.2.6. --- 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 9c93a5477b..6166b0d006 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -39852,14 +39852,14 @@ be efficient and easy to use.") (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.5") + (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "0xj4nlxrpmwzdlj4q3vnhwy7gd1634ff7yjsnaf609ap0q23mxb1")))) + "0frbkdylyz630y7rjyif0whf74r89ca5bmhk9djcwz8nqfs2jygb")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs From 1a7612a64cbe923a68b9f26b9cc81ce38fdbf9e6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 159/440] gnu: r-foreign: Update to 0.8-85. * gnu/packages/statistics.scm (r-foreign): Update to 0.8-85. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c3444560fd..f5268bb0b6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -603,14 +603,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-84") + (version "0.8-85") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0jc5r5wiqqbkni2xjdd24hic1xvfi151m9lnqhni52jnqw1g7v8p")))) + "1azca97fhwb1pzgrjw2xscfh2k7bfryp6wjsdcx2y4h7305d4ych")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") From 8f68be3264004b17ae9e2bef0c878fab07462d8f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 160/440] gnu: r-labeling: Update to 0.4.3. * gnu/packages/statistics.scm (r-labeling): Update to 0.4.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f5268bb0b6..4b1d7ef896 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1005,13 +1005,13 @@ non-estimable cases correctly.") (define-public r-labeling (package (name "r-labeling") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "labeling" version)) (sha256 - (base32 "0rfikd9gy70b8qz87q9axcwv8nmn9mbxfdwypxi0sghpfs9df8p0")))) + (base32 "1wk4wa1s8f17b5lf8vs5hxsmyadp2ccmyg4hamq7sdvlrk14yby6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/labeling") (synopsis "Axis labeling algorithms") From 44dfcc013a9af9de179b821f8bf71d6949ce8703 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 161/440] gnu: r-knitr: Update to 1.44. * gnu/packages/statistics.scm (r-knitr): Update to 1.44. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4b1d7ef896..c9b4cc518a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1576,13 +1576,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.43") + (version "1.44") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0g6m9s53qyf34ba4db97k31sxg2ikndfp747229sm6ilikmbla9x")))) + "015ylljvx0q2himch4k813021nvh0l7p5x3aqdkj3w0ax8x8k3ki")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-xfun r-yaml)) From 800aab705c802dda1c10eee0104a0a1e8513c961 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 162/440] gnu: r-dplyr: Update to 1.1.3. * gnu/packages/statistics.scm (r-dplyr): Update to 1.1.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c9b4cc518a..e78744d15d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1827,13 +1827,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "1qwn00ai7k6km0z9kl6aa1qjkfz8j3prlgdfxr1pr5s47a5c6862")))) + "0hhpzv66rqz7z8vdryzjdkp4flmjvzxrx1pwpxnbmjqgvd3s4hv8")))) (build-system r-build-system) (propagated-inputs (list r-cli From fcf5c595e2989cdeaf8d08414118b47adbb9e5da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 163/440] gnu: r-rcpparmadillo: Update to 0.12.6.4.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.6.4.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e78744d15d..27e9f95e73 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2963,13 +2963,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.6.1.0") + (version "0.12.6.4.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0saga8anaahyrvvynggg168756rv8d9gyq8sryjgnx5pp4jbz6ck")))) + "1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs From 894c89b1d87b2c9c30df79d5f038f1c0df1802be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 164/440] gnu: r-rematch: Update to 2.0.0. * gnu/packages/statistics.scm (r-rematch): Update to 2.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 27e9f95e73..843d0d9992 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4717,14 +4717,14 @@ distribution).") (define-public r-rematch (package (name "r-rematch") - (version "1.0.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "rematch" version)) (sha256 (base32 - "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4")))) + "09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm")))) (build-system r-build-system) (home-page "https://github.com/MangoTheCat/rematch") (synopsis "Match regular expressions with a nicer API") From fd1d1e11a29e7d2cd674c1c51f3499234bbf4bc4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 165/440] gnu: r-deoptimr: Update to 1.1-2. * gnu/packages/statistics.scm (r-deoptimr): Update to 1.1-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 843d0d9992..791b811eff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5586,14 +5586,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.1-1") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "1appp5xgayafda6f5pcdsxaskqs831rb21znx44r8nyb9gvg0f6z")))) + "0swycypiyxkvhn1438q0wysz2c4ky6zjw89w62dggbciqwk8xdbq")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") From 97e5c897c4ba22ce8b9955eec4a683fdcf9a7ef6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 166/440] gnu: r-lmom: Update to 3.0. * gnu/packages/statistics.scm (r-lmom): Update to 3.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 791b811eff..b647ec0b61 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7232,13 +7232,13 @@ Annealing\" @url{doi:10.1145/3025453.3025912}.") (define-public r-lmom (package (name "r-lmom") - (version "2.9") + (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "lmom" version)) (sha256 - (base32 "145va4dhl767mywk36xcmqilm21sfkqhcqi0s07qgq3k39sn4gin")))) + (base32 "1482kbb4cm65m2d1xlxml93yjd3d43iiap6nvzg5vd33i9iyh2jb")))) (properties `((upstream-name . "lmom"))) (build-system r-build-system) (native-inputs (list gfortran)) From 3d402fbf1d950c1d7c194d5cdd1bc17e884ab6eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 167/440] gnu: r-desctools: Update to 0.99.50. * gnu/packages/statistics.scm (r-desctools): Update to 0.99.50. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b647ec0b61..00eb6c7f1b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7316,13 +7316,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.49") + (version "0.99.50") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "0s2zh8xz06c45rbwcypgsa8shby66nm6sj90cb9d1bwb60mws8j5")))) + (base32 "1awfhbv7klvkwxki4lvxj086yiwqyys95jnss8q5qqn7wyfz170v")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs From 2afa9353a0f69dabf4ddec54b58b60308092c794 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 00:04:16 +0200 Subject: [PATCH 168/440] gnu: r-reghelper: Update to 1.1.2. * gnu/packages/statistics.scm (r-reghelper): Update to 1.1.2. [propagated-inputs]: Add r-rlang. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 00eb6c7f1b..d8fde36cd3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -7553,16 +7553,16 @@ generating and manipulating colors in R.") (define-public r-reghelper (package (name "r-reghelper") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "reghelper" version)) (sha256 (base32 - "0v1987rs6kcpizfhrp3hxsyx9arn5vsbapjfgj9478j73mm844ji")))) + "1vd8kd719kyjp65zym6zx3vax1q2kbhpl6la71d5aa59s54ylri3")))) (properties `((upstream-name . "reghelper"))) (build-system r-build-system) - (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme)) + (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang)) (home-page "https://github.com/jeff-hughes/reghelper") (synopsis "Helper Functions for Regression Analysis") (description From 028ebb8edb133bec27c6c7ae1f604dcb090ed127 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Thu, 14 Sep 2023 06:50:42 +0200 Subject: [PATCH 169/440] gnu: libwebp: Replace with 1.3.2. [fixes CVE-2023-4863] * gnu/packages/image.scm (libwebp/fixed): Update to 1.3.2. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 403409975a..a632a02139 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1475,7 +1475,7 @@ channels.") (package (inherit libwebp) (name "libwebp") - (version "1.3.1") + (version "1.3.2") (source (origin (method git-fetch) @@ -1485,7 +1485,7 @@ channels.") (file-name (git-file-name name version)) (sha256 (base32 - "1aas6gwy7kfcq34cil781kcsl286khh9grwcx7k4d2n1g7zcpl3m")))))) + "1x37795gpc63g1ma9kqw4q3dikwhrjklixqzjjsj6viqksa19z41")))))) (define-public libmng (package From 6e06c0032cd0f4f3b49d38b226b082e1c4e4d429 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 170/440] gnu: r-genomeinfodb: Update to 1.36.3. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.3. --- 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 0b44257b16..0fd32ddacb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7195,13 +7195,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.2") + (version "1.36.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0bd46s7ch4j70n0snjf2nyx8gzkxn7d563jh5i3i0wzb647f5hbg")))) + "04bh4481jcj91xdh11ic4519jczck6zmysbpnpbbhykanp31z4pf")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From a1245f559d1291cac1b8578157fbbb0f565f0219 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 171/440] gnu: r-genomicdatacommons: Update to 1.24.3. * gnu/packages/bioconductor.scm (r-genomicdatacommons): Update to 1.24.3. [propagated-inputs]: Add r-tidyr. --- 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 0fd32ddacb..165f704934 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7254,13 +7254,13 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "0dgvhi6nbc1qvrdwww2r39gxd2xmbadvy03lxh5nny9pyhhdlz3l")))) + "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -7273,6 +7273,7 @@ alignments.") r-readr r-rlang r-tibble + r-tidyr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicDataCommons") From 7f983fb73024a3f0429b8a78bde74a8fdd059ff4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 172/440] gnu: r-shinymethyl: Update to 1.36.1. * gnu/packages/bioconductor.scm (r-shinymethyl): Update to 1.36.1. --- 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 165f704934..aa7b491191 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9813,13 +9813,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "1rqwwglj0475gr14bxazfmcvsy7rq6nlw2zcswa684751wy15w0r")))) + "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs From 8fe9e14917973c2039079be9440f0acd9b91cfe5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 173/440] gnu: r-tcgautils: Update to 1.20.4. * gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.20.4. [propagated-inputs]: Add r-biocbaseutils. --- 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 aa7b491191..43952be0aa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9963,16 +9963,17 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.20.2") + (version "1.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "0nnfrd5x3mii9adizvz79jinlxn2lhg4civ9v0wwygmdhk7rrm1n")))) + "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi + r-biocbaseutils r-biocgenerics r-genomeinfodb r-genomicdatacommons From 8cfd6e804ab5917d161f3880bd1f9d70b2d1fb4b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 174/440] gnu: r-greylistchip: Update to 1.32.1. * gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.32.1. --- 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 43952be0aa..2f2d649e4f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11110,13 +11110,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s")))) + "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs From 9232ef79865439cc6584e8942550f8d6fb70a1c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 175/440] gnu: r-clusterprofiler: Update to 4.8.3. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.8.3. --- 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 2f2d649e4f..69795311a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14422,14 +14422,14 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.8.2") + (version "4.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4")))) + "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) From ebaf944cddd7a7fd5e9ba825a9c17dfda2cfe223 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:19 +0200 Subject: [PATCH 176/440] gnu: r-s4arrays: Update to 1.0.6. * gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.6. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69795311a7..e37ce4d424 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -19663,13 +19663,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c")))) + "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs From c8e7ea8a8be82ac9296e0bcea9b4b83c0a656179 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:20 +0200 Subject: [PATCH 177/440] gnu: r-rhdf5lib: Update to 1.22.1. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.22.1. --- 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 e37ce4d424..abf35d72fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -19927,14 +19927,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1j8i4rmq85n7jys86a9zyj1n4qn7bhc1sqgcq8dyh7zqfdvb9bcw")) + "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9")) (modules '((guix build utils))) (snippet '(begin From cf5cb0875b06b5823e9de8bbd01ddd8c0b0d15a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 08:57:20 +0200 Subject: [PATCH 178/440] gnu: r-delayedmatrixstats: Update to 1.22.6. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.6. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index abf35d72fb..8e13044b1a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -20550,14 +20550,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.22.5") + (version "1.22.6") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1bzbsfds5zki6iazj53y6kps8bvn7zdysbmpf9359sv6zshk18fv")))) + "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) From 180502f28fbed79228549738fd550894dbdc2dc7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:08:54 +0300 Subject: [PATCH 179/440] gnu: debootstrap: Update to 1.0.132. * gnu/packages/debian.scm (debootstrap): Update to 1.0.132. --- gnu/packages/debian.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index ef3c5f1f2c..78cdd0d3f4 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -190,7 +190,7 @@ contains the archive keys used for that.") (define-public debootstrap (package (name "debootstrap") - (version "1.0.128") + (version "1.0.132") (source (origin (method git-fetch) @@ -199,7 +199,7 @@ contains the archive keys used for that.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0hc7xc6qvnmjlpf3j6bm25kf0j1ifvv5j7a0iljfmbag4idxc9jv")))) + (base32 "1l6mc3i2wqfhmhj85x9qiiqchqp9br6gg54hv1xs08h8xndmfchf")))) (build-system gnu-build-system) (arguments (list From 6226b8f72d87583322b075d4c51f253f9b13bc07 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:12:28 +0300 Subject: [PATCH 180/440] gnu: debootstrap: Hardcode location of archive keyrings. * gnu/packages/debian.scm (debootstrap)[arguments]: Adjust custom 'patch-source phase to hardcode the location of the archive keyrings. --- gnu/packages/debian.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index 78cdd0d3f4..f011802ed3 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -226,6 +226,12 @@ contains the archive keys used for that.") (substitute* "debootstrap" (("=/usr") (string-append "=" #$output)) (("/usr/bin/dpkg") (search-input-file inputs "/bin/dpkg"))) + ;; Include the keyring locations by default. + (substitute* (find-files "scripts") + (("keyring.*(debian-archive-keyring.gpg)"_ keyring) + (string-append "keyring " debian "/share/keyrings/" keyring)) + (("keyring.*(ubuntu-archive-keyring.gpg)" _ keyring) + (string-append "keyring " ubuntu "/share/keyrings/" keyring))) ;; Ensure PATH works both in guix and within the debian chroot ;; workaround for: https://bugs.debian.org/929889 (substitute* "functions" From 0ce57ea4a17139038c79a00057635e89103c76f6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 11:31:41 +0300 Subject: [PATCH 181/440] gnu: dpkg: Update to 1.22.0. * gnu/packages/debian.scm (dpkg): Update to 1.22.0. [arguments]: Wrap another script in the custom 'wrap-scripts phase. --- gnu/packages/debian.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index f011802ed3..6e40096199 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -341,7 +341,7 @@ distributions such as Debian and Trisquel.") (define-public dpkg (package (name "dpkg") - (version "1.21.22") + (version "1.22.0") (source (origin (method git-fetch) @@ -350,7 +350,7 @@ distributions such as Debian and Trisquel.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0b5czgif5g6pdjzcw60hzzj0i1llxvajf3nlx115axmpa3y4iynd")))) + (base32 "1p7f2mgrn2iy0xfysxfq4pjbbhbhb2rp649bsik0x25jrck4if83")))) (build-system gnu-build-system) (arguments (list #:modules @@ -388,6 +388,7 @@ distributions such as Debian and Trisquel.") `("PATH" ":" prefix (,(string-append #$output "/bin"))))) (list "dpkg-architecture" + "dpkg-buildapi" "dpkg-buildflags" "dpkg-buildpackage" "dpkg-checkbuilddeps" From c36d4760c6a32864c10809b996e1c093928a3653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 11:16:29 +0200 Subject: [PATCH 182/440] gnu: perl-cworld-dekker: Drop labels from inputs. * gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use G-expression and avoid references to labeled inputs. [inputs]: Drop labels. --- gnu/packages/bioinformatics.scm | 134 ++++++++++++++++---------------- 1 file changed, 67 insertions(+), 67 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa88692204..c78f017a24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19246,77 +19246,77 @@ large-scale data-analysis.") "1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych")))) (build-system perl-build-system) (arguments - `(#:modules ((guix build perl-build-system) + (list + #:modules '((guix build perl-build-system) (guix build utils) (srfi srfi-26)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'hardcode-references - (lambda* (#:key inputs #:allow-other-keys) - (let ((bedtools (assoc-ref inputs "bedtools")) - (r (assoc-ref inputs "r-minimal"))) - (substitute* '("scripts/python/getEigenVectors.py" - "scripts/python/matrix2EigenVectors.py") - (("bedtools intersect") - (string-append bedtools "/bin/bedtools intersect"))) - (substitute* "lib/cworld/dekker.pm" - (("bedtools --version") - (string-append bedtools "/bin/bedtools --version"))) - (substitute* '("scripts/perl/correlateMatrices.pl" - "scripts/perl/matrix2scaling.pl" - "scripts/perl/matrix2distance.pl" - "scripts/perl/coverageCorrect.pl" - "scripts/perl/matrix2anchorPlot.pl" - "scripts/python/matrix2EigenVectors.py" - "scripts/python/matrix2insulation-lite.py" - "scripts/perl/matrix2compartment.pl" - "scripts/perl/anchorPurge.pl" - "scripts/perl/applyCorrection.pl" - "scripts/perl/compareInsulation.pl" - "scripts/perl/fillMissingData.pl" - "scripts/perl/matrix2loess.pl" - "scripts/python/getEigenVectors.py" - "scripts/perl/aggregateBED.pl" - "scripts/perl/collapseMatrix.pl" - "scripts/perl/matrix2direction.pl" - "scripts/perl/singletonRemoval.pl" - "lib/cworld/dekker.pm" - "scripts/perl/matrix2insulation.pl") - (("(`|\")Rscript" _ pre) - (string-append pre r "/bin/Rscript")))))) - (add-after 'install 'install-scripts - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share/cworld-dekker"))) - (mkdir-p share) - (copy-recursively "scripts" share) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'hardcode-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bedtools #$(this-package-input "bedtools")) + (r #$(this-package-input "r-minimal"))) + (substitute* '("scripts/python/getEigenVectors.py" + "scripts/python/matrix2EigenVectors.py") + (("bedtools intersect") + (string-append bedtools "/bin/bedtools intersect"))) + (substitute* "lib/cworld/dekker.pm" + (("bedtools --version") + (string-append bedtools "/bin/bedtools --version"))) + (substitute* '("scripts/perl/correlateMatrices.pl" + "scripts/perl/matrix2scaling.pl" + "scripts/perl/matrix2distance.pl" + "scripts/perl/coverageCorrect.pl" + "scripts/perl/matrix2anchorPlot.pl" + "scripts/python/matrix2EigenVectors.py" + "scripts/python/matrix2insulation-lite.py" + "scripts/perl/matrix2compartment.pl" + "scripts/perl/anchorPurge.pl" + "scripts/perl/applyCorrection.pl" + "scripts/perl/compareInsulation.pl" + "scripts/perl/fillMissingData.pl" + "scripts/perl/matrix2loess.pl" + "scripts/python/getEigenVectors.py" + "scripts/perl/aggregateBED.pl" + "scripts/perl/collapseMatrix.pl" + "scripts/perl/matrix2direction.pl" + "scripts/perl/singletonRemoval.pl" + "lib/cworld/dekker.pm" + "scripts/perl/matrix2insulation.pl") + (("(`|\")Rscript" _ pre) + (string-append pre r "/bin/Rscript")))))) + (add-after 'install 'install-scripts + (lambda _ + (let ((share (string-append #$output "/share/cworld-dekker"))) + (mkdir-p share) + (copy-recursively "scripts" share) - ;; Make all scripts executable and wrap them. - (let ((r (find-files share "\\.R$")) - (py (find-files share "\\.py$")) - (pl (find-files share "\\.pl$")) - (wrap (lambda* (script var #:optional (extra "")) - (let ((path (string-append (getenv var) - extra))) - (wrap-program script - `(,var ":" prefix (,path))))))) - (for-each (cut chmod <> #o555) (append r py pl)) - (for-each (cut wrap <> "PERL5LIB" - (string-append ":" out - "/lib/perl5/site_perl")) - pl) - (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) + ;; Make all scripts executable and wrap them. + (let ((r (find-files share "\\.R$")) + (py (find-files share "\\.py$")) + (pl (find-files share "\\.pl$")) + (wrap (lambda* (script var #:optional (extra "")) + (let ((path (string-append (getenv var) + extra))) + (wrap-program script + `(,var ":" prefix (,path))))))) + (for-each (cut chmod <> #o555) (append r py pl)) + (for-each (cut wrap <> "PERL5LIB" + (string-append ":" #$output + "/lib/perl5/site_perl")) + pl) + (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) (inputs - `(("libgd" ,gd) - ("perl-gd" ,perl-gd) - ("bedtools" ,bedtools) - ("python" ,python-wrapper) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-h5py" ,python-h5py) - ("python-scikit-learn" ,python-scikit-learn) - ("r-minimal" ,r-minimal))) + (list gd + perl-gd + bedtools + python-wrapper + python-scipy + python-numpy + python-matplotlib + python-h5py + python-scikit-learn + r-minimal)) (native-inputs (list perl-module-build)) (home-page "https://github.com/dekkerlab/cworld-dekker") From e5f7c14ef6c951f02ca710fad1869db3aedff4b5 Mon Sep 17 00:00:00 2001 From: c4droid Date: Thu, 14 Sep 2023 17:29:26 +0800 Subject: [PATCH 183/440] gnu: python-requests_ntlm: Update to 1.2.0. * gnu/packages/python-web.scm (python-requests_ntlm): Update to 1.2.0. Signed-off-by: Efraim Flashner --- gnu/packages/python-web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 93fd2d2278..12f0ce6208 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3215,17 +3215,17 @@ HTTP via a UNIX domain socket.") (define-public python-requests_ntlm (package (name "python-requests_ntlm") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (pypi-uri "requests_ntlm" version)) (sha256 (base32 - "0wgbqzaq9w7bas16b7brdb75f91bh3275fb459093bk1ihpck2ci")))) + "1a0np7lk8ma1plv1s4aw5q9h2z3aljprkl9qsfypqcaf0zsqbhik")))) (build-system python-build-system) (propagated-inputs - (list python-cryptography python-ntlm-auth python-requests)) + (list python-cryptography python-pyspnego python-requests)) (home-page "https://github.com/requests/requests-ntlm") (synopsis "NTLM authentication support for Requests") From 2643fa3513ef93fc98a1bbf368f456b163fcf191 Mon Sep 17 00:00:00 2001 From: Kjartan Oli Agustsson Date: Wed, 23 Aug 2023 22:35:11 +0000 Subject: [PATCH 184/440] home: services: redshift: Use redshift package specified in configuration MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/home/services/desktop.scm (redshift-shepherd-service): Use the redshift package specified by config. Signed-off-by: Ludovic Courtès --- gnu/home/services/desktop.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/home/services/desktop.scm b/gnu/home/services/desktop.scm index 626918fd9e..c4da116100 100644 --- a/gnu/home/services/desktop.scm +++ b/gnu/home/services/desktop.scm @@ -172,7 +172,7 @@ format.")) ;; FIXME: This fails to start if Home is first activated from a ;; non-X11 session. (start #~(make-forkexec-constructor - (list #$(file-append redshift "/bin/redshift") + (list #$(file-append (home-redshift-configuration-redshift config) "/bin/redshift") "-c" #$config-file))) (stop #~(make-kill-destructor)) (actions (list (shepherd-configuration-action config-file)))))) From e645a53d87be1132bb7f8c3c0afc5967e061fb94 Mon Sep 17 00:00:00 2001 From: Ramin Honary Date: Thu, 24 Aug 2023 17:57:51 +0900 Subject: [PATCH 185/440] gnu: Add stklos. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/scheme.scm (stklos): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/scheme.scm | 45 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 43 insertions(+), 2 deletions(-) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 44e0130573..ad06d7db06 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -42,8 +42,8 @@ (define-module (gnu packages scheme) #:use-module (gnu packages) #:use-module ((guix licenses) - #:select (gpl2+ lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3+ asl2.0 bsd-3 - cc-by-sa4.0 non-copyleft expat public-domain)) + #:select (gpl2 gpl2+ lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3+ asl2.0 + bsd-3 cc-by-sa4.0 non-copyleft expat public-domain)) #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) @@ -1235,3 +1235,44 @@ time compilation and compiled macros.") (description "Gerbil mode provides font-lock, indentation, navigation, and REPL for Gerbil code within Emacs."))) + +(define-public stklos + (package + (name "stklos") + (version "1.70") + (source (origin + (method url-fetch) + ;; TODO: Unbundle pcre, libgc, and libffi. + (uri (string-append "https://stklos.net/download/stklos-" + version ".tar.gz")) + (sha256 + (base32 + "1iw3pgycjz3kz3jd1855v2ngf8ib2almpf8v058n1mkj1qd2b88m")))) + (build-system gnu-build-system) + (arguments + (list + #:modules `((ice-9 ftw) + ,@%gnu-build-system-modules) + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'patch-sh-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash (which "bash"))) + (substitute* "configure" + (("/bin/sh") bash))))) + (add-after 'configure 'patch-rm-references + (lambda _ + (let ((rm (which "rm"))) + (substitute* (find-files "." "^Makefile$") + (("/bin/rm") rm)))))))) + (properties + '((release-monitoring-url . "https://stklos.net/download.html"))) + (home-page "https://stklos.net") + (synopsis "R7RS Scheme with CLOS-like object system") + (description + "STklos is a free Scheme system mostly compliant with the languages +features defined in R7RS small. The aim of this implementation is to be fast +as well as light. The implementation is based on an ad-hoc Virtual +Machine. STklos can also be compiled as a library and embedded in an +application.") + (license gpl2+))) From 08e8c3483fa16b4fc9b1fbd92f52bbc778f65249 Mon Sep 17 00:00:00 2001 From: Timotej Lazar Date: Fri, 25 Aug 2023 14:31:23 +0200 Subject: [PATCH 186/440] gnu: syncthing: Update to 1.23.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The uraggregate binary was merged into ursrv, so don’t attempt to install it. * gnu/packages/syncthing.scm (syncthing): Update to 1.23.7. [arguments]: Build with go-1.20. Signed-off-by: Ludovic Courtès --- gnu/packages/syncthing.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 414395251b..fd30360006 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -46,7 +46,7 @@ (define-public syncthing (package (name "syncthing") - (version "1.23.6") + (version "1.23.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/syncthing/syncthing" @@ -54,7 +54,7 @@ "/syncthing-source-v" version ".tar.gz")) (sha256 (base32 - "03myinspq61aiis29mq0xjigj5rh5jd8m0d9xakf43vi7pqgwjbc")))) + "1891dqcsg5r034bw19qjm6qg0zi1g0djcllp2c550zq7v1sdvn0q")))) (build-system go-build-system) ;; The primary Syncthing executable goes to "out", while the auxiliary ;; server programs and utility tools go to "utils". This reduces the size @@ -64,7 +64,7 @@ (list #:modules '((srfi srfi-26) ; for cut (guix build utils) (guix build go-build-system)) - #:go go-1.19 + #:go go-1.20 #:import-path "github.com/syncthing/syncthing" ;; We don't need to install the source code for end-user applications. #:install-source? #f @@ -101,7 +101,7 @@ "stdisco" "stdiscosrv" "stevents" "stfileinfo" "stfinddevice" "stfindignored" "stgenfiles" "strelaypoolsrv" "strelaysrv" "stsigtool" - "stvanity" "stwatchfile" "uraggregate" "ursrv"))))) + "stvanity" "stwatchfile" "ursrv"))))) (add-after 'install 'install-docs (lambda _ From de64e412f3684d54bd2a485920cd3287a551f793 Mon Sep 17 00:00:00 2001 From: fanquake Date: Thu, 24 Aug 2023 09:47:33 +0100 Subject: [PATCH 187/440] gnu: tor: Update to 0.4.8.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/tor.scm (tor): Update to 0.4.8.5. * gnu/packages/tor.scm (tor)[arguments]<#:configure-flags>: Add "--enable-gpl". * gnu/packages/patches/tor-remove-defensive-assert.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/tor.scm (tor)[source]: Add patch to remove defensive assert. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + .../patches/tor-remove-defensive-assert.patch | 28 +++++++++++++++++++ gnu/packages/tor.scm | 8 ++++-- 3 files changed, 34 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/tor-remove-defensive-assert.patch diff --git a/gnu/local.mk b/gnu/local.mk index 924d497057..8dd363dd79 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -2018,6 +2018,7 @@ dist_patch_DATA = \ %D%/packages/patches/tofi-32bit-compat.patch \ %D%/packages/patches/tootle-glib-object-naming.patch \ %D%/packages/patches/tootle-reason-phrase.patch \ + %D%/packages/patches/tor-remove-defensive-assert.patch \ %D%/packages/patches/transcode-ffmpeg.patch \ %D%/packages/patches/transfig-gcc10-fno-common.patch \ %D%/packages/patches/trytond-add-egg-modules-to-path.patch \ diff --git a/gnu/packages/patches/tor-remove-defensive-assert.patch b/gnu/packages/patches/tor-remove-defensive-assert.patch new file mode 100644 index 0000000000..7207ec867a --- /dev/null +++ b/gnu/packages/patches/tor-remove-defensive-assert.patch @@ -0,0 +1,28 @@ +This patch removes a call to `tor_assert_nonfatal_unreached()` in +`relay_key_is_unavailable_()` that is only called when Tor is compiled +without relay support. + +Unfortunately, the non-fatal assertion causes a BUG log +message to appear for clients when they start up without relay support +for each CPU worker we spawn. This makes it spotting issues during +bootstrap harder particularly for our iOS developers. + +Since the call sites to `get_master_identity_key()` handles `NULL` +values already, we do not think this will be an issue later on. + +Reported by Benjamin Erhart (@tla) from Guardian Project. + +Fixes tpo/core/tor#40848. + +diff --git a/src/feature/relay/routerkeys.h b/src/feature/relay/routerkeys.h +index 7b6d80773c..b97615a9c9 100644 +--- a/src/feature/relay/routerkeys.h ++++ b/src/feature/relay/routerkeys.h +@@ -53,7 +53,6 @@ void routerkeys_free_all(void); + static inline void * + relay_key_is_unavailable_(void) + { +- tor_assert_nonfatal_unreached(); + return NULL; + } + #define relay_key_is_unavailable(type) \ diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 7fec88656f..44e62b63cc 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -63,18 +63,20 @@ (define-public tor (package (name "tor") - (version "0.4.7.14") + (version "0.4.8.5") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "1y2xwrji1rvk6h0k15705yra5s74h72h2g84x02zr0338vv6gb55")))) + "06g1awb4piqvgxa97pyswxgjzkpj8rx3iy2jbiaygvi99b8wymv9")) + (patches (search-patches "tor-remove-defensive-assert.patch")))) (build-system gnu-build-system) (arguments (list #:configure-flags - #~(list "--enable-lzma" + #~(list "--enable-gpl" + "--enable-lzma" "--enable-zstd") #:phases #~(modify-phases %standard-phases From 6c72db7314b6c355a2bd956da840e9a07a5b1929 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Sat, 9 Sep 2023 17:26:00 +0800 Subject: [PATCH 188/440] gnu: neofetch: Fix cross-compiling. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/admin.scm (neofetch): Fix cross-compiling. [arguments]: Use Gexp. Signed-off-by: Ludovic Courtès --- gnu/packages/admin.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 2492890ee5..98ed3d4e61 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -36,7 +36,7 @@ ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Morgan Smith ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer -;;; Copyright © 2021 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2021, 2023 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2021 Stefan Reichör ;;; Copyright © 2021 qblade ;;; Copyright © 2021 Hyunseok Kim @@ -4008,12 +4008,12 @@ Intel DRM Driver.") "0i7wpisipwzk0j62pzaigbiq42y1mn4sbraz4my2jlz6ahwf00kv")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; there are no tests - #:make-flags - (list (string-append "PREFIX=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) ; no configure script + (list #:tests? #f ; there are no tests + #:make-flags + #~(list (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) ; no configure script (home-page "https://github.com/dylanaraps/neofetch") (synopsis "System information script") (description "Neofetch is a command-line system information tool written in From 9aeb9e7cc83d5d0e1aed7b34fb5a357645fd86a9 Mon Sep 17 00:00:00 2001 From: Skyler Date: Thu, 7 Sep 2023 02:01:51 +0000 Subject: [PATCH 189/440] gnu: rottlog: Add gawk as an input. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This avoids an issue where rottlog will delete the entire /tmp directory if gawk is not installed. See . * gnu/packages/admin.scm (rottlog): Add gawk input, also update the patch-paths build phase for awk invocations. Signed-off-by: Ludovic Courtès --- gnu/packages/admin.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 98ed3d4e61..1b2324bfc7 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1978,7 +1978,11 @@ at once based on a Perl regular expression.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "rc/rc" (("/usr/sbin/sendmail") - (search-input-file inputs "/bin/mail"))))) + (search-input-file inputs "/bin/mail"))) + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "src/rottlog" + (("awk") + (search-input-file inputs "/bin/awk")))))) (add-after 'build 'set-packdir (lambda _ ;; Set a default location for archived logs. @@ -1997,7 +2001,7 @@ at once based on a Perl regular expression.") (lambda _ (invoke "make" "install-info")))))) (native-inputs (list autoconf automake texinfo util-linux)) ; for 'cal' - (inputs (list coreutils mailutils)) + (inputs (list coreutils gawk mailutils)) (home-page "https://www.gnu.org/software/rottlog/") (synopsis "Log rotation and management") (description From 40a76a7750586c05b85619a8a6e69610005edbc8 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 17:46:48 +0800 Subject: [PATCH 190/440] gnu: npiet: Fix cross-compilation. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/piet.scm (npiet)[arguments]<#:phases>: Use SEARCH-INPUT-FILE replace WHICH. Signed-off-by: Ludovic Courtès --- gnu/packages/piet.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/piet.scm b/gnu/packages/piet.scm index 824efe59de..8e5a313e82 100644 --- a/gnu/packages/piet.scm +++ b/gnu/packages/piet.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Jesse Gibbons ;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,10 +47,12 @@ `(#:phases (modify-phases %standard-phases (add-after 'install 'wrap-binaries - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (wrap-program (string-append out "/bin/npietedit") - `("PATH" ":" prefix (,(dirname (which "wish"))))) + `("PATH" ":" prefix + (,(dirname + (search-input-file inputs "bin/wish"))))) #t)))))) (inputs (list gd giflib libpng tk)) From 62e138706507bab7e342c2b75fcaaa92f9440597 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 17:46:49 +0800 Subject: [PATCH 191/440] gnu: npiet: Use gexps. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/piet.scm (npiet): Use Gexp. [arguments]: Use Gexp and remove tail #t. Signed-off-by: Ludovic Courtès --- gnu/packages/piet.scm | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/gnu/packages/piet.scm b/gnu/packages/piet.scm index 8e5a313e82..0b16299482 100644 --- a/gnu/packages/piet.scm +++ b/gnu/packages/piet.scm @@ -21,6 +21,7 @@ (define-module (gnu packages piet) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix build-system gnu) @@ -44,16 +45,17 @@ "0nl59fhdqqr7nslxdirdn8nvlq5wws67c7jyx2ckbmxbc9h8bv9d")))) (build-system gnu-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'wrap-binaries - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/npietedit") - `("PATH" ":" prefix - (,(dirname - (search-input-file inputs "bin/wish"))))) - #t)))))) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'install 'wrap-binaries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out + "/bin/npietedit") + `("PATH" ":" prefix + (,(dirname + (search-input-file + inputs "bin/wish"))))))))))) (inputs (list gd giflib libpng tk)) (native-inputs (list groff)) From 6d12c16299c1654a909c69d52bcb99b02cca0962 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 14 Sep 2023 17:18:09 +0200 Subject: [PATCH 192/440] =?UTF-8?q?doc:=20Make=20=E2=80=9Ccrash=20course?= =?UTF-8?q?=E2=80=9D=20xref=20more=20visible.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * doc/guix.texi (Using the Configuration System): Move the “Do not panic” note right after the first example. Clarify wording. --- doc/guix.texi | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 339dcb2a41..7e42a7151c 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -16834,24 +16834,37 @@ instance to support new system services. The operating system is configured by providing an @code{operating-system} declaration in a file that can then be passed to the @command{guix system} command (@pxref{Invoking guix system}). A -simple setup, with the default system services, the default Linux-Libre -kernel, initial RAM disk, and boot loader looks like this: +simple setup, with the default Linux-Libre +kernel, initial RAM disk, and a couple of system services added to those +provided by default looks like this: @findex operating-system @lisp @include os-config-bare-bones.texi @end lisp -This example should be self-describing. Some of the fields defined +The configuration is declarative and hopefully mostly self-describing. +It is actually code in the Scheme programming language; the whole +@code{(operating-system @dots{})} expression produces a @dfn{record} +with a number of @dfn{fields}. +Some of the fields defined above, such as @code{host-name} and @code{bootloader}, are mandatory. Others, such as @code{packages} and @code{services}, can be omitted, in -which case they get a default value. +which case they get a default value. @xref{operating-system Reference}, +for details about all the available fields. -Below we discuss the effect of some of the most important fields -(@pxref{operating-system Reference}, for details about all the available -fields), and how to @dfn{instantiate} the operating system using +Below we discuss the effect of some of the most important fields, +and how to @dfn{instantiate} the operating system using @command{guix system}. +@quotation Do not panic +@cindex Scheme programming language, getting started +Intimidated by the Scheme language or curious about it? The Cookbook +has a short section to get started that explains the fundamentals, which +you will find helpful when hacking your configuration. @xref{A Scheme +Crash Course,,, guix-cookbook, GNU Guix Cookbook}. +@end quotation + @unnumberedsubsec Bootloader @cindex legacy boot, on Intel machines @@ -17025,14 +17038,6 @@ Alternatively, the @code{modify-services} macro can be used: (delete avahi-service-type)) @end lisp -@quotation Do not panic -@cindex Scheme programming language, getting started -Intimidated by the Scheme language or curious about it? The Cookbook -has a short section to get started that explains the fundamentals, which -you will find helpful when hacking your configuration. @xref{A Scheme -Crash Course,,, guix-cookbook, GNU Guix Cookbook}. -@end quotation - @unnumberedsubsec Instantiating the System Assuming the @code{operating-system} declaration From 55da0930e30e0ee1b3da1b9aee5851e9ccfca32c Mon Sep 17 00:00:00 2001 From: Lars Bilke Date: Thu, 7 Sep 2023 15:06:03 +0200 Subject: [PATCH 193/440] gnu: openmpi: Enable PMIx. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/mpi.scm (openmpi)[arguments]: Pass “--with-pmix=internal”. Signed-off-by: Ludovic Courtès --- gnu/packages/mpi.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index 4d2458344f..baf6ce11e0 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -247,6 +247,12 @@ bind processes, and much more.") "--enable-openib-rdmacm" "--enable-openib-rdmacm-ibaddr" + ;; Enable support for the 'Process Management + ;; Interface for Exascale' (PMIx) used e.g. by + ;; Slurm for the management communication and + ;; coordination of MPI processes. + "--with-pmix=internal" + ;; Enable support for SLURM's Process Manager ;; Interface (PMI). ,(string-append "--with-pmi=" From 258729b928e14f0349a109d0a9a1d56a8e68e139 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:25:53 +0800 Subject: [PATCH 194/440] gnu: makefile2graph: fix cross-compile. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (makefile2graph): fix cross-compile. [arguments]: Use gexp and CC-FOR-TARGET. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 1c21ad475b..4335c57150 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2021 lu hui ;;; Copyright © 2021, 2022 Foo Chuan Wei ;;; Copyright © 2022 Michael Rohleder +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -773,11 +774,13 @@ produce colored output.") (base32 "1gjfk3d8qg3cla7qd2y7r9s03whlfwy83q8k76xfcnqrjjfavdgk")))) (build-system gnu-build-system) (arguments - '(#:test-target "test" - #:make-flags (list "CC=gcc" (string-append "prefix=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure)))) + (list + #:test-target "test" + #:make-flags #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "prefix=" #$output)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure)))) (native-inputs (list graphviz)) (home-page "https://github.com/lindenb/makefile2graph") From ca5fae4f26f2f35412a96fe2042883341ca62182 Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:51:08 +0800 Subject: [PATCH 195/440] gnu: uncrustify: Update to 0.77.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (uncrustify): Update to 0.77.1. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 4335c57150..a9e94dab25 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -794,7 +794,7 @@ independent targets.") (define-public uncrustify (package (name "uncrustify") - (version "0.75.1") + (version "0.77.1") (source (origin (method git-fetch) (uri (git-reference @@ -803,7 +803,7 @@ independent targets.") (file-name (git-file-name name version)) (sha256 (base32 - "1mzzzd4alajjdshbjd2a5mddqcpag8yyss72n09mfpialzyf7g60")))) + "17x9p5pqgzjchi9xhskp4kq7ag4chmsgbkvwym5m2b9zwm6qykpm")))) (build-system cmake-build-system) (native-inputs `(("python" ,python-wrapper))) From c0bfa12666cc6dc706981c76b9ee5c7f9006932d Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 18:51:09 +0800 Subject: [PATCH 196/440] gnu: uncrustify: use new style and gexp. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/code.scm (uncrustify): use new style and gexp. [native-inputs]: remove label. [arguments]: use gexp and remove tail #t. Signed-off-by: Ludovic Courtès --- gnu/packages/code.scm | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index a9e94dab25..b716f32599 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -805,20 +805,18 @@ independent targets.") (base32 "17x9p5pqgzjchi9xhskp4kq7ag4chmsgbkvwym5m2b9zwm6qykpm")))) (build-system cmake-build-system) - (native-inputs - `(("python" ,python-wrapper))) + (native-inputs (list python-wrapper)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-etc - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Configuration samples are not installed by default. - (let* ((output (assoc-ref outputs "out")) - (etcdir (string-append output "/etc"))) - (for-each (lambda (l) - (install-file l etcdir)) - (find-files "etc" "\\.cfg$"))) - #t))))) + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-etc + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Configuration samples are not installed by default. + (let* ((output (assoc-ref outputs "out")) + (etcdir (string-append output "/etc"))) + (for-each (lambda (l) + (install-file l etcdir)) + (find-files "etc" "\\.cfg$")))))))) (home-page "https://uncrustify.sourceforge.net/") (synopsis "Code formatter for C and other related languages") (description From 50725212f0578b98ad4bac9786ca954ae22125cc Mon Sep 17 00:00:00 2001 From: Sughosha Date: Fri, 16 Jun 2023 14:44:00 +0000 Subject: [PATCH 197/440] gnu: dpf-plugins: Update to 1.7. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Message-Id: <23da89c3cbf2358ac70d387ebd714abe03b6758e.1686926462.git.sughosha@proton.me> From: Sughosha Date: Fri, 16 Jun 2023 16:22:57 +0200 Subject: [PATCH 1/2] gnu: dpf-plugins: Update to 1.7. * gnu/packages/music.scm (dpf-plugins): Update to 1.7. Signed-off-by: Ludovic Courtès --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index cf74a2cd36..3f17a054ca 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -6517,7 +6517,7 @@ curl/include/curl/curl.h") (define-public dpf-plugins (package (name "dpf-plugins") - (version "1.4") + (version "1.7") (source (origin (method git-fetch) @@ -6527,7 +6527,7 @@ curl/include/curl/curl.h") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0y7qvpfm34g6f7d786c6c9043dlbg5c4h71l2s24dsc9m8i7x2ww")))) + (base32 "082f3f78x6k58j78mqr57qhw40f5s8fmcbkhl36nn3vbcsa07bzg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target From 0a6ad454a3ec01e402403f500bb90fe55fc232b7 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sat, 8 Jul 2023 11:50:16 +0300 Subject: [PATCH 198/440] gnu: nanosvg: Add a patch for PrusaSlicer 2.6. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/graphics.scm (nanosvg): Add a patch that is required to build PrusaSlicer 2.6. * gnu/packages/patches/nanosvg-prusa-slicer.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/graphics.scm | 8 +- .../patches/nanosvg-prusa-slicer.patch | 248 ++++++++++++++++++ 3 files changed, 256 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/nanosvg-prusa-slicer.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8dd363dd79..0d6e6846ee 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1636,6 +1636,7 @@ dist_patch_DATA = \ %D%/packages/patches/mutter-fix-inverted-test.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/m17n-lib-1.8.0-use-pkg-config-for-freetype.patch \ + %D%/packages/patches/nanosvg-prusa-slicer.patch \ %D%/packages/patches/nautilus-extension-search-path.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ %D%/packages/patches/ncftp-reproducible.patch \ diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 8edc93f702..9362666274 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -36,6 +36,7 @@ ;;; Copyright © 2023 Sharlatan Hellseher ;;; Copyright © 2023 David Thompson ;;; Copyright © 2023 Eric Bavier +;;; Copyright © 2023 Artyom V. Poptsov ;;; ;;; This file is part of GNU Guix. ;;; @@ -2643,7 +2644,12 @@ a tetrahedral mesh, isovalue discretization and Lagrangian movement; (file-name (git-file-name name version)) (sha256 (base32 - "1pkzv75kavkhrbdd2kvq755jyr0vamgrfr7lc33dq3ipkzmqvs2l")))) + "1pkzv75kavkhrbdd2kvq755jyr0vamgrfr7lc33dq3ipkzmqvs2l")) + ;; This patch required to build PrusaSlicer 2.6. + ;; + ;; It is taken from + ;; + (patches (search-patches "nanosvg-prusa-slicer.patch")))) (build-system cmake-build-system) (arguments (list #:tests? #f ;no test suite #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) diff --git a/gnu/packages/patches/nanosvg-prusa-slicer.patch b/gnu/packages/patches/nanosvg-prusa-slicer.patch new file mode 100644 index 0000000000..dc11e9365c --- /dev/null +++ b/gnu/packages/patches/nanosvg-prusa-slicer.patch @@ -0,0 +1,248 @@ +From abcd277ea45e9098bed752cf9c6875b533c0892f Mon Sep 17 00:00:00 2001 +From: AlbrechtS +Date: Sun, 4 Feb 2018 23:47:38 +0100 +Subject: [PATCH] Modify rasterizer to support non-square X,Y axes scaling. + +Add new function nsvgRasterizeXY() similar to nsvgRasterize() but with +separate scaling factors for x-axis and y-axis. +--- + src/nanosvgrast.h | 78 +++++++++++++++++++++++++++++++---------------- + 1 file changed, 51 insertions(+), 27 deletions(-) + +diff --git a/src/nanosvgrast.h b/src/nanosvgrast.h +index 17ba3b0..a83db27 100644 +--- a/src/nanosvgrast.h ++++ b/src/nanosvgrast.h +@@ -22,6 +22,12 @@ + * + */ + ++/* Modified by FLTK to support non-square X,Y axes scaling. ++ * ++ * Added: nsvgRasterizeXY() ++*/ ++ ++ + #ifndef NANOSVGRAST_H + #define NANOSVGRAST_H + +@@ -46,6 +52,9 @@ typedef struct NSVGrasterizer NSVGrasterizer; + unsigned char* img = malloc(w*h*4); + // Rasterize + nsvgRasterize(rast, image, 0,0,1, img, w, h, w*4); ++ ++ // For non-square X,Y scaling, use ++ nsvgRasterizeXY(rast, image, 0,0,1,1, img, w, h, w*4); + */ + + // Allocated rasterizer context. +@@ -55,7 +64,7 @@ NSVGrasterizer* nsvgCreateRasterizer(void); + // r - pointer to rasterizer context + // image - pointer to image to rasterize + // tx,ty - image offset (applied after scaling) +-// scale - image scale ++// scale - image scale (assumes square aspect ratio) + // dst - pointer to destination image data, 4 bytes per pixel (RGBA) + // w - width of the image to render + // h - height of the image to render +@@ -64,6 +73,12 @@ void nsvgRasterize(NSVGrasterizer* r, + NSVGimage* image, float tx, float ty, float scale, + unsigned char* dst, int w, int h, int stride); + ++// As above, but allow X and Y axes to scale independently for non-square aspects ++void nsvgRasterizeXY(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, ++ float sx, float sy, ++ unsigned char* dst, int w, int h, int stride); ++ + // Deletes rasterizer context. + void nsvgDeleteRasterizer(NSVGrasterizer*); + +@@ -370,7 +385,7 @@ static void nsvg__flattenCubicBez(NSVGrasterizer* r, + nsvg__flattenCubicBez(r, x1234,y1234, x234,y234, x34,y34, x4,y4, level+1, type); + } + +-static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float scale) ++static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float sx, float sy) + { + int i, j; + NSVGpath* path; +@@ -378,13 +393,13 @@ static void nsvg__flattenShape(NSVGrasterizer* r, NSVGshape* shape, float scale) + for (path = shape->paths; path != NULL; path = path->next) { + r->npoints = 0; + // Flatten path +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, 0); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, 0); + for (i = 0; i < path->npts-1; i += 3) { + float* p = &path->pts[i*2]; +- nsvg__flattenCubicBez(r, p[0]*scale,p[1]*scale, p[2]*scale,p[3]*scale, p[4]*scale,p[5]*scale, p[6]*scale,p[7]*scale, 0, 0); ++ nsvg__flattenCubicBez(r, p[0]*sx,p[1]*sy, p[2]*sx,p[3]*sy, p[4]*sx,p[5]*sy, p[6]*sx,p[7]*sy, 0, 0); + } + // Close path +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, 0); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, 0); + // Build edges + for (i = 0, j = r->npoints-1; i < r->npoints; j = i++) + nsvg__addEdge(r, r->points[j].x, r->points[j].y, r->points[i].x, r->points[i].y); +@@ -734,7 +749,7 @@ static void nsvg__prepareStroke(NSVGrasterizer* r, float miterLimit, int lineJoi + } + } + +-static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float scale) ++static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float sx, float sy) + { + int i, j, closed; + NSVGpath* path; +@@ -742,15 +757,16 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + float miterLimit = shape->miterLimit; + int lineJoin = shape->strokeLineJoin; + int lineCap = shape->strokeLineCap; +- float lineWidth = shape->strokeWidth * scale; ++ const float sw = (sx + sy) / 2; // average scaling factor ++ const float lineWidth = shape->strokeWidth * sw; // FIXME (?) + + for (path = shape->paths; path != NULL; path = path->next) { + // Flatten path + r->npoints = 0; +- nsvg__addPathPoint(r, path->pts[0]*scale, path->pts[1]*scale, NSVG_PT_CORNER); ++ nsvg__addPathPoint(r, path->pts[0]*sx, path->pts[1]*sy, NSVG_PT_CORNER); + for (i = 0; i < path->npts-1; i += 3) { + float* p = &path->pts[i*2]; +- nsvg__flattenCubicBez(r, p[0]*scale,p[1]*scale, p[2]*scale,p[3]*scale, p[4]*scale,p[5]*scale, p[6]*scale,p[7]*scale, 0, NSVG_PT_CORNER); ++ nsvg__flattenCubicBez(r, p[0]*sx,p[1]*sy, p[2]*sx,p[3]*sy, p[4]*sx,p[5]*sy, p[6]*sx,p[7]*sy, 0, NSVG_PT_CORNER); + } + if (r->npoints < 2) + continue; +@@ -796,7 +812,7 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + dashOffset -= shape->strokeDashArray[idash]; + idash = (idash + 1) % shape->strokeDashCount; + } +- dashLen = (shape->strokeDashArray[idash] - dashOffset) * scale; ++ dashLen = (shape->strokeDashArray[idash] - dashOffset) * sw; + + for (j = 1; j < r->npoints2; ) { + float dx = r->points2[j].x - cur.x; +@@ -818,7 +834,7 @@ static void nsvg__flattenShapeStroke(NSVGrasterizer* r, NSVGshape* shape, float + // Advance dash pattern + dashState = !dashState; + idash = (idash+1) % shape->strokeDashCount; +- dashLen = shape->strokeDashArray[idash] * scale; ++ dashLen = shape->strokeDashArray[idash] * sw; + // Restart + cur.x = x; + cur.y = y; +@@ -987,7 +1003,7 @@ static inline int nsvg__div255(int x) + } + + static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* cover, int x, int y, +- float tx, float ty, float scale, NSVGcachedPaint* cache) ++ float tx, float ty, float sx, float sy, NSVGcachedPaint* cache) + { + + if (cache->type == NSVG_PAINT_COLOR) { +@@ -1028,9 +1044,9 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + int i, cr, cg, cb, ca; + unsigned int c; + +- fx = ((float)x - tx) / scale; +- fy = ((float)y - ty) / scale; +- dx = 1.0f / scale; ++ fx = ((float)x - tx) / sx; ++ fy = ((float)y - ty) / sy; ++ dx = 1.0f / sx; + + for (i = 0; i < count; i++) { + int r,g,b,a,ia; +@@ -1073,9 +1089,9 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + int i, cr, cg, cb, ca; + unsigned int c; + +- fx = ((float)x - tx) / scale; +- fy = ((float)y - ty) / scale; +- dx = 1.0f / scale; ++ fx = ((float)x - tx) / sx; ++ fy = ((float)y - ty) / sy; ++ dx = 1.0f / sx; + + for (i = 0; i < count; i++) { + int r,g,b,a,ia; +@@ -1114,7 +1130,7 @@ static void nsvg__scanlineSolid(unsigned char* dst, int count, unsigned char* co + } + } + +-static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, float scale, NSVGcachedPaint* cache, char fillRule) ++static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, float sx, float sy, NSVGcachedPaint* cache, char fillRule) + { + NSVGactiveEdge *active = NULL; + int y, s; +@@ -1196,7 +1212,7 @@ static void nsvg__rasterizeSortedEdges(NSVGrasterizer *r, float tx, float ty, fl + if (xmin < 0) xmin = 0; + if (xmax > r->width-1) xmax = r->width-1; + if (xmin <= xmax) { +- nsvg__scanlineSolid(&r->bitmap[y * r->stride] + xmin*4, xmax-xmin+1, &r->scanline[xmin], xmin, y, tx,ty, scale, cache); ++ nsvg__scanlineSolid(&r->bitmap[y * r->stride] + xmin*4, xmax-xmin+1, &r->scanline[xmin], xmin, y, tx,ty, sx, sy, cache); + } + } + +@@ -1364,8 +1380,9 @@ static void dumpEdges(NSVGrasterizer* r, const char* name) + } + */ + +-void nsvgRasterize(NSVGrasterizer* r, +- NSVGimage* image, float tx, float ty, float scale, ++void nsvgRasterizeXY(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, ++ float sx, float sy, + unsigned char* dst, int w, int h, int stride) + { + NSVGshape *shape = NULL; +@@ -1396,7 +1413,7 @@ void nsvgRasterize(NSVGrasterizer* r, + r->freelist = NULL; + r->nedges = 0; + +- nsvg__flattenShape(r, shape, scale); ++ nsvg__flattenShape(r, shape, sx, sy); + + // Scale and translate edges + for (i = 0; i < r->nedges; i++) { +@@ -1414,14 +1431,14 @@ void nsvgRasterize(NSVGrasterizer* r, + // now, traverse the scanlines and find the intersections on each scanline, use non-zero rule + nsvg__initPaint(&cache, &shape->fill, shape->opacity); + +- nsvg__rasterizeSortedEdges(r, tx,ty,scale, &cache, shape->fillRule); ++ nsvg__rasterizeSortedEdges(r, tx,ty, sx, sy, &cache, shape->fillRule); + } +- if (shape->stroke.type != NSVG_PAINT_NONE && (shape->strokeWidth * scale) > 0.01f) { ++ if (shape->stroke.type != NSVG_PAINT_NONE && (shape->strokeWidth * sx) > 0.01f) { + nsvg__resetPool(r); + r->freelist = NULL; + r->nedges = 0; + +- nsvg__flattenShapeStroke(r, shape, scale); ++ nsvg__flattenShapeStroke(r, shape, sx, sy); + + // dumpEdges(r, "edge.svg"); + +@@ -1441,7 +1458,7 @@ void nsvgRasterize(NSVGrasterizer* r, + // now, traverse the scanlines and find the intersections on each scanline, use non-zero rule + nsvg__initPaint(&cache, &shape->stroke, shape->opacity); + +- nsvg__rasterizeSortedEdges(r, tx,ty,scale, &cache, NSVG_FILLRULE_NONZERO); ++ nsvg__rasterizeSortedEdges(r, tx,ty,sx, sy, &cache, NSVG_FILLRULE_NONZERO); + } + } + +@@ -1453,6 +1470,13 @@ void nsvgRasterize(NSVGrasterizer* r, + r->stride = 0; + } + ++void nsvgRasterize(NSVGrasterizer* r, ++ NSVGimage* image, float tx, float ty, float scale, ++ unsigned char* dst, int w, int h, int stride) ++{ ++ nsvgRasterizeXY(r,image, tx, ty, scale, scale, dst, w, h, stride); ++} ++ + #endif // NANOSVGRAST_IMPLEMENTATION + + #endif // NANOSVGRAST_H From a5d207f0db20933501712c037703cb7cb27adbbc Mon Sep 17 00:00:00 2001 From: Zheng Junjie Date: Wed, 6 Sep 2023 23:43:53 +0800 Subject: [PATCH 199/440] gnu: kwin: Unwrap executable name for desktop file search. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit see https://github.com/NixOS/nixpkgs/pull/116549 * gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/kde-plasma.scm (kwin)[origin]: Use it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/kde-plasma.scm | 1 + ...ecutable-name-for-dot-desktop-search.patch | 89 +++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0d6e6846ee..a94fce9248 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1479,6 +1479,7 @@ dist_patch_DATA = \ %D%/packages/patches/kobodeluxe-midicon-segmentation-fault.patch \ %D%/packages/patches/kobodeluxe-graphics-window-signed-char.patch \ %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch \ + %D%/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch\ %D%/packages/patches/kodi-mesa-eglchromium.patch \ %D%/packages/patches/laby-make-install.patch \ %D%/packages/patches/laby-use-tmpdir-from-runtime.patch \ diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 11586a6ce2..331ab28cd1 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -1210,6 +1210,7 @@ KDE Frameworks components.") (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) + (patches (search-patches "kwin-unwrap-executable-name-for-dot-desktop-search.patch")) (sha256 (base32 "0bssp76lzqqlan5pfg6wjf4z9c6pl6p66ri8p82vqqw406x5bzyb")))) diff --git a/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch b/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch new file mode 100644 index 0000000000..8f67553138 --- /dev/null +++ b/gnu/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch @@ -0,0 +1,89 @@ +origin patch from nixos. + +see https://github.com/NixOS/nixpkgs/blob/2457551a54ffbd93b7d8f84af8b8fb3aac5cbdd5/pkgs/desktops/plasma-5/kwin/0001-NixOS-Unwrap-executable-name-for-.desktop-search.patch + +--- + src/guix_utils.h | 41 +++++++++++++++++++++++++++++++++++++++++ + src/service_utils.h | 4 +++- + src/waylandwindow.cpp | 5 ++++- + 3 files changed, 48 insertions(+), 2 deletions(-) + create mode 100644 src/guix_utils.h + +diff a/src/guix_utils.h b/src/guix_utils.h +new file mode 100644 +index 0000000..726065d +--- /dev/null ++++ b/src/guix_utils.h +@@ -0,0 +1,24 @@ ++#ifndef GUIX_UTILS_H ++#define GUIX_UTILS_H ++ ++// kwin ++#include ++ ++namespace KWin ++{ ++ ++static QString unwrapExecutablePath(const QString &in_executablePath) ++{ ++ QString executablePath(in_executablePath); ++ ++ while (executablePath.endsWith("-real") && executablePath[executablePath.lastIndexOf("/")+1] == QChar('.')) { ++ executablePath.remove(executablePath.length() - 5, 5); ++ executablePath.remove(executablePath.lastIndexOf("/")+1, 1); ++ } ++ ++ return executablePath; ++} ++ ++}// namespace ++ ++#endif // GUIX_UTILS_H +diff a/src/utils/serviceutils.h b/src/utils/serviceutils.h +index 8a70c1f..475b15d 100644 +--- a/src/utils/serviceutils.h ++++ b/src/utils/serviceutils.h +@@ -19,6 +19,7 @@ + #include + //KF + #include ++#include "guix_utils.h" + + namespace KWin + { +@@ -26,8 +27,9 @@ namespace KWin + const static QString s_waylandInterfaceName = QStringLiteral("X-KDE-Wayland-Interfaces"); + const static QString s_dbusRestrictedInterfaceName = QStringLiteral("X-KDE-DBUS-Restricted-Interfaces"); + +-static QStringList fetchProcessServiceField(const QString &executablePath, const QString &fieldName) ++static QStringList fetchProcessServiceField(const QString &in_executablePath, const QString &fieldName) + { ++ const QString executablePath = unwrapExecutablePath(in_executablePath); + // needed to be able to use the logging category in a header static function + static QLoggingCategory KWIN_UTILS ("KWIN_UTILS", QtWarningMsg); + const auto servicesFound = KApplicationTrader::query([&executablePath] (const KService::Ptr &service) { +diff a/src/waylandwindow.cpp b/src/waylandwindow.cpp +index fd2c0c1..ae8cf96 100644 +--- a/src/waylandwindow.cpp ++++ b/src/waylandwindow.cpp +@@ -10,6 +10,7 @@ + #include "screens.h" + #include "wayland_server.h" + #include "workspace.h" ++#include "guix_utils.h" + + #include + #include +@@ -173,7 +174,9 @@ void WaylandWindow::updateIcon() + + void WaylandWindow::updateResourceName() + { +- const QFileInfo fileInfo(surface()->client()->executablePath()); ++ const QString in_path = surface()->client()->executablePath(); ++ const QString path = unwrapExecutablePath(in_path); ++ const QFileInfo fileInfo(path); + if (fileInfo.exists()) { + const QByteArray executableFileName = fileInfo.fileName().toUtf8(); + setResourceClass(executableFileName, executableFileName); +-- +2.32.0 \ No newline at end of file From f59a1dc924f6cfd3bddb3dae2e56ffb585097b4e Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Wed, 6 Sep 2023 14:38:56 -0400 Subject: [PATCH 200/440] gnu: armagetronad: Update to 0.2.9.1.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (armagetronad): Update to 0.2.9.1.1. [inputs]: Add sdl-mixer to fix game audio. Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 78063fa625..1167443825 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -491,27 +491,25 @@ Doom clone shooter game.") (define-public armagetronad (package (name "armagetronad") - (version "0.2.9.1.0") + (version "0.2.9.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/armagetronad/stable/" version "/armagetronad-" version ".tbz")) (sha256 (base32 - "18gn4sg4j5sw38ngb90sl50raliplrsgjcvy8fjwry733k0cgdjr")))) + "0cpxvzbssyf45fmanp1d6l992wln8zkjx4z2flgx27fg1rqdw5zn")))) (build-system gnu-build-system) - (native-inputs - (list pkg-config)) - (inputs - (list libxml2 - sdl - sdl-image - freeglut - libpng - libjpeg-turbo)) + (native-inputs (list pkg-config)) + (inputs (list libxml2 + (sdl-union (list sdl sdl-image sdl-mixer)) + freeglut + libpng + libjpeg-turbo)) (home-page "https://www.armagetronad.org") (synopsis "Tron clone in 3D") - (description "Armagetron Advanced is a multiplayer game in 3d that + (description + "Armagetron Advanced is a multiplayer game in 3d that attempts to emulate and expand on the lightcycle sequence from the movie Tron. It's an old school arcade game slung into the 21st century. Highlights include a customizable playing arena, HUD, unique graphics, and AI bots. For From c057507a0bac3ee5885a4ef055c9fea44683a1c3 Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Wed, 6 Sep 2023 20:56:20 -0700 Subject: [PATCH 201/440] gnu: icewm: Update to 3.4.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/wm.scm (icewm): Update to 3.4.1 Signed-off-by: Ludovic Courtès --- gnu/packages/wm.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index aaff618248..9ef60ec668 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -789,7 +789,7 @@ desktop environment.") (define-public icewm (package (name "icewm") - (version "3.3.4") + (version "3.4.1") (source (origin (method url-fetch) (uri (string-append @@ -797,7 +797,7 @@ desktop environment.") version "/icewm-" version ".tar.lz")) (sha256 (base32 - "124w00yq35mj859nf321bpy36ij7a0kblcg95axxahz4l6fhxfxf")))) + "0fr79i6r2sjr27lv4wik8lvcnrrapd28lzhy4gnqffzds0sqx64r")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) (inputs (list fontconfig From 9620b9d29858c05c774c15c3011bd610ce7ab671 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:50 -0400 Subject: [PATCH 202/440] gnu: libftdi: Update package style. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm: Re-order #:use-module statements. (libftdi): Wrap long lines; reformat gently. [license]: Use "license:" prefix. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index e39e0b3d71..4cfa1d3424 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -18,12 +18,12 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages libftdi) - #:use-module (guix licenses) + #:use-module (guix build-system cmake) #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) - #:use-module (gnu packages libusb) - #:use-module (guix build-system cmake)) + #:use-module (gnu packages libusb)) (define-public libftdi (package @@ -32,18 +32,17 @@ (source (origin (method url-fetch) (uri (string-append - "http://www.intra2net.com/en/developer/libftdi/download/libftdi1-" - version ".tar.bz2")) + "http://www.intra2net.com/en/developer/libftdi/download/" + "libftdi1-" version ".tar.bz2")) (sha256 (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) (propagated-inputs - (list libusb)) ; required by libftdi1.pc + (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") (synopsis "FTDI USB driver with bitbang mode") (description - "libFTDI is a library to talk to FTDI chips: FT232BM, -FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular -bitbangmode.") - (license lgpl2.1))) + "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, +FT2232D, FT245R and FT232H including the popular bitbangmode.") + (license license:lgpl2.1))) From ea2376a4f5f0bd82ac0b74521b656123fc39fba5 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:51 -0400 Subject: [PATCH 203/440] gnu: libftdi: Use HTTPS for package source. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[source]: Use HTTPS. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 4cfa1d3424..b881aa5cc2 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -32,7 +32,7 @@ (source (origin (method url-fetch) (uri (string-append - "http://www.intra2net.com/en/developer/libftdi/download/" + "https://www.intra2net.com/en/developer/libftdi/download/" "libftdi1-" version ".tar.bz2")) (sha256 (base32 From dcef5c7179816583bc008f4719092a0171d791dd Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:52 -0400 Subject: [PATCH 204/440] gnu: libftdi: Do not build example programs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]: Add with "-DEXAMPLES" configure flag. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index b881aa5cc2..74df12a354 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -20,6 +20,7 @@ (define-module (gnu packages libftdi) #:use-module (guix build-system cmake) #:use-module (guix download) + #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) @@ -38,6 +39,8 @@ (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DEXAMPLES=OFF"))) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") From ea67b8571d0ed2132956d0c2857b26faf835f0c9 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:53 -0400 Subject: [PATCH 205/440] gnu: libftdi: Install libraries to /lib instead of /lib64. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]<#:configure-flags>: Add "-DLIB_SUFFIX". Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 74df12a354..1e97793a93 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -40,7 +40,10 @@ "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) (arguments - (list #:configure-flags #~(list "-DEXAMPLES=OFF"))) + (list + #:configure-flags + #~(list "-DEXAMPLES=OFF" + "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") From d92c71f1d63cd89e4805c4dfde8f4deed9d037cf Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:54 -0400 Subject: [PATCH 206/440] gnu: libftdi: Build ftdi_eeprom. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[arguments]<#:configure-flags>: Add "-DCMAKE_INSTALL_DOCDIR". [native-inputs]: Add with pkg-config. [inputs]: Add with libconfuse. [license]: Add GPL version 2. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 1e97793a93..b3fb717905 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -24,7 +24,9 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) - #:use-module (gnu packages libusb)) + #:use-module (gnu packages libusb) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages textutils)) (define-public libftdi (package @@ -42,8 +44,14 @@ (arguments (list #:configure-flags - #~(list "-DEXAMPLES=OFF" + #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" + #$output "/share/doc/" #$name "-" #$version) + "-DEXAMPLES=OFF" "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 + (native-inputs + (list pkg-config)) + (inputs + (list libconfuse)) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") @@ -51,4 +59,5 @@ (description "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular bitbangmode.") - (license license:lgpl2.1))) + (license (list license:gpl2 ; ftdi_eeprom + license:lgpl2.1)))) ; main library From fce3d00cdb045fe8714be62d67ba3a0c303f4ea0 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:55 -0400 Subject: [PATCH 207/440] gnu: libftdi: Build C++ bindings. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Enabling the C++ bindings allows the test suite to be run, although this fails without access to the host's USB interface. * gnu/packages/libftdi.scm (libftdi)[arguments]: Add #:test-target, #:tests?. (inputs): Add boost. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index b3fb717905..0a996b05e7 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -24,6 +24,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (gnu packages) + #:use-module (gnu packages boost) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) #:use-module (gnu packages textutils)) @@ -47,11 +48,13 @@ #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" - "-DLIB_SUFFIX=''"))) ; place libraries in /lib, not /lib64 + "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + #:test-target "check" + #:tests? #f)) ; tests fail without access to USB (native-inputs (list pkg-config)) (inputs - (list libconfuse)) + (list boost libconfuse)) (propagated-inputs (list libusb)) ; required by libftdi1.pc (home-page "https://www.intra2net.com/en/developer/libftdi/") @@ -59,5 +62,5 @@ (description "libFTDI is a library to talk to FTDI chips: FT232BM, FT245BM, FT2232C, FT2232D, FT245R and FT232H including the popular bitbangmode.") - (license (list license:gpl2 ; ftdi_eeprom + (license (list license:gpl2 ; ftdi_eeprom, C++ bindings license:lgpl2.1)))) ; main library From 856eeedcbc65add655a40878ebed81aecd44a377 Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:56 -0400 Subject: [PATCH 208/440] gnu: libftdi: Build Python bindings. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[outputs]: Add "python". [arguments]<#:phases>: Add with "install-python-binding" phase. [native-inputs]: Add python, swig. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 0a996b05e7..773b0ec73e 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2023 Simon South ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,15 +19,19 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages libftdi) + #:use-module (guix build utils) #:use-module (guix build-system cmake) #:use-module (guix download) #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages swig) #:use-module (gnu packages textutils)) (define-public libftdi @@ -42,6 +47,7 @@ (base32 "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) (build-system cmake-build-system) + (outputs '("out" "python")) (arguments (list #:configure-flags @@ -49,10 +55,26 @@ #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'install-python-binding + (lambda _ + (let* ((python-version + #$(version-major+minor (package-version python))) + (python-lib-path + (string-append "/lib/python" python-version))) + (mkdir-p (string-append #$output:python "/lib")) + (mkdir-p (string-append #$output:python "/share/libftdi")) + (rename-file (string-append #$output python-lib-path) + (string-append #$output:python python-lib-path)) + (rename-file (string-append #$output + "/share/libftdi/examples") + (string-append #$output:python + "/share/libftdi/examples")))))) #:test-target "check" #:tests? #f)) ; tests fail without access to USB (native-inputs - (list pkg-config)) + (list pkg-config python swig)) (inputs (list boost libconfuse)) (propagated-inputs From 6c4868aca9e098fd7c830ba681ae0735aa752bdd Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:57 -0400 Subject: [PATCH 209/440] gnu: libftdi: Update to 1.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/libftdi.scm (libftdi): Update to 1.5. [source]: Apply patch. [arguments]<#:configure-flags>: Add "-DFTDIPP", "-DPYTHON_BINDINGS". Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/libftdi.scm | 10 +++-- .../libftdi-fix-paths-when-FTDIPP-set.patch | 39 +++++++++++++++++++ 3 files changed, 47 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch diff --git a/gnu/local.mk b/gnu/local.mk index a94fce9248..4c3de24d73 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1449,6 +1449,7 @@ dist_patch_DATA = \ %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/julia-Use-MPFR-4.2.patch \ + %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch \ %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \ %D%/packages/patches/libobjc2-unbundle-robin-map.patch \ %D%/packages/patches/librime-fix-build-with-gcc10.patch \ diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 773b0ec73e..bdfc635379 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -37,7 +37,7 @@ (define-public libftdi (package (name "libftdi") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (string-append @@ -45,7 +45,9 @@ "libftdi1-" version ".tar.bz2")) (sha256 (base32 - "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc")))) + "0jdh5r499wbz83vmpskczq5m3cfc1mcv8xqisj5i95k1r3lr2w3w")) + (patches + (search-patches "libftdi-fix-paths-when-FTDIPP-set.patch")))) (build-system cmake-build-system) (outputs '("out" "python")) (arguments @@ -54,7 +56,9 @@ #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) "-DEXAMPLES=OFF" - "-DLIB_SUFFIX=''") ; place libraries in /lib, not /lib64 + "-DFTDIPP=ON" + "-DLIB_SUFFIX=''" ; place libraries in /lib, not /lib64 + "-DPYTHON_BINDINGS=ON") #:phases #~(modify-phases %standard-phases (add-after 'install 'install-python-binding diff --git a/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch b/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch new file mode 100644 index 0000000000..0a81cceb26 --- /dev/null +++ b/gnu/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch @@ -0,0 +1,39 @@ +commit cdb28383402d248dbc6062f4391b038375c52385 +Author: Fabrice Fontaine +Date: Fri Jul 17 21:25:03 2020 +0200 + + CMakeLists.txt: fix paths when FTDIPP is set + + Use the same project name (i.e. libftdi1 and not libftdipp1) when FTDIPP + is enabled as suggested by Aurelien Jarno in + http://developer.intra2net.com/mailarchive/html/libftdi/2020/msg00044.html + + Without this change, the libftdi1.pc config file defines the include + path as /usr/local/include/libftdipp1 while the ftdi.h file is actually + installed in /usr/local/include/libftdi1 + + This is an issue for example for libsigrok which will fail on: + + In file included from src/hardware/asix-sigma/protocol.c:27: + src/hardware/asix-sigma/protocol.h:28:10: fatal error: ftdi.h: No such file or directory + 28 | #include + | ^~~~~~~~ + + Fixes: + - http://autobuild.buildroot.org/results/1427f44e36752c337791597fab47a1889552a2fe + + Signed-off-by: Fabrice Fontaine + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 5aecafc..3b0b87c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -136,7 +136,7 @@ endif () + + add_subdirectory(src) + if ( FTDIPP ) +- project(libftdipp1 C CXX) ++ project(libftdi1 C CXX) + add_subdirectory(ftdipp) + endif () + if ( PYTHON_BINDINGS ) From a5bc9f233f630e06b05f3029b181ba951502c00d Mon Sep 17 00:00:00 2001 From: Simon South Date: Thu, 7 Sep 2023 12:37:58 -0400 Subject: [PATCH 210/440] gnu: libftdi: Build API documentation. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libftdi.scm (libftdi)[outputs]: Add "doc" output. [arguments]<#:configure-flags>: Add "-DDOCUMENTATION". <#:phases>: Add "install-documentation" phase. [native-inputs]: Add doxygen, graphviz. Signed-off-by: Ludovic Courtès --- gnu/packages/libftdi.scm | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index bdfc635379..02efcbbbc0 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -28,6 +28,8 @@ #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) + #:use-module (gnu packages documentation) + #:use-module (gnu packages graphviz) #:use-module (gnu packages libusb) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -49,12 +51,13 @@ (patches (search-patches "libftdi-fix-paths-when-FTDIPP-set.patch")))) (build-system cmake-build-system) - (outputs '("out" "python")) + (outputs '("out" "doc" "python")) (arguments (list #:configure-flags #~(list (string-append "-DCMAKE_INSTALL_DOCDIR=" #$output "/share/doc/" #$name "-" #$version) + "-DDOCUMENTATION=ON" "-DEXAMPLES=OFF" "-DFTDIPP=ON" "-DLIB_SUFFIX=''" ; place libraries in /lib, not /lib64 @@ -74,11 +77,20 @@ (rename-file (string-append #$output "/share/libftdi/examples") (string-append #$output:python - "/share/libftdi/examples")))))) + "/share/libftdi/examples"))))) + (add-after 'install-python-binding 'install-documentation + (lambda _ + (let ((share (string-append #$output:doc "/share"))) + (copy-recursively "doc/man" + (string-append share "/man")) + (copy-recursively "doc/html" + (string-append share "/doc/" + #$name "-" #$version + "/html")))))) #:test-target "check" #:tests? #f)) ; tests fail without access to USB (native-inputs - (list pkg-config python swig)) + (list doxygen graphviz pkg-config python swig)) (inputs (list boost libconfuse)) (propagated-inputs From 1149cc1b9f2f3124f890c76497b826d7f959cec2 Mon Sep 17 00:00:00 2001 From: "Artyom V. Poptsov" Date: Sun, 10 Sep 2023 10:18:44 +0300 Subject: [PATCH 211/440] gnu: go-ipfs: Update to 0.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ipfs.scm (go-ipfs): Update to 0.13.0. [inputs]: Add GO-GOLANG-ORG-X-{EXP,TEXT}. Signed-off-by: Ludovic Courtès --- gnu/packages/ipfs.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ipfs.scm b/gnu/packages/ipfs.scm index 141653176b..1e4a7cca3a 100644 --- a/gnu/packages/ipfs.scm +++ b/gnu/packages/ipfs.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2019, 2020 Martin Becze ;;; Copyright © 2020, 2021, 2022 Michael Rohleder ;;; Copyright © 2022 Maxime Devos +;;; Copyright © 2023 Artyom V. Poptsov ;;; ;;; This file is part of GNU Guix. ;;; @@ -220,7 +221,7 @@ written in Go.") (define-public go-ipfs (package (name "go-ipfs") - (version "0.11.0") + (version "0.13.0") (source (origin (method url-fetch/tarbomb) @@ -228,7 +229,7 @@ written in Go.") "https://dist.ipfs.io/go-ipfs/v" version "/go-ipfs-source.tar.gz")) (sha256 - (base32 "13pmj83hwpz6mk7x52qn0cjnfqxqw2qri3r0k4b270w3bafcccwm")) + (base32 "1cx47ais2zn62c0r7lmrpfzia2gjyr61qi8my5wg3pj3dfr0fhkq")) (file-name (string-append name "-" version "-source")) (modules '((guix build utils))) (snippet '(for-each delete-file-recursively @@ -350,6 +351,8 @@ written in Go.") go-golang-org-x-term go-golang-org-x-tools go-golang-org-x-xerrors + go-golang-org-x-exp + go-golang-org-x-text go-lukechampine-com-blake3)) (native-inputs (append (if (%current-target-system) From b2cc649999ed97b62517dcfb7cf21ee731c97487 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Sun, 10 Sep 2023 15:21:24 +0200 Subject: [PATCH 212/440] gnu: glibc/hurd: Add unsubmitted getauxval patch from upstream. This support building of gdk-pixbuf, gobject-introspection. * gnu/packages/patches/glibc-hurd-getauxval.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (glibc/hurd)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/base.scm | 3 +- .../patches/glibc-hurd-getauxval.patch | 34 +++++++++++++++++++ 3 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/glibc-hurd-getauxval.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4c3de24d73..8862fbfbb9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1287,6 +1287,7 @@ dist_patch_DATA = \ %D%/packages/patches/glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch \ %D%/packages/patches/glibc-2.37-versioned-locpath.patch \ %D%/packages/patches/glibc-hurd-clock_t_centiseconds.patch \ + %D%/packages/patches/glibc-hurd-getauxval.patch \ %D%/packages/patches/glibc-hurd-gettyent.patch \ %D%/packages/patches/glibc-hurd-mach-print.patch \ %D%/packages/patches/glibc-hurd-signal-sa-siginfo.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 5a3d5aced5..786b080ae4 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -1463,7 +1463,8 @@ command.") "glibc-2.37-hurd-clock_t_centiseconds.patch" "glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch" "glibc-hurd-mach-print.patch" - "glibc-hurd-gettyent.patch")))) + "glibc-hurd-gettyent.patch" + "glibc-hurd-getauxval.patch")))) (supported-systems %hurd-systems))) (define-public glibc/hurd-headers diff --git a/gnu/packages/patches/glibc-hurd-getauxval.patch b/gnu/packages/patches/glibc-hurd-getauxval.patch new file mode 100644 index 0000000000..815371b2d0 --- /dev/null +++ b/gnu/packages/patches/glibc-hurd-getauxval.patch @@ -0,0 +1,34 @@ +Taken from https://salsa.debian.org/glibc-team/glibc/-/blob/5af8e3701c63ad202b652b5051bec592b8385820/debian/patches/hurd-i386/unsubmitted-getaux_at_secure.diff + +This fixes gdk-pixbuf, gobject-introspection. + +FIXME: sysdeps/mach/hurd/i386/init-first.c should instead pass an auxv +to __libc_start_main + +Index: glibc-2.33/misc/getauxval.c +=================================================================== +--- glibc-2.33.orig/misc/getauxval.c ++++ glibc-2.33/misc/getauxval.c +@@ -19,6 +19,7 @@ + #include + #include + #include ++#include + + bool + __getauxval2 (unsigned long int type, unsigned long int *result) +@@ -27,6 +28,14 @@ __getauxval2 (unsigned long int type, un + ElfW(auxv_t) *p; + #endif + ++#ifdef AT_SECURE ++ if (type == AT_SECURE) ++ { ++ *result = __libc_enable_secure; ++ return true; ++ } ++#endif ++ + if (type == AT_HWCAP) + { + *result = GLRO(dl_hwcap); From 1d5f1a5462491bf877999525466fb83c55e7e66d Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 14 Sep 2023 19:14:21 +0200 Subject: [PATCH 213/440] gnu: glib-next: Disable failing tests on the Hurd. * gnu/packages/glib.scm (glib-next)[arguments]: In phase `disable-tests', disable four extra failing tests when building on the Hurd. --- gnu/packages/glib.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index e2a0bbdcdf..b5eb4602da 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -532,7 +532,21 @@ functions for strings and common data structures.") (string-append "//" all "\n")) (("^ g_assert_cmpfloat \\(elapsed, ==.*" all) (string-append "//" all "\n")))) - '()))))))) + '()) + #$@(if (system-hurd?) + '((with-directory-excursion "gio/tests" + ;; FAIL + (substitute* '("appmonitor.c" + "gdbus-server-auth.c" + "live-g-file.c" + "socket.c") + (("return (g_test_run|session_bus_run)" all call) + (string-append "return 0;// " call)) + ((" (ret|rtv|result) = (g_test_run|session_bus_run)" + all var call) + (string-append " " var " = 0;// " call)) + (("[ \t]*g_test_add_func.*;") "")))) + '()))))))) (native-inputs (modify-inputs (package-native-inputs glib) (append desktop-file-utils))) From 0c1aa354048f82023e6d2043bfecc4fd58bc9b58 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 14 Sep 2023 23:12:23 +0200 Subject: [PATCH 214/440] gnu: python-cython: Support building on the Hurd. * gnu/packages/python-xyz.scm (python-cython)[arguments]: In phase `check', skip failing tests on the Hurd. --- gnu/packages/python-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dd43fb3cd1..2230310a03 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -142,6 +142,7 @@ ;;; Copyright © 2023 Parnikkapore ;;; Copyright © 2023 Foundation Devices, Inc. ;;; Copyright © c4droid +;;; Copyright © 2023 Janneke Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -7129,6 +7130,11 @@ provides additional functionality on the produced Mallard documents.") ,@(if (not (target-64bit?)) '("-x" "run.parallel") '()) + ,@(if (system-hurd?) + '("-x" "test_class_ref" + "-x" "test_compiler_directives" + "-x" "test_lang_version") + '()) ;; This test fails when running on 24 cores. "-x" "cpp_stl_conversion"))))))) (home-page "https://cython.org/") From dca96f27ed5b870109c26836d32d991fcfbedaab Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Wed, 12 Jul 2023 14:57:58 +0100 Subject: [PATCH 215/440] gnu: Add bffe. * gnu/packages/package-management.scm (bffe): New variable. --- gnu/packages/package-management.scm | 53 +++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 51a5d52131..daf2d3b0c0 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -961,6 +961,59 @@ transactions from C or Python.") ;; The whole is GPLv2+; librpm itself is dual-licensed LGPLv2+ | GPLv2+. (license license:gpl2+))) +(define-public bffe + (let ((commit "634d3444c094dd594bdf2b15b9a71055462ae676") + (revision "1")) + (package + (name "bffe") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.cbaines.net/guix/bffe") + (commit commit))) + (sha256 + (base32 + "0z13hyaq6bs2j3hnr7ys2vsyx2554zy69ka21savywx0ci3hhfk3")) + (file-name (string-append name "-" version "-checkout")))) + (build-system gnu-build-system) + (native-inputs + (list pkg-config + autoconf + automake + + ;; Guile libraries are needed here for cross-compilation. + guile-next + guile-gnutls + guile-json-4 + guix + guix-data-service + guix-build-coordinator + guile-fibers-1.3 + guile-prometheus + guile-lib)) + (inputs + (list guile-next)) + (propagated-inputs + (list guile-gnutls + guile-json-4 + guix + guix-data-service + guix-build-coordinator + guile-fibers-1.3 + guile-prometheus + guile-lib)) + (home-page "https://git.cbaines.net/guix/bffe") + (synopsis "Build Farm Front-end for Guix") + (description + "The BFFE of Build Farm Front-end is an experimental frontend for Guix +build farms. It works together with the Guix Data Service and Guix Build +Coordinator to submit builds and monitor the activity. + +It functions as a Guile library, with the @code{run-bffe-service} procedure in +the @code{(bffe)} module as the entry point.") + (license license:gpl3+)))) + (define-public python-anaconda-client (package (name "python-anaconda-client") From 82abf6ddadc6139148660440a064e60ae68f238e Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 26 Aug 2023 10:08:56 +0100 Subject: [PATCH 216/440] services: guix: Add bffe-service-type. This is intended to replace the functionality of the Guix Build Coordinator queue builds script, and also provide a web interface for build farms. * gnu/services/guix.scm (): New record type. (bffe-configuration, bffe-configuration?, bffe-configuration-package, bffe-configuration-user, bffe-configuration-group, bffe-configuration-arguments bffe-configuration-extra-environment-variables): New procedures. (bffe-service-type): New variable. * gnu/tests/guix.scm (%test-bffe): New variable. * doc/guix.texi (Guix Services): Document the new service. --- doc/guix.texi | 59 ++++++++++++++++++++ gnu/services/guix.scm | 127 +++++++++++++++++++++++++++++++++++++++++- gnu/tests/guix.scm | 81 ++++++++++++++++++++++++++- 3 files changed, 265 insertions(+), 2 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 7e42a7151c..46cc8e1b80 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -38088,6 +38088,65 @@ File name of the file system key for the target volume. @node Guix Services @subsection Guix Services +@subsubheading Build Farm Front-End (BFFE) +The @uref{https://git.cbaines.net/guix/bffe/,Build Farm Front-End} +assists with building Guix packages in bulk. It's responsible for +submitting builds and displaying the status of the build farm. + +@defvar bffe-service-type +Service type for the Build Farm Front-End. Its value must be a +@code{bffe-configuration} object. +@end defvar + +@deftp {Data Type} bffe-configuration +Data type representing the configuration of the Build Farm Front-End. + +@table @asis +@item @code{package} (default: @code{bffe}) +The Build Farm Front-End package to use. + +@item @code{user} (default: @code{"bffe"}) +The system user to run the service as. + +@item @code{group} (default: @code{"bffe"}) +The system group to run the service as. + +@item @code{arguments} +A list of arguments to the Build Farm Front-End. These are passed to +the @code{run-bffe-service} procedure when starting the service. + +For example, the following value directs the Build Farm Front-End to +submit builds for derivations available from @code{data.guix.gnu.org} to +the Build Coordinator instance assumed to be running on the same +machine. + +@example +(list + #:build + (list + (build-from-guix-data-service + (data-service-url "https://data.guix.gnu.org") + (build-coordinator-url "http://127.0.0.1:8746") + (branches '("master")) + (systems '("x86_64-linux" "i686-linux")) + (systems-and-targets + (map (lambda (target) + (cons "x86_64-linux" target)) + '("aarch64-linux-gnu" + "i586-pc-gnu"))) + (build-priority (const 0)))) + #:web-server-args + '(#:event-source "https://example.com" + #:controller-args + (#:title "example.com build farm"))) +@end example + +@item @code{extra-environment-variables} (default: @var{'()}) +Extra environment variables to set via the shepherd service. + +@end table +@end deftp + @subsubheading Guix Build Coordinator The @uref{https://git.cbaines.net/guix/build-coordinator/,Guix Build Coordinator} aids in distributing derivation builds among machines diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm index 99b21f52d8..9b19a48cfd 100644 --- a/gnu/services/guix.scm +++ b/gnu/services/guix.scm @@ -140,7 +140,17 @@ nar-herder-cached-compression-configuration-type nar-herder-cached-compression-configuration-level nar-herder-cached-compression-configuration-directory - nar-herder-cached-compression-configuration-directory-max-size)) + nar-herder-cached-compression-configuration-directory-max-size + + bffe-configuration + bffe-configuration? + bffe-configuration-package + bffe-configuration-user + bffe-configuration-group + bffe-configuration-arguments + bffe-configuration-extra-environment-variables + + bffe-service-type)) ;;;; Commentary: ;;; @@ -1030,3 +1040,118 @@ ca-certificates.crt file in the system profile." nar-herder-account))) (description "Run a Nar Herder server."))) + + +;;; +;;; Build Farm Front-end (BFFE) +;;; + +(define-record-type* + bffe-configuration make-bffe-configuration + bffe-configuration? + (package bffe-configuration-package + (default bffe)) + (user bffe-configuration-user + (default "bffe")) + (group bffe-configuration-group + (default "bffe")) + (arguments bffe-configuration-arguments) + (extra-environment-variables + bffe-configuration-extra-environment-variables + (default '()))) + +(define (bffe-shepherd-services config) + (define bffe-package + (bffe-configuration-package config)) + + (define start-script + (program-file + "run-bffe" + (with-extensions (cons + bffe-package + ;; This is a poorly constructed Guile load path, + ;; since it contains things that aren't Guile + ;; libraries, but it means that the Guile + ;; libraries needed for BFFE don't need to be + ;; individually specified here. + (map second (package-transitive-propagated-inputs + bffe-package))) + #~(begin + (use-modules (bffe) + (bffe manage-builds)) + + (setvbuf (current-output-port) 'line) + (setvbuf (current-error-port) 'line) + + (simple-format #t "starting the bffe:\n ~A\n" + (current-filename)) + + (apply run-bffe-service + (append + (list #:pid-file "/var/run/bffe/pid") + #$(bffe-configuration-arguments config))))) + #:guile guile-3.0)) + + (match-record config + (package user group arguments extra-environment-variables) + + (list + (shepherd-service + (documentation "Build Farm Front-end") + (provision '(bffe)) + (requirement '(networking)) + (start #~(make-forkexec-constructor + (list #$start-script) + #:user #$user + #:group #$group + #:pid-file "/var/run/bffe/pid" + #:directory "/var/lib/bffe" + #:environment-variables + `(,(string-append + "GUIX_LOCPATH=" #$glibc-utf8-locales "/lib/locale") + "LC_ALL=en_US.utf8" + #$@extra-environment-variables) + #:log-file "/var/log/bffe/server.log")) + (stop #~(make-kill-destructor)))))) + +(define (bffe-activation config) + #~(begin + (use-modules (guix build utils)) + + (define %user + (getpw #$(bffe-configuration-user config))) + + (chmod "/var/lib/bffe" #o755) + + (mkdir-p "/var/log/bffe") + + ;; Allow writing the PID file + (mkdir-p "/var/run/bffe") + (chown "/var/run/bffe" (passwd:uid %user) (passwd:gid %user)))) + +(define (bffe-account config) + (match-record config + (user group) + (list (user-group + (name group) + (system? #t)) + (user-account + (name user) + (group group) + (system? #t) + (comment "BFFE user") + (home-directory "/var/lib/bffe") + (shell (file-append shadow "/sbin/nologin")))))) + +(define bffe-service-type + (service-type + (name 'bffe) + (extensions + (list (service-extension shepherd-root-service-type + bffe-shepherd-services) + (service-extension activation-service-type + bffe-activation) + (service-extension account-service-type + bffe-account))) + (description + "Run the Build Farm Front-end."))) diff --git a/gnu/tests/guix.scm b/gnu/tests/guix.scm index ad0980a10c..240ded4825 100644 --- a/gnu/tests/guix.scm +++ b/gnu/tests/guix.scm @@ -37,7 +37,8 @@ #:use-module (ice-9 match) #:export (%test-guix-build-coordinator %test-guix-data-service - %test-nar-herder)) + %test-nar-herder + %test-bffe)) ;;; ;;; Guix Build Coordinator @@ -325,3 +326,81 @@ host all all ::1/128 trust")))))) (name "nar-herder") (description "Connect to a running Nar Herder server.") (value (run-nar-herder-test)))) + + +;;; +;;; Build Farm Front-end +;;; + +(define %bffe-os + (simple-operating-system + (service dhcp-client-service-type) + (service guix-build-coordinator-service-type) + (service bffe-service-type + (bffe-configuration + (arguments + #~(list + #:web-server-args + '(#:port 8767 + #:controller-args + (#:title "Test title")))))))) + +(define (run-bffe-test) + (define os + (marionette-operating-system + %bffe-os + #:imported-modules '((gnu services herd) + (guix combinators)))) + + (define forwarded-port 8767) + + (define vm + (virtual-machine + (operating-system os) + (memory-size 1024) + (port-forwardings `((,forwarded-port . 8767))))) + + (define test + (with-imported-modules '((gnu build marionette)) + #~(begin + (use-modules (srfi srfi-11) (srfi srfi-64) + (gnu build marionette) + (web uri) + (web client) + (web response)) + + (define marionette + (make-marionette (list #$vm))) + + (test-runner-current (system-test-runner #$output)) + (test-begin "bffe") + + (test-assert "service running" + (marionette-eval + '(begin + (use-modules (gnu services herd)) + (match (start-service 'bffe) + (#f #f) + (('service response-parts ...) + (match (assq-ref response-parts 'running) + ((pid) (number? pid)))))) + marionette)) + + (test-equal "http-get" + 200 + (let-values + (((response text) + (http-get #$(simple-format + #f "http://localhost:~A/" forwarded-port) + #:decode-body? #t))) + (response-code response))) + + (test-end)))) + + (gexp->derivation "bffe-test" test)) + +(define %test-bffe + (system-test + (name "bffe") + (description "Connect to a running Build Farm Front-end.") + (value (run-bffe-test)))) From 92498fad27a304ab73f66bd4944007c150012a07 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 8 Sep 2023 12:51:53 -0700 Subject: [PATCH 217/440] gnu: diffoscope: Update to 250. * gnu/packages/diffoscope.scm (diffoscope): Update to 250. [native-inputs]: Add html2text and u-boot-tools. Signed-off-by: Christopher Baines --- gnu/packages/diffoscope.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm index 86f0c779ef..1b8b77d7a4 100644 --- a/gnu/packages/diffoscope.scm +++ b/gnu/packages/diffoscope.scm @@ -74,7 +74,7 @@ (define-public diffoscope (package (name "diffoscope") - (version "247") + (version "250") (source (origin (method git-fetch) @@ -83,7 +83,7 @@ (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0c81pvdq0bz47sk3gcgpm2l3g5hxdi2s1jz05krv1cr2bd0sfq4j")))) + (base32 "12cdsgxlva1gcry16w9x44ji9asar1n8p9q6rv2jd1gr9fi6l0sz")))) (build-system python-build-system) (arguments (list @@ -188,6 +188,7 @@ gnumeric gnupg hdf5 + html2text imagemagick libarchive llvm @@ -206,6 +207,7 @@ sqlite squashfs-tools tcpdump + u-boot-tools unzip wabt xxd From af1d2c031032b2b0330a3093a41b16f7699f29b9 Mon Sep 17 00:00:00 2001 From: Sergey Trofimov Date: Fri, 8 Sep 2023 17:57:39 +0200 Subject: [PATCH 218/440] gnu: squid: Update to 6.3. Signed-off-by: Christopher Baines --- gnu/packages/networking.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 6c22129a98..1eb464673d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1998,14 +1998,14 @@ TCP connection, TLS handshake and so on) in the terminal.") (define-public squid (package (name "squid") - (version "4.17") + (version "6.3") (source (origin (method url-fetch) - (uri (string-append "http://www.squid-cache.org/Versions/v4/squid-" + (uri (string-append "http://www.squid-cache.org/Versions/v6/squid-" version ".tar.xz")) (sha256 - (base32 "060lwghn6q982bay11ia38c86kd8w6mjgy68n58v31kwik08m4nb")))) + (base32 "1yj869jnbdv1fb604j6g602dyvfnw7ahh9sh7mbqjpbsd9cgb83l")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 4c031bb86f2a82c9e37ce37981abc2779fcd8b68 Mon Sep 17 00:00:00 2001 From: Jussi Timperi Date: Mon, 11 Sep 2023 12:06:48 +0300 Subject: [PATCH 219/440] gnu: pasystray: Update to 0.8.2. * gnu/packages/pulseaudio.scm (pasystray): Update to 0.8.2. Signed-off-by: Christopher Baines --- gnu/packages/pulseaudio.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm index ef4f8ba8cf..dd0d3985c0 100644 --- a/gnu/packages/pulseaudio.scm +++ b/gnu/packages/pulseaudio.scm @@ -385,16 +385,16 @@ volume levels of the sinks (get, set, decrease, increase, toggle mute, etc).") (define-public pasystray (package (name "pasystray") - (version "0.7.1") + (version "0.8.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/christophgysin/pasystray") - (commit (string-append name "-" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0xx1bm9kimgq11a359ikabdndqg5q54pn1d1dyyjnrj0s41168fk")))) + (base32 "1zf79pfmm7wa1l9yyab2g6lf0j81v1mrp406262rd21g4prx1921")))) (build-system gnu-build-system) (arguments `(#:phases From a0510561935e3327099df558e9dd9bdffe850441 Mon Sep 17 00:00:00 2001 From: Andrew Jose Date: Wed, 13 Sep 2023 13:24:35 +0530 Subject: [PATCH 220/440] gnu: delve: Update to 1.21.0. * gnu/packages/debug.scm (delve): Update to 1.21.0. [propagated-inputs]: Remove go. Signed-off-by: Christopher Baines --- gnu/packages/debug.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index e2a29a3ae9..febc041e53 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -892,11 +892,10 @@ to aid in debugging.") (home-page "https://www.gnu.org/software/ddd/") (license license:gpl3+))) - (define-public delve (package (name "delve") - (version "1.9.1") + (version "1.21.0") (source (origin (method git-fetch) @@ -906,14 +905,13 @@ to aid in debugging.") (file-name (git-file-name name version)) (sha256 (base32 - "07jch3yd1pgqviyy18amn23gazbzi7l51f210c3vmc707v3vbbqr")))) + "1gdynx4gp02lj47znnf638kkbmmsl24a9fis81a2fg3pdrg6jg3c")))) (build-system go-build-system) (arguments (list #:import-path "github.com/go-delve/delve/cmd/dlv" #:unpack-path "github.com/go-delve/delve" #:install-source? #f #:phases #~(modify-phases %standard-phases (delete 'check)))) - (propagated-inputs (list go)) (home-page "https://github.com/go-delve/delve") (synopsis "Debugger for the Go programming language") (description "Delve is a debugger for the Go programming language.") From 61a89de7d7e6517cd393dd1f3cf93004a5a3bdf2 Mon Sep 17 00:00:00 2001 From: Nicolas Graves Date: Thu, 14 Sep 2023 14:15:35 +0200 Subject: [PATCH 221/440] gnu: emacs-sway: Update to 0.7. * gnu/packages/emacs-xyz.scm (emacs-sway): Update to 0.7. Signed-off-by: Andrew Tropin --- gnu/packages/emacs-xyz.scm | 39 ++++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a4c6f45feb..c4de0e1d1f 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -12440,30 +12440,27 @@ The following completions are currently available: (license license:gpl3+))) (define-public emacs-sway - ;; Commit from Nicola's fork (dash free version with various improvments) - (let ((commit "838ef531a30fe616f0141adbdabc132d4edfd374") - (revision "0")) - (package - (name "emacs-sway") - (version (git-version "0.6.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/thblt/sway.el") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0ddaz8my3z4ca2z81kf1h8773pyx8h0l0ra3ssqd1rq5j0041wdh")))) - (build-system emacs-build-system) - (home-page "https://github.com/thblt/sway.el") - (synopsis "Communication with the Sway window manager") - (description - "This is a basic library to control the Sway window manager from Emacs. + (package + (name "emacs-sway") + (version "0.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/thblt/sway.el") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w29dkl7s835zgwnc4jx1cp84s6mmwbvlil8z2c31psy0rlajc6i")))) + (build-system emacs-build-system) + (home-page "https://github.com/thblt/sway.el") + (synopsis "Communication with the Sway window manager") + (description + "This is a basic library to control the Sway window manager from Emacs. Its main use case is in combination with popup managers like Shackle, to use frames instead of windows while still giving focus to existing frames instead of duplicating them.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-sweet-theme (let ((commit "78f741806ecebe01224bf54d09ad80e306652508") From 9549266ba42cc31a9442ddd78af592e824f2d061 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 13:18:43 +0300 Subject: [PATCH 222/440] gnu: julia-freetype2-jll: Update to 2.13.1+0. * gnu/packages/julia-jll.scm (julia-freetype2-jll): Update to 2.13.1+0. [arguments]: Remove trailing #t from phases. --- gnu/packages/julia-jll.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm index 35e06c7124..753651cb9e 100644 --- a/gnu/packages/julia-jll.scm +++ b/gnu/packages/julia-jll.scm @@ -401,7 +401,7 @@ build tree Yggdrasil.") (define-public julia-freetype2-jll (package (name "julia-freetype2-jll") - (version "2.10.4+0") + (version "2.13.1+0") (source (origin (method git-fetch) @@ -410,7 +410,7 @@ build tree Yggdrasil.") (commit (string-append "FreeType2-v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03lgmb59lipc3bi7z22j4a53bbjmcwkf0xzpwan889p1ix3ry1lr")))) + (base32 "1kngkk3kkf6dam8g4g2ajvzvydzxbgpgxlcpsg7nm7q6r5b4b4db")))) (build-system julia-build-system) (arguments '(#:tests? #f ; No runtests.jl @@ -426,8 +426,7 @@ build tree Yggdrasil.") "generate_wrapper_header(\"FreeType2\", \"" (assoc-ref inputs "freetype") "\")\n")))) ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$")) - #t))))) + (find-files "src/wrappers/" "\\.jl$"))))))) (inputs (list freetype)) (propagated-inputs From 69580997bd1b383659b990a5e1e46817e371fa8c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Sep 2023 13:28:57 +0300 Subject: [PATCH 223/440] gnu: julia-structarrays: Add missing input. * gnu/packages/julia-xyz.scm (julia-structarrays)[propagated-inputs]: Add julia-adapt. --- gnu/packages/julia-xyz.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index bbb8085492..a1e65332fa 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -6084,7 +6084,8 @@ with ANSI escape sequences.") "test/runtests.jl") (("Int64") "Int32")))))))) (propagated-inputs - (list julia-dataapi + (list julia-adapt + julia-dataapi julia-staticarrays julia-tables)) (native-inputs From 9c9d6c3dab0a3c83ca30664d0461807d0289579b Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 15 Sep 2023 10:50:31 +0100 Subject: [PATCH 224/440] services: bffe: Use guile from the package. Rather than hardcoding a particular guile in the service definition. * gnu/services/guix.scm (bffe-shepherd-services): Use guile from the package. * gnu/packages/package-management.scm (bffe)[inputs]: Remove unnecessary guile-next input. --- gnu/packages/package-management.scm | 2 -- gnu/services/guix.scm | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index daf2d3b0c0..d2e0cdecd7 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -992,8 +992,6 @@ transactions from C or Python.") guile-fibers-1.3 guile-prometheus guile-lib)) - (inputs - (list guile-next)) (propagated-inputs (list guile-gnutls guile-json-4 diff --git a/gnu/services/guix.scm b/gnu/services/guix.scm index 9b19a48cfd..fe602efb99 100644 --- a/gnu/services/guix.scm +++ b/gnu/services/guix.scm @@ -1090,7 +1090,7 @@ ca-certificates.crt file in the system profile." (append (list #:pid-file "/var/run/bffe/pid") #$(bffe-configuration-arguments config))))) - #:guile guile-3.0)) + #:guile (lookup-package-native-input bffe-package "guile-next"))) (match-record config (package user group arguments extra-environment-variables) From eeeaf13984b96ca8856532559d5ab755c560e42c Mon Sep 17 00:00:00 2001 From: Vincent Prat Date: Mon, 26 Jun 2023 11:44:47 +0200 Subject: [PATCH 225/440] gnu: python-mypy: Update to 1.4.1. * gnu/packages/python-check.scm (python-mypy): Update to 1.4.1. [origin]: Switch to PyPI. [arguments]: Don't skip the testImports test. Signed-off-by: Christopher Baines --- gnu/packages/python-check.scm | 23 +++++------------------ 1 file changed, 5 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 87e15b4560..3a718954c5 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -1834,24 +1834,14 @@ supported by the MyPy typechecker.") (define-public python-mypy (package (name "python-mypy") - (version "0.971") + (version "1.4.1") (source (origin - ;; Because of https://github.com/python/mypy/issues/9584, the - ;; mypyc/analysis directory is missing in the PyPI archive, leading to - ;; test failures. - (method git-fetch) - (uri (git-reference - (url "https://github.com/python/mypy") - (commit (string-append "v" version)) - ;; Fetch git submodules otherwise typeshed is not fetched. - ;; Typeshed is a collection of Python sources type annotation - ;; (data) files. - (recursive? #t))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (pypi-uri "mypy" version)) (sha256 (base32 - "0i8swdynms1wpiprgqn24za6mx8rlgxr2jash3cb5xi8jyf58n97")))) + "06svfmqbnb45pydy8lcrr12wqhhla5dl888w0g4f3wm1ismxkg4v")))) (build-system python-build-system) (arguments `(#:phases @@ -1859,10 +1849,7 @@ supported by the MyPy typechecker.") (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? - (invoke "pytest" "-vv" "mypyc" - ;; XXX: This test gets an unexpected DeprecationWarning - ;; from recent versions of setuptools. Ignore for now. - "-k" "not testImports"))))))) + (invoke "pytest" "mypyc"))))))) (native-inputs (list python-attrs python-lxml From 444cab7f05686c0b0ca75b61eb69866c6d7536dc Mon Sep 17 00:00:00 2001 From: Hilton Chain Date: Sun, 2 Jul 2023 18:01:32 +0800 Subject: [PATCH 226/440] gnu: go-github-com-tdewolff-minify-v2: Update to 2.12.7. * gnu/packages/golang.scm (go-github-com-tdewolff-minify-v2): Update to 2.12.7 Signed-off-by: Christopher Baines --- gnu/packages/golang.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index cbd4bafd20..3d19b48e9f 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -3673,7 +3673,7 @@ per-goroutine.") (define-public go-github-com-tdewolff-minify-v2 (package (name "go-github-com-tdewolff-minify-v2") - (version "2.12.6") + (version "2.12.7") (source (origin (method git-fetch) (uri (git-reference @@ -3682,7 +3682,7 @@ per-goroutine.") (file-name (git-file-name name version)) (sha256 (base32 - "0h006wpfkl0ls0skqxblwcanrhmphgq5q0ii26l2ayh7s99cgmy3")))) + "0qhslaq885zbqs83nvbi29yh09b89kkb6ycami8lz28wkwrlayap")))) (build-system go-build-system) (arguments (list #:import-path "github.com/tdewolff/minify/v2" From b696fb41bc0dfcb7130a5aa6d69aff2ae191c283 Mon Sep 17 00:00:00 2001 From: kiasoc5 Date: Tue, 4 Jul 2023 14:28:56 -0400 Subject: [PATCH 227/440] gnu: libostree: Update to 2023.5. * gnu/packages/package-management.scm (libostree): Update to 2023.5. Signed-off-by: Christopher Baines --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index d2e0cdecd7..e899817093 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1921,7 +1921,7 @@ for packaging and deployment of cross-compiled Windows applications.") (define-public libostree (package (name "libostree") - (version "2022.7") + (version "2023.5") (source (origin (method url-fetch) @@ -1929,7 +1929,7 @@ for packaging and deployment of cross-compiled Windows applications.") "https://github.com/ostreedev/ostree/releases/download/v" (version-major+minor version) "/libostree-" version ".tar.xz")) (sha256 - (base32 "07s14awf9ynlp84s08dkbwj9i18g93y0yf0k87nbks4l3hkakqlb")))) + (base32 "056v7bz40dx8k2j2pfypc4shl6ijzvx1gy8r0kaw66py67xklndw")))) (build-system gnu-build-system) (arguments '(#:phases From edca2863bcb52388fe454e14136264a4f7490273 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Fri, 15 Sep 2023 21:57:57 +0200 Subject: [PATCH 228/440] tests: Fix "package-transitive-supported-systems, implicit inputs". MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This is a follow-up to commit 0e08ad7f19d5b29a4883468552b5d213a7bdb66e gnu: linux-libre-headers: Remove i586-gnu from supported-systems. See also . * tests/packages.scm ("package-transitive-supported-systems, implicit inputs"): Filter expectiation with target-linux?, as %current-system is linux. Co-authored-by: Ludovic Courtès --- tests/packages.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/packages.scm b/tests/packages.scm index 2b4f9f8e90..a623628447 100644 --- a/tests/packages.scm +++ b/tests/packages.scm @@ -494,7 +494,7 @@ (member "boo" keys)))) (test-equal "package-transitive-supported-systems, implicit inputs" - %supported-systems + (filter target-linux? %supported-systems) ;; Here GNU-BUILD-SYSTEM adds implicit inputs that build only on ;; %SUPPORTED-SYSTEMS. Thus the others must be ignored. From 213516f0baf92b6f50bd0c2e005625c0b3421a6f Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Fri, 15 Sep 2023 22:20:59 +0200 Subject: [PATCH 229/440] gnu: beignet: Fix build. * gnu/packages/opencl.scm (beignet)[arguments]: Add configure flag. --- gnu/packages/opencl.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index 85b063b136..caafa6beaf 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -240,7 +240,10 @@ the system.") (list (string-append "-DCLANG_LIBRARY_DIR=" (assoc-ref %build-inputs "clang@3.7") "/lib") "-DENABLE_GL_SHARING=ON" - "-DEXPERIMENTAL_DOUBLE=ON") + "-DEXPERIMENTAL_DOUBLE=ON" + ;; disable OCL ICD, which is probably this project: + ;; https://github.com/OCL-dev/ocl-icd + "-DOCLICD_COMPAT=0") #:phases (modify-phases %standard-phases From 3341b22f594398b3aa3ff930d99b74a78abd1a30 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 230/440] gnu: Add ocl-icd. * gnu/packages/opencl.scm (ocl-icd): New public variable. --- gnu/packages/opencl.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index caafa6beaf..7275dfb573 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -197,6 +197,31 @@ possible (known) properties of the OpenCL platform and devices available on the system.") (license license:cc0))) +(define-public ocl-icd + (package + (name "ocl-icd") + (version "2.3.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OCL-dev/ocl-icd") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0y0lnxb6zlhfb5vxxib5n1vvxa4b23qc0j3lsih6yjz9j37mj7wz")))) + (build-system gnu-build-system) + (native-inputs + (list autoconf automake libtool ruby)) + (home-page "https://github.com/OCL-dev/ocl-icd") + (synopsis "Generic OpenCL @acronym{ICD, Installable Client Driver} loader") + (description + "This package provides an OpenCL @acronym{ICD, Installable Client Driver} +loader. It maintains a YAML database of all known and guessed function pointers +from vendor-specific drivers. It also delivers a skeleton of bindings to +incorporate inside an OpenCL implementation to give it ICD functionalities.") + (license license:bsd-2))) + (define-public beignet (package (name "beignet") From 1ad4d00a9522289b94bb230674ffb585f1dcf417 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 231/440] gnu: beignet: Fix build. * gnu/packages/opencl.scm (beignet)[inputs]: Add ocl-icd. --- gnu/packages/opencl.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index 7275dfb573..56eecec603 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -255,6 +255,7 @@ incorporate inside an OpenCL implementation to give it ICD functionalities.") ("libxext" ,libxext) ("mesa-utils" ,mesa-utils) ("ncurses" ,ncurses) + ("ocl-icd" ,ocl-icd) ("opencl-icd-loader" ,opencl-icd-loader) ("opencl-headers" ,opencl-headers) ("xextproto" ,xextproto) From 40e78353a4699b8edb6600d82df648914c9110b9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 232/440] Revert "gnu: beignet: Fix build." This reverts commit 213516f0baf92b6f50bd0c2e005625c0b3421a6f, which removed ICD support entirely. --- gnu/packages/opencl.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index 56eecec603..74b250cb9d 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -266,10 +266,7 @@ incorporate inside an OpenCL implementation to give it ICD functionalities.") (list (string-append "-DCLANG_LIBRARY_DIR=" (assoc-ref %build-inputs "clang@3.7") "/lib") "-DENABLE_GL_SHARING=ON" - "-DEXPERIMENTAL_DOUBLE=ON" - ;; disable OCL ICD, which is probably this project: - ;; https://github.com/OCL-dev/ocl-icd - "-DOCLICD_COMPAT=0") + "-DEXPERIMENTAL_DOUBLE=ON") #:phases (modify-phases %standard-phases From 7a006d72b4e87828b2cfbe37462644b5271fb0f5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 13 Sep 2023 23:05:59 -0400 Subject: [PATCH 233/440] gnu: linux-libre: Update to 6.4.16. * gnu/packages/linux.scm (linux-libre-6.4-version): Update to 6.4.16. (linux-libre-6.4-pristine-source, deblob-scripts-6.5): Update hashes. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 91109c41d9..d088f2836b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -490,17 +490,17 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.4-version "6.4.15") +(define-public linux-libre-6.4-version "6.4.16") (define-public linux-libre-6.4-gnu-revision "gnu") (define deblob-scripts-6.4 (linux-libre-deblob-scripts linux-libre-6.4-version linux-libre-6.4-gnu-revision (base32 "012d16rjprxdv9frf7kcakpikvw7l0s3kvj4kkp9flzdg3j8wxpz") - (base32 "1rwm09anyn4py1g877f9vh6ya86y2hfvlqx51bpa53dci5k0b0ds"))) + (base32 "02zizxf0dp4291hbvjrif04m19h8rrc55c11qinlrm0p19s9srcx"))) (define-public linux-libre-6.4-pristine-source (let ((version linux-libre-6.4-version) - (hash (base32 "1phlx375ln5pslw5vjqm029cdv6pzf4ang10xlrf90x5sb4fgy93"))) + (hash (base32 "0zgj1z97jyx7wf12zrnlcp0mj4cl43ais9qsy6dh1jwylf2fq9ln"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.4))) From 5b236fbcccc123d4ccda6063b36c8d6f6c1a57f6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 13 Sep 2023 23:06:22 -0400 Subject: [PATCH 234/440] gnu: linux-libre 6.1: Update to 6.1.53. * gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.53. (linux-libre-6.1-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 d088f2836b..51147406ec 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -508,7 +508,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; -(define-public linux-libre-6.1-version "6.1.52") +(define-public linux-libre-6.1-version "6.1.53") (define-public linux-libre-6.1-gnu-revision "gnu") (define deblob-scripts-6.1 (linux-libre-deblob-scripts @@ -518,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11"))) (define-public linux-libre-6.1-pristine-source (let ((version linux-libre-6.1-version) - (hash (base32 "0lis73mxnl7hxz8lyja6sfgmbym944l3k1h7dab6b4mw1nckfxsn"))) + (hash (base32 "0zpdg3fcc12iyjhfs5w7cw75700z4i8m9jcg38mlzlhh92hf0msz"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.1))) From 33e64b4509d595eb324790c9a7e134de10d2f491 Mon Sep 17 00:00:00 2001 From: Vivien Kraus Date: Tue, 12 Sep 2023 22:31:37 +0200 Subject: [PATCH 235/440] gnu: ocaml: Allow not to build the native compiler. Build "defaultentry", not "world.opt", so that the build system decides whether to build the native compiler or just the bytecode compiler. The native compiler is not available for 32-bit architectures. * gnu/packages/ocaml.scm (ocaml-5.0)[arguments]: Change make-flags. Signed-off-by: Andreas Enge --- gnu/packages/ocaml.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 8ff755aea9..ea9d3e3594 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -219,7 +219,7 @@ This package produces a native @command{ocamlc} and a bytecode @command{ocamllex (arguments `(#:configure-flags '("--enable-ocamltest") #:test-target "tests" - #:make-flags '("world.opt") + #:make-flags '("defaultentry") #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-/bin/sh-references From f2a8b26df8148496856509606f34e552e64cdad7 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 16 Sep 2023 09:04:18 +0100 Subject: [PATCH 236/440] gnu: guix-build-coordinator: Update to 0-89.9c42dcb. * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-89.9c42dcb. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index e899817093..b068fc5f15 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1501,8 +1501,8 @@ environments.") "0k9zkdyyzir3fvlbcfcqy17k28b51i20rpbjwlx2i1mwd2pw9cxc"))))))) (define-public guix-build-coordinator - (let ((commit "cbded42c284cca4ecaaebbf0a666cf89efc465a7") - (revision "88")) + (let ((commit "9c42dcb726fc925606b12695e195ae1dc7e28cc3") + (revision "89")) (package (name "guix-build-coordinator") (version (git-version "0" revision commit)) @@ -1513,7 +1513,7 @@ environments.") (commit commit))) (sha256 (base32 - "1z2wdf5h4dxq9g7a6j7nvmrsqcibrfm8nmkakqgz7ipcxyk0vzjx")) + "18m368rgmaiscmr1jlz77qkfw5fp4m8szgh90l6wbi9w68yfmr4n")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments From 54fd990973cf1fc6cfc50130f715761c5a2406f5 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 16 Sep 2023 09:15:43 +0100 Subject: [PATCH 237/440] gnu: rust-1.55: Remove i586-gnu from supported-systems. * gnu/packages/rust.scm (rust-1.55)[supported-systems]: Remove i586-gnu. --- gnu/packages/rust.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index 5cfdeffa81..38db41549a 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -544,6 +544,7 @@ ar = \"" binutils "/bin/ar" "\" (search-path-specification (variable "LIBRARY_PATH") (files '("lib" "lib64"))))) + (supported-systems (delete "i586-gnu" %supported-systems)) (synopsis "Compiler for the Rust programming language") (description "Rust is a systems programming language that provides memory safety and thread safety guarantees.") From 6a7cda20993aea36aa6e21e4a08b630f0d888d6d Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 16 Sep 2023 09:16:29 +0100 Subject: [PATCH 238/440] gnu: ecl: Remove i586-gnu from supported-systems. * gnu/packages/lisp.scm (ecl)[supported-systems]: Remove i586-gnu. --- gnu/packages/lisp.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index 6f425a6e4a..ef30f0087c 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -346,6 +346,7 @@ interface to the Tk widget system.") (files '("etc"))))) (home-page "https://ecl.common-lisp.dev/") (synopsis "Embeddable Common Lisp") + (supported-systems (delete "i586-gnu" %supported-systems)) (description "ECL is an implementation of the Common Lisp language as defined by the ANSI X3J13 specification. Its most relevant features are: a bytecode compiler and interpreter, being able to compile Common Lisp with any From bd6c377ca0e337aa26899b88f82539edb5aaedd0 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 16 Sep 2023 09:16:54 +0100 Subject: [PATCH 239/440] gnu: sbcl: Remove i586-gnu from supported-systems. * gnu/packages/lisp.scm (sbcl)[supported-systems]: Remove i586-gnu. --- gnu/packages/lisp.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index ef30f0087c..7abdbc8b6c 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -669,6 +669,7 @@ an interpreter, a compiler, a debugger, and much more.") (variable "XDG_CONFIG_DIRS") (files '("etc"))))) (home-page "https://www.sbcl.org/") + (supported-systems (delete "i586-gnu" %supported-systems)) (synopsis "Common Lisp implementation") (description "Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. In addition to the compiler and runtime system for ANSI Common From eeec8371890fc95c60112da299dde78b21c948c2 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 16 Sep 2023 09:18:34 +0100 Subject: [PATCH 240/440] gnu: bffe: Update to 0-2.722c37e. * gnu/packages/package-management.scm (bffe): Update to 0-2.722c37e. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index b068fc5f15..cbda40f78b 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -962,8 +962,8 @@ transactions from C or Python.") (license license:gpl2+))) (define-public bffe - (let ((commit "634d3444c094dd594bdf2b15b9a71055462ae676") - (revision "1")) + (let ((commit "722c37ec8a23835edfc85cba3d89868592a2ed2d") + (revision "2")) (package (name "bffe") (version (git-version "0" revision commit)) @@ -974,7 +974,7 @@ transactions from C or Python.") (commit commit))) (sha256 (base32 - "0z13hyaq6bs2j3hnr7ys2vsyx2554zy69ka21savywx0ci3hhfk3")) + "05i4awyirp440pk4vwa0sf46gi801zv839qm1i2z7jipm1xfwaxx")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs From d0e3fd2dc42c3bcba96fd8e4256b1283d589d7d9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 241/440] gnu: evdi: Update to 1.14.1. * gnu/packages/linux.scm (evdi): Update to 1.14.1. [source]: Use a Git tag. Remove patch. * gnu/packages/patches/evdi-fix-build-with-linux-6.2.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/linux.scm | 23 +++--- .../evdi-fix-build-with-linux-6.2.patch | 72 ------------------- 3 files changed, 11 insertions(+), 85 deletions(-) delete mode 100644 gnu/packages/patches/evdi-fix-build-with-linux-6.2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8862fbfbb9..c52917a4c5 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1120,7 +1120,6 @@ dist_patch_DATA = \ %D%/packages/patches/esmini-use-pkgconfig.patch \ %D%/packages/patches/esmtp-add-lesmtp.patch \ %D%/packages/patches/eudev-rules-directory.patch \ - %D%/packages/patches/evdi-fix-build-with-linux-6.2.patch \ %D%/packages/patches/exercism-disable-self-update.patch \ %D%/packages/patches/extempore-unbundle-external-dependencies.patch \ %D%/packages/patches/extundelete-e2fsprogs-1.44.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 51147406ec..73fa52e487 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1548,20 +1548,19 @@ is also needed for the @code{tuxedo-control-center} (short tcc) package.") (define-public evdi (package (name "evdi") - (version "1.12.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DisplayLink/evdi") - (commit "bdc258b25df4d00f222fde0e3c5003bf88ef17b5"))) - (file-name (git-file-name name version)) - (patches (search-patches "evdi-fix-build-with-linux-6.2.patch")) - (sha256 - (base32 - "1yi7mbyvxm9lsx6i1xbwp2bihwgzhwxkydk1kbngw5a5kw9azpws")))) + (version "1.14.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DisplayLink/evdi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vfbph6bdb206zgdp0bvpqck2zvkx1367xdxbavv41qsmgkxhvbs")))) (build-system linux-module-build-system) (arguments - (list #:tests? #f ;no test suite + (list #:tests? #f ;no test suite #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ diff --git a/gnu/packages/patches/evdi-fix-build-with-linux-6.2.patch b/gnu/packages/patches/evdi-fix-build-with-linux-6.2.patch deleted file mode 100644 index 0c53cd2ef7..0000000000 --- a/gnu/packages/patches/evdi-fix-build-with-linux-6.2.patch +++ /dev/null @@ -1,72 +0,0 @@ -Fix the build with Linux 6.2: - -https://github.com/DisplayLink/evdi/issues/402 - -Patch copied from upstream pull request: - -https://github.com/DisplayLink/evdi/pull/401 - -From a90ecd5f0f09e976e4b8784fa16b92804138b1bd Mon Sep 17 00:00:00 2001 -From: listout -Date: Wed, 22 Feb 2023 13:09:40 +0530 -Subject: [PATCH] Original patch was suggested by Crashdummyy. - -Since commit 9877d8f6bc374912b08dfe862cddbb78b395a5ef -feild fbdev has been renamed to info in struct drm_fb_helper. - -Fixes: https://github.com/DisplayLink/evdi/issues/402 -Fixes: https://github.com/DisplayLink/evdi/issues/394 -Fixes: https://github.com/DisplayLink/evdi/issues/384 -Signed-off-by: listout ---- - module/evdi_fb.c | 16 ++++++++++++++++ - 1 file changed, 16 insertions(+) - -diff --git a/module/evdi_fb.c b/module/evdi_fb.c -index 6b367fe8..f5de81f1 100644 ---- a/module/evdi_fb.c -+++ b/module/evdi_fb.c -@@ -405,7 +405,11 @@ static int evdifb_create(struct drm_fb_helper *helper, - fb = &efbdev->efb.base; - - efbdev->helper.fb = fb; -+#if KERNEL_VERSION(6, 2, 0) <= LINUX_VERSION_CODE -+ efbdev->helper.info = info; -+#else - efbdev->helper.fbdev = info; -+#endif - - strcpy(info->fix.id, "evdidrmfb"); - -@@ -459,8 +463,13 @@ static void evdi_fbdev_destroy(__always_unused struct drm_device *dev, - { - struct fb_info *info; - -+#if KERNEL_VERSION(6, 2, 0) <= LINUX_VERSION_CODE -+ if (efbdev->helper.info) { -+ info = efbdev->helper.info; -+#else - if (efbdev->helper.fbdev) { - info = efbdev->helper.fbdev; -+#endif - unregister_framebuffer(info); - if (info->cmap.len) - fb_dealloc_cmap(&info->cmap); -@@ -537,10 +546,17 @@ void evdi_fbdev_unplug(struct drm_device *dev) - return; - - efbdev = evdi->fbdev; -+#if KERNEL_VERSION(6, 2, 0) <= LINUX_VERSION_CODE -+ if (efbdev->helper.info) { -+ struct fb_info *info; -+ -+ info = efbdev->helper.info; -+#else - if (efbdev->helper.fbdev) { - struct fb_info *info; - - info = efbdev->helper.fbdev; -+#endif - #if KERNEL_VERSION(5, 6, 0) <= LINUX_VERSION_CODE || defined(EL8) - unregister_framebuffer(info); - #else From 6f9d658e63ab3d3e57d330d226bb5d35c66ef0eb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 242/440] gnu: libevdi: Update to 1.14.1. * gnu/packages/linux.scm (libevdi): Update to 1.14.1. [source]: Use a Git tag. --- gnu/packages/linux.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 73fa52e487..8f420d0178 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9977,20 +9977,20 @@ libraries are found or why they cannot be located.") (define-public libevdi (package (name "libevdi") - (version "1.12.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DisplayLink/evdi") - (commit "bdc258b25df4d00f222fde0e3c5003bf88ef17b5"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1yi7mbyvxm9lsx6i1xbwp2bihwgzhwxkydk1kbngw5a5kw9azpws")))) + (version "1.14.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DisplayLink/evdi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vfbph6bdb206zgdp0bvpqck2zvkx1367xdxbavv41qsmgkxhvbs")))) (build-system gnu-build-system) (inputs (list libdrm)) (arguments - (list #:tests? #f ;no test suite + (list #:tests? #f ;no test suite #:make-flags #~'("CC=gcc") #:phases #~(modify-phases %standard-phases (delete 'configure) From c507f15d48b32af5e9860f55f751fe626732929c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 243/440] gnu: libevdi: Inherit from evdi. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (libevdi)[inherit]: …from evdi. [version, source, home-page]: Likewise. --- gnu/packages/linux.scm | 64 ++++++++++++++++++------------------------ 1 file changed, 27 insertions(+), 37 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8f420d0178..e1b6bebc54 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1548,7 +1548,7 @@ is also needed for the @code{tuxedo-control-center} (short tcc) package.") (define-public evdi (package (name "evdi") - (version "1.14.1") + (version "1.14.1") ;inherited by libevdi (source (origin (method git-fetch) @@ -1573,6 +1573,32 @@ that enables management of multiple screens, allowing user-space programs to take control over what happens with the image.") (license license:gpl2))) +(define-public libevdi + (package + (inherit evdi) + (name "libevdi") + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;no test suite + #:make-flags #~'("CC=gcc") + #:phases #~(modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'chdir + (lambda _ + (chdir "library"))) + (replace 'install + (lambda* _ + (let* ((lib (string-append #$output "/lib"))) + (mkdir-p lib) + (install-file "libevdi.so" lib))))))) + (inputs (list libdrm)) + (synopsis "User-space EVDI library") + (description + "Libevdi is a library that gives applications easy access to +@acronym{EVDI, Extensible Virtual Display Interface} devices on +various operating systems.") + (license license:lgpl2.1))) + (define-public ec (package (name "ec") @@ -9974,42 +10000,6 @@ system.") libraries are found or why they cannot be located.") (license license:expat))) -(define-public libevdi - (package - (name "libevdi") - (version "1.14.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DisplayLink/evdi") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0vfbph6bdb206zgdp0bvpqck2zvkx1367xdxbavv41qsmgkxhvbs")))) - (build-system gnu-build-system) - (inputs (list libdrm)) - (arguments - (list #:tests? #f ;no test suite - #:make-flags #~'("CC=gcc") - #:phases #~(modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'chdir - (lambda _ - (chdir "library"))) - (replace 'install - (lambda* _ - (let* ((lib (string-append #$output "/lib"))) - (mkdir-p lib) - (install-file "libevdi.so" lib))))))) - (home-page "https://github.com/DisplayLink/evdi") - (synopsis "User-space EVDI library") - (description - "Libevdi is a library that gives applications easy access to -@acronym{EVDI, Extensible Virtual Display Interface} devices on -various operating systems.") - (license license:lgpl2.1))) - (define-public touchegg (package (name "touchegg") From 012d068354f555b191e5ebb4b28941b76c13fd38 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 244/440] gnu: evdi: Expand description. * gnu/packages/linux.scm (evdi)[synopsis, description]: Expand. --- gnu/packages/linux.scm | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index e1b6bebc54..5df7fbf982 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1566,11 +1566,18 @@ is also needed for the @code{tuxedo-control-center} (short tcc) package.") (lambda _ (chdir "module")))))) (home-page "https://github.com/DisplayLink/evdi") - (synopsis "EVDI Linux kernel module") + (synopsis + "@acronym{EVDI, Extensible Virtual Display Interface} Linux kernel module") (description - "The @acronym{EVDI, Extensible Virtual Display Interface} is a Linux kernel module -that enables management of multiple screens, allowing user-space programs to -take control over what happens with the image.") + "The @acronym{EVDI, Extensible Virtual Display Interface} is a Linux kernel +module that enables management of multiple screens, allowing user-space programs +to take control over what happens with the image. It is essentially a virtual +display for which applications using the @code{libevdi} library can add, remove, +and receive screen updates. + +The EVDI driver uses the standard Linux @acronym{DRM, Direct Rendering Manager}. +Its displays can be controlled by standard tools such as @command{xrandr} and +display settings applets in graphical environments") (license license:gpl2))) (define-public libevdi From c5657608c6eded81dd064271690a507118342328 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 245/440] gnu: libevdi: Expand description. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (libevdi)[synopsis]: Use @acronym. [description]: Replace ‘on various operating systems’, which is not guaranteed, with something that is. --- gnu/packages/linux.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5df7fbf982..a8856fe965 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1599,11 +1599,12 @@ display settings applets in graphical environments") (mkdir-p lib) (install-file "libevdi.so" lib))))))) (inputs (list libdrm)) - (synopsis "User-space EVDI library") + (synopsis + "@acronym{EVDI, Extensible Virtual Display Interface} user-space library") (description "Libevdi is a library that gives applications easy access to -@acronym{EVDI, Extensible Virtual Display Interface} devices on -various operating systems.") +@acronym{EVDI, Extensible Virtual Display Interface} devices provided by the +@code{evdi} driver package. ") (license license:lgpl2.1))) (define-public ec From 128ddcda76ee801257ba0d7c9ca58c191e3fb7fc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 246/440] gnu: libevdi: Fix cross-compilation. * gnu/packages/linux.scm (libevdi)[arguments]: Use CC-FOR-TARGET. --- gnu/packages/linux.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a8856fe965..8ce44ab2d4 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1587,7 +1587,8 @@ display settings applets in graphical environments") (build-system gnu-build-system) (arguments (list #:tests? #f ;no test suite - #:make-flags #~'("CC=gcc") + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target))) #:phases #~(modify-phases %standard-phases (delete 'configure) (add-after 'unpack 'chdir From b7ed26b1a7846299f03aab2bbaa7b89dadd01c8e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 247/440] gnu: bfs: Update to 3.0.2. * gnu/packages/admin.scm (bfs): Update to 3.0.2. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 1b2324bfc7..50cfe0c628 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -5995,7 +5995,7 @@ Discover other RouterOS devices or @command{mactelnetd} hosts. (define-public bfs (package (name "bfs") - (version "3.0.1") + (version "3.0.2") (source (origin (method git-fetch) (uri (git-reference @@ -6004,7 +6004,7 @@ Discover other RouterOS devices or @command{mactelnetd} hosts. (file-name (git-file-name name version)) (sha256 (base32 - "1ffma9p82bl0ai4h439cnhvcyyy8x593m27xlf16gsg6knpldm58")))) + "055qn2bhnyk9k96w8aviz7v4wip9hwsv7ak1m3yygm1x3fhdyhyz")))) (build-system gnu-build-system) (arguments (list #:make-flags #~(list (string-append "CC=" From f4be30e3b9b350856637a9a816c6d6acdd520cbd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 248/440] gnu: dmidecode: Update to 3.5. * gnu/packages/admin.scm (dmidecode): Update to 3.5. --- gnu/packages/admin.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 50cfe0c628..5a69f2051d 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2442,14 +2442,14 @@ network, which causes enabled computers to power on.") (define-public dmidecode (package (name "dmidecode") - (version "3.4") + (version "3.5") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/dmidecode/dmidecode-" version ".tar.xz")) (sha256 - (base32 "04i2ahvqinkrnzfsbswplv9wff36xf9b3snvriwrjz26v18sijs3")))) + (base32 "0wy0khw02sr59f43fdahh6as1xc3jv7n8abj59p1j9cfxqsngmvr")))) (build-system gnu-build-system) (arguments (list #:tests? #f ; no 'check' target @@ -2458,7 +2458,7 @@ network, which causes enabled computers to power on.") (string-append "prefix=" #$output)) #:phases #~(modify-phases %standard-phases - (delete 'configure)))) ; no configure script + (delete 'configure)))) ; no configure script (home-page "https://www.nongnu.org/dmidecode/") (synopsis "Read hardware information from the BIOS") (description From 721030e1e808d509193e21cb09c94270c6aba5f9 Mon Sep 17 00:00:00 2001 From: mikadoZero Date: Tue, 21 Mar 2023 19:23:20 +0000 Subject: [PATCH 249/440] gnu: psmisc: Make description more informative. The text for the description is taken from the psmisc README. * gnu/packages/linux.scm (psmisc)[description]: Make description more informative. Co-authored-by: Bruno Victal Co-authored-by: Tobias Geerinckx-Rice Signed-off-by: Tobias Geerinckx-Rice f psmisc desc --- gnu/packages/linux.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8ce44ab2d4..1d34cf8ae6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2108,9 +2108,15 @@ deviation, and minimum and maximum values. It can show a nice histogram too.") (home-page "https://gitlab.com/psmisc/psmisc") (synopsis "Small utilities that use the proc file system") (description - "This PSmisc package is a set of some small useful utilities that -use the proc file system. We're not about changing the world, but -providing the system administrator with some help in common tasks.") + "psmisc is a set of small utilities that use the proc file system. +@itemize @bullet +@item @command{fuser} identifies processes using files or sockets; +@item @command{killall} kills processes by name; +@item @command{prtstat} prints statistics of a process; +@item @command{pslog} prints the log file(s) of a process; +@item @command{pstree} shows the currently running processes as a tree; +@item @command{peekfd} shows the data travelling over a file descriptor. +@end itemize") (license license:gpl2+))) (define-public util-linux From 32b4f59433df620ab8f4b9a6c523f8ef9500d75d Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Tue, 21 Mar 2023 19:23:21 +0000 Subject: [PATCH 250/440] gnu: psmisc: Use G-Expressions. * gnu/packages/linux.scm (psmisc): Use G-Expressions. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/linux.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 1d34cf8ae6..9a49c090aa 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2098,12 +2098,12 @@ deviation, and minimum and maximum values. It can show a nice histogram too.") (base32 "12z5786dnf37n8wvv73wdcqp3nvsqzhwdk3ajna0mag4yz1fqdyw")))) (build-system gnu-build-system) (arguments - `(,@(if (%current-target-system) - '(#:configure-flags - (list - "ac_cv_func_malloc_0_nonnull=yes" - "ac_cv_func_realloc_0_nonnull=yes")) - '()))) + (list + #:configure-flags + (if (%current-target-system) + #~(list "ac_cv_func_malloc_0_nonnull=yes" + "ac_cv_func_realloc_0_nonnull=yes") + #~'()))) (inputs (list ncurses)) (home-page "https://gitlab.com/psmisc/psmisc") (synopsis "Small utilities that use the proc file system") From f2cfb4a85c82882c571274573fd7ff646d380b63 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Sat, 24 Jun 2023 15:17:42 +0200 Subject: [PATCH 251/440] locale: Set %default-locale-definitions to glibc/hurd on the Hurd. * gnu/system/locale.scm (%default-locale-libcs): Use only glib/hurd when building on the Hurd. --- gnu/system/locale.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/system/locale.scm b/gnu/system/locale.scm index 6895b209dc..bc572baeb9 100644 --- a/gnu/system/locale.scm +++ b/gnu/system/locale.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014-2017, 2019-2021, 2023 Ludovic Courtès ;;; Copyright © 2018 Mark H Weaver +;;; Copyright © 2023 Janneke Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -147,7 +148,9 @@ data format changes between libc versions." (define %default-locale-libcs ;; The libcs for which we build locales by default. - (list glibc-2.33 glibc)) + (if (system-hurd?) + (list glibc/hurd) + (list glibc-2.33 glibc))) (define %default-locale-definitions ;; Arbitrary set of locales that are built by default. They are here mostly From 64929be426f7f5fd17ee718da631aff73c7bbe51 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Wed, 14 Jun 2023 12:14:54 +0200 Subject: [PATCH 252/440] system: hurd: Add procps to %base-packages/hurd. * gnu/system/hurd.scm (%base-packages/hurd): Add procps. --- gnu/system/hurd.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/system/hurd.scm b/gnu/system/hurd.scm index 22dafae622..5f3538663d 100644 --- a/gnu/system/hurd.scm +++ b/gnu/system/hurd.scm @@ -34,6 +34,7 @@ #:use-module (gnu packages guile-xyz) #:use-module (gnu packages hurd) #:use-module (gnu packages less) + #:use-module (gnu packages linux) #:use-module (gnu packages texinfo) #:use-module (gnu services) #:use-module (gnu services base) @@ -71,7 +72,7 @@ (list shepherd-0.8 hurd netdde bash coreutils file findutils grep sed diffutils patch gawk tar gzip bzip2 xz lzip guile-3.0-latest guile-colorized guile-readline - net-base inetutils less shadow sudo which + net-base inetutils less procps shadow sudo which info-reader)) (define %base-services/hurd From bd303443be97c5aa5f8696f6f1ecc5e40b919874 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Sat, 16 Sep 2023 15:15:53 +0200 Subject: [PATCH 253/440] system: hurd: Add nss-certs to %base-packages/hurd. This fixes the recently added "rewrite-url, to-version specified" test. * gnu/system/hurd.scm (%base-packages/hurd): Add nss-certs. --- gnu/system/hurd.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/system/hurd.scm b/gnu/system/hurd.scm index 5f3538663d..ec81217330 100644 --- a/gnu/system/hurd.scm +++ b/gnu/system/hurd.scm @@ -26,6 +26,7 @@ #:use-module (gnu packages admin) #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages certs) #:use-module (gnu packages compression) #:use-module (gnu packages cross-base) #:use-module (gnu packages file) @@ -72,7 +73,7 @@ (list shepherd-0.8 hurd netdde bash coreutils file findutils grep sed diffutils patch gawk tar gzip bzip2 xz lzip guile-3.0-latest guile-colorized guile-readline - net-base inetutils less procps shadow sudo which + net-base nss-certs inetutils less procps shadow sudo which info-reader)) (define %base-services/hurd From 41df5c5289c970b40a002a32dcfdcb61ddc5a2f5 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Sat, 16 Sep 2023 15:16:59 +0200 Subject: [PATCH 254/440] system: hurd: Override locale-libcs harder. This really removes the locale-2.33 dependency running `guix system build bare-hurd.tmpl' on the Hurd, that somehow still managed to leak-in? * gnu/system/hurd.scm (%base-packages/hurd)[locale-libcs]: New field. --- gnu/system/hurd.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/system/hurd.scm b/gnu/system/hurd.scm index ec81217330..3b138bef65 100644 --- a/gnu/system/hurd.scm +++ b/gnu/system/hurd.scm @@ -129,6 +129,7 @@ (file-systems '()) (packages %base-packages/hurd) (timezone "GNUrope") + (locale-libcs (list glibc/hurd)) (name-service-switch #f) (essential-services (hurd-default-essential-services this-operating-system)) (setuid-programs %setuid-programs/hurd))) From df174ed4467ca30ade37678c1406196ab1e22fe4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 255/440] gnu: nmon: Update to 16p. * gnu/packages/admin.scm (nmon): Update to 16p. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 5a69f2051d..e4d2b6a824 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1271,13 +1271,13 @@ IPv6, proxies, and Unix sockets.") (define-public nmon (package (name "nmon") - (version "16n") + (version "16p") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/nmon/lmon" version ".c")) (sha256 - (base32 "1wpm2f30414b87kpbr9hbidblr5cmfby5skwqd0fkpi5v712q0f0")))) + (base32 "0akbkv70zffdmc5p51r02rlxd8b3jvkgl64rjsd29qr5cxgh9ijx")))) (build-system gnu-build-system) (arguments (list #:tests? #f ; no test suite From 39db6489e8e7a6dc0e37c1d23345753a5cdf5cab Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 256/440] gnu: inxi-minimal: Update to 3.3.29-1. * gnu/packages/admin.scm (inxi-minimal): Update to 3.3.29-1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index e4d2b6a824..0cf38bed9a 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4496,7 +4496,7 @@ Python loading in HPC environments.") (let ((real-name "inxi")) (package (name "inxi-minimal") - (version "3.3.28-1") + (version "3.3.29-1") (source (origin (method git-fetch) @@ -4505,7 +4505,7 @@ Python loading in HPC environments.") (commit version))) (file-name (git-file-name real-name version)) (sha256 - (base32 "0h00dasmw3crci8kwpa503jljy3c5r2fsdhpbbczhsgznhlr8pbi")))) + (base32 "05z0vydfmkva61kj14p6jxy7dr8qwd024a7nn8pib57q4qnjm4r8")))) (build-system trivial-build-system) (inputs (list bash-minimal From 4c4ff2e1f077786d85c47ceeec10340a864e17f1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 257/440] gnu: vsftpd: Fix build with recent OpenSSL. * gnu/packages/ftp.scm (vsftpd)[arguments]: Add "-Wno-deprecated-declarations" to CFLAGS. Reported by helioscultist in #guix. --- gnu/packages/code.scm | 2 +- gnu/packages/ftp.scm | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index b716f32599..497b3bfd75 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -893,7 +893,7 @@ the C, C++, C++/CLI, Objective‑C, C#, and Java programming languages.") (define-public indent (package (name "indent") - (version "2.2.12") + (version "2.2.13") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/indent/indent-" version diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 5edbc412ea..80e346d658 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -266,6 +266,9 @@ directory comparison and more.") (arguments `(#:make-flags (list (string-append "CC=" ,(cc-for-target)) + ;; Work around, e.g., “ssl.c:149:7: error: ‘EC_KEY_free’ is + ;; deprecated: Since OpenSSL 3.0 [-Werror=deprecated-declarations]” + "CFLAGS=-Wno-deprecated-declarations" ;; vsf_findlibs.sh looks only for hard-coded {/usr,}/lib file names ;; that will never exist on Guix. Manage libraries ourselves. "LDFLAGS=-lcap -lpam" From 04fad62acdcffa50c18528ce71f015907b9eb558 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 258/440] gnu: indent: Update to 2.2.13. * gnu/packages/code.scm (indent): Finish update to 2.2.13, partially pushed in commit 4c4ff2e1f077786d85c47ceeec10340a864e17f1. --- gnu/packages/code.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 497b3bfd75..a982e111e9 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -899,7 +899,7 @@ the C, C++, C++/CLI, Objective‑C, C#, and Java programming languages.") (uri (string-append "mirror://gnu/indent/indent-" version ".tar.gz")) (sha256 - (base32 "12xvcd16cwilzglv9h7sgh4h1qqjd1h8s48ji2dla58m4706hzg7")))) + (base32 "15c0ayp9rib7hzvrcxm5ijs0mpagw5y8kf5w0jr9fryfqi7n6r4y")))) (build-system gnu-build-system) (arguments `(#:phases From e4fdf062dcd1d7ad7ab8b0d50119a315d3df3095 Mon Sep 17 00:00:00 2001 From: Liliana Marie Prikler Date: Fri, 15 Sep 2023 21:53:27 +0200 Subject: [PATCH 259/440] gnu: python-pyxel: Update to 1.4.3-2.be75b72. * gnu/packages/game-development.scm (python-pyxel): Update to 1.4.3-2.be75b72. [version]: Use git-version even though it is a release. [source]: Use commit. : Adjust accordingly. --- gnu/packages/game-development.scm | 96 +++++++++++++++++-------------- 1 file changed, 52 insertions(+), 44 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index c25dadb39e..215c12e2d9 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1646,53 +1646,61 @@ games.") (license license:expat))) (define-public python-pyxel - (package - (name "python-pyxel") - (version "1.4.3") - (source - (origin - (method git-fetch) - (uri - (git-reference - (url "https://github.com/kitao/pyxel") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0bwsgb5yq5s479cnf046v379zsn5ybp5195kbfvzr9l11qbaicm9")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "pyxel/core/bin"))))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; "Tests" are actually example programs that never halt. - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-build-files - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "setup.py" - (("\"pyxel\\.core\\.bin\\.(.*)\"," all arch) - (if (string=? arch "linux") - all - ""))) - (substitute* "pyxel/core/Makefile" - (("`sdl2-config") - (string-append "`sdl2-config --prefix=" - (assoc-ref inputs "sdl2")))))) - (add-before 'build 'prebuild - (lambda _ - (invoke "make" "-C" "pyxel/core")))))) - (inputs - `(("gifsicle" ,gifsicle) - ("sdl2" ,(sdl-union (list sdl2 sdl2-image))))) - (home-page "https://github.com/kitao/pyxel") - (synopsis "Retro game engine for Python") - (description "Pyxel is a game engine inspired by retro gaming consoles. + ;; Note to updaters: Use commit and revision even if you're bumping + ;; to a release, as upstream is known to "reuse" tags. + ;; See for more information. + (let ((commit "be75b724cae9e10e56a82a5421f9dd65390f1a06") + (revision "2")) + (package + (name "python-pyxel") + ;; This is the latest version to not require Rust… + (version (git-version "1.4.3" revision commit)) + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/kitao/pyxel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03ch79cmh9fxvq6c2f3zc2snzczhqi2n01f254lsigckc7d5wz08")) + (modules '((guix build utils))) + (snippet + #~(begin + (substitute* "pyxel/__init__.py" + (("from collections import MutableSequence") + "from collections.abc import MutableSequence")))))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; "Tests" are actually example programs that never halt. + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-build-files + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "setup.py" + (("\"pyxel\\.core\\.bin\\.(.*)\"," all arch) + (if (string=? arch "linux") + all + ""))) + (substitute* "pyxel/core/Makefile" + (("`sdl2-config") + (string-append "`sdl2-config --prefix=" + (assoc-ref inputs "sdl2")))))) + (add-before 'build 'prebuild + (lambda _ + (invoke "make" "-C" "pyxel/core")))))) + (inputs + `(("gifsicle" ,gifsicle) + ("sdl2" ,(sdl-union (list sdl2 sdl2-image))))) + (home-page "https://github.com/kitao/pyxel") + (synopsis "Retro game engine for Python") + (description "Pyxel is a game engine inspired by retro gaming consoles. It has a fixed 16-color palette, can hold up to 3 image banks and 8 tilemaps (256x256 pixels each) and 4 sound channels with 64 definable sounds. It also comes with a built-in image and sound editor.") - (license license:expat))) + (license license:expat)))) (define-public grafx2 (package From 0dc83ce53b8bad8473c80689ba212d9f9bb712b3 Mon Sep 17 00:00:00 2001 From: raingloom Date: Sat, 16 Sep 2023 14:03:11 +0200 Subject: [PATCH 260/440] gnu: gnome-dictionary: Fix build. * gnu/packages/patches/gnome-dictionary-meson-i18n.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it here. * gnu/packages/gnome.scm (gnome-dictionary): Use it here. Signed-off-by: Liliana Marie Prikler Fixes: gnome-dictionary-40.0: fails configure --- gnu/local.mk | 1 + gnu/packages/gnome.scm | 4 +- .../patches/gnome-dictionary-meson-i18n.patch | 52 +++++++++++++++++++ 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/gnome-dictionary-meson-i18n.patch diff --git a/gnu/local.mk b/gnu/local.mk index c52917a4c5..672050723f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1306,6 +1306,7 @@ dist_patch_DATA = \ %D%/packages/patches/gnash-fix-giflib-version.patch \ %D%/packages/patches/gnome-2048-fix-positional-argument.patch \ %D%/packages/patches/gnome-control-center-libexecdir.patch \ + %D%/packages/patches/gnome-dictionary-meson-i18n.patch \ %D%/packages/patches/gnome-online-miners-tracker-3.patch \ %D%/packages/patches/gnome-settings-daemon-gc.patch \ %D%/packages/patches/gnome-session-support-elogind.patch \ diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 36fe1a80a1..908b5782b5 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -10497,7 +10497,9 @@ like automatic language detection, text-to-speech and clipboard buttons.") name "-" version ".tar.xz")) (sha256 (base32 - "1d8dhcfys788vv27v34i3s3x3jdvdi2kqn2a5p8c937a9hm0qr9f")))) + "1d8dhcfys788vv27v34i3s3x3jdvdi2kqn2a5p8c937a9hm0qr9f")) + (patches + (search-patches "gnome-dictionary-meson-i18n.patch")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t diff --git a/gnu/packages/patches/gnome-dictionary-meson-i18n.patch b/gnu/packages/patches/gnome-dictionary-meson-i18n.patch new file mode 100644 index 0000000000..fea45af69a --- /dev/null +++ b/gnu/packages/patches/gnome-dictionary-meson-i18n.patch @@ -0,0 +1,52 @@ +From 71933f6586475b36c70ef325373fe6d50c7a034f Mon Sep 17 00:00:00 2001 +From: Jan Beich +Date: Mon, 24 Jan 2022 11:13:54 +0000 +Subject: [PATCH] meson: drop unused argument for i18n.merge_file() + +Ignored in Meson < 0.60.0, deprecated since 0.60.1 and fatal since 0.61.0. + +data/appdata/meson.build:3:5: ERROR: Function does not take positional arguments. +data/meson.build:6:5: ERROR: Function does not take positional arguments. +data/meson.build:49:5: ERROR: Function does not take positional arguments. +--- + data/appdata/meson.build | 2 +- + data/meson.build | 4 ++-- + 2 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/data/appdata/meson.build b/data/appdata/meson.build +index 1dc4ed7..e44a58e 100644 +--- a/data/appdata/meson.build ++++ b/data/appdata/meson.build +@@ -1,6 +1,6 @@ + appdata_conf = configuration_data() + appdata_conf.set('application_id', application_id) +-i18n.merge_file('appdata', ++appdata_file = i18n.merge_file( + input: configure_file( + input: 'org.gnome.Dictionary.appdata.xml.in.in', + output: 'org.gnome.Dictionary.appdata.xml.in', +diff --git a/data/meson.build b/data/meson.build +index 660e6b8..7ec7251 100644 +--- a/data/meson.build ++++ b/data/meson.build +@@ -3,7 +3,7 @@ subdir('appdata') + desktop_conf = configuration_data() + desktop_conf.set('icon', application_id) + desktop_conf.set('application_id', application_id) +-i18n.merge_file('desktop', ++desktop_file = i18n.merge_file( + input: configure_file( + input: 'org.gnome.Dictionary.desktop.in.in', + output: 'org.gnome.Dictionary.desktop.in', +@@ -45,7 +45,7 @@ sources = [ + ] + + foreach s: sources +- i18n.merge_file('sources', ++ i18n.merge_file( + input: '@0@.in'.format(s), + output: s, + install: true, +-- +2.41.0 + From 6b4d305b192ea61d1d60a57779fe389ce1f62703 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 261/440] gnu: conky: Update to 1.19.4. * gnu/packages/conky.scm (conky): Update to 1.19.4. --- gnu/packages/conky.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index 54b525a04e..bd26cdd015 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -40,7 +40,7 @@ (package (name "conky") (home-page "https://github.com/brndnmtthws/conky") - (version "1.19.3") + (version "1.19.4") (source (origin (method git-fetch) @@ -49,7 +49,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "079s6icvcrryhj71qya4rnyc6pdjq488l0gjqrrblycgzppn1pas")))) + (base32 "03zzssdg1qdv83p4c3dbjgr0g1n0spc0ndk9bds1rd2n82i6g6sy")))) (build-system cmake-build-system) (arguments `(#:configure-flags From 6415fd680d35b51c82bbf69aa74032337873a82e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 262/440] gnu: libzen: Update to 0.4.41. * gnu/packages/cpp.scm (libzen): Update to 0.4.41. --- gnu/packages/cpp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 72f04b25a0..4ee7f375d7 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -298,7 +298,7 @@ various formats, including @code{json}.") (define-public libzen (package (name "libzen") - (version "0.4.40") + (version "0.4.41") (source (origin (method url-fetch) ;; Warning: This source has proved unreliable 1 time at least. @@ -309,7 +309,7 @@ various formats, including @code{json}.") "libzen_" version ".tar.bz2")) (sha256 (base32 - "17pnp5i1ppcxhxnfs9qlkzzy35h23pkdwhsgpbqdkf8lab2f4hsm")))) + "0b8yj3rmmcv2fn3b5bnchfkk82fy4w5446c70sxccvfa7myps8zb")))) (native-inputs (list autoconf automake libtool)) (build-system gnu-build-system) From d6381a2f16791c4f21bcce67891e6e5842af8e24 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 263/440] gnu: knot: Update to 3.3.1. * gnu/packages/dns.scm (knot): Update to 3.3.1. --- gnu/packages/dns.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 51e88e29bb..33715d6b19 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -844,7 +844,7 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "3.2.9") + (version "3.3.1") (source (origin (method git-fetch) @@ -853,7 +853,7 @@ Extensions} (DNSSEC).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1kxmplngnlpd6j9nbzq1c1z02ipd38ypnppy7frg5crn83phfbxm")) + (base32 "0l29809wcpx4q1d87539799c4mai0vvfkzkbmrba186mn47p3lsd")) (modules '((guix build utils))) (snippet '(begin @@ -863,9 +863,8 @@ Extensions} (DNSSEC).") ;; Remove bundled libraries to ensure we always use the system's. (with-directory-excursion "src/contrib" (for-each delete-file-recursively - (list "libbpf" - ;; TODO: package this for DoQ (‘QUIC’) support. - "libngtcp2"))))))) + ;; TODO: package libngtcp2 for DoQ (‘QUIC’) support. + '("libngtcp2"))))))) (build-system gnu-build-system) (outputs (list "out" "doc" "lib" "tools")) (arguments From 39a29fc4c180e16c78f78036a2986a26d1a883fc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 264/440] gnu: exfatprogs: Update to 1.2.1. * gnu/packages/file-systems.scm (exfatprogs): Update to 1.2.1. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index a500fdb708..ad4c078268 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -716,7 +716,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (define-public exfatprogs (package (name "exfatprogs") - (version "1.2.0") + (version "1.2.1") (source (origin (method git-fetch) @@ -725,7 +725,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "02a6178brikg12wl80h9qgxyhpm6mly0jnml0rs9phb7lkbv9kzh")))) + (base32 "1g5aqhjz0l58kvmis1j5b5qkn58hjs582f36ygiqkgxvp4njkny4")))) (build-system gnu-build-system) (arguments `(#:configure-flags From 952a0ce2800e4fe9165184151412858ed8d34760 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 265/440] gnu: exfat-utils: Update to 1.4.0. * gnu/packages/file-systems.scm (exfat-utils): Update to 1.4.0. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index ad4c078268..0d98e23e93 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -373,7 +373,7 @@ always possible.") (define-public exfat-utils (package (name "exfat-utils") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) @@ -381,7 +381,7 @@ always possible.") "https://github.com/relan/exfat/releases/download/v" version "/exfat-utils-" version ".tar.gz")) (sha256 - (base32 "0da8f8mm1sbwqp7prh78qk33xm0b8kk2d5is7mh2szlhgdxd1syz")))) + (base32 "0sdzflmwcxjjliq1yqhidy46kbkvj16kxrbrgsj0ci0hjgx7a594")))) (build-system gnu-build-system) (home-page "https://github.com/relan/exfat") (synopsis "Utilities to manipulate exFAT file systems") From ee17fdfe42daab9ef7849a2d204fc69179daf1bf Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Fri, 9 Jun 2023 12:44:14 -0300 Subject: [PATCH 266/440] gnu: python-typeguard: Add dependency on python-setuptools-scm. * gnu/packages/python-xyz.scm (python-typeguard)[native-inputs]: Add python-setuptools-scm. --- 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 2230310a03..dd3f987475 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24125,8 +24125,10 @@ based on the CPython 2.7 and 3.7 parsers.") ;; XXX: These fail when installed as a library: ;; https://github.com/agronholm/typeguard/issues/176 "not usefixtures and not test_cached_module"))))))) - (native-inputs - (list python-mypy python-pytest python-typing-extensions)) + (native-inputs (list python-mypy + python-pytest + python-setuptools-scm + python-typing-extensions)) (home-page "https://github.com/agronholm/typeguard") (synopsis "Run-time type checker for Python") (description From 70b8682eaa94b5a6517a8fe733eb599ca2a778e3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 29 Jul 2023 14:52:53 -0300 Subject: [PATCH 267/440] gnu: Add python-jaxtyping. * gnu/packages/machine-learning.scm (python-jaxtyping): New variable. --- gnu/packages/machine-learning.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fd0be8d500..92a60d1616 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -2060,6 +2060,31 @@ physics-informed learning. It includes implementations for the PINN MFNN (multifidelity neural network) algorithms.") (license license:lgpl2.1+))) +(define-public python-jaxtyping + (package + (name "python-jaxtyping") + (version "0.2.21") + (source (origin + (method url-fetch) + (uri (pypi-uri "jaxtyping" version)) + (sha256 + (base32 + "19qmsnbn4wv2jl99lpn622qs49mrfxmx8s9pr5y8izzgdjq1fvii")))) + (build-system pyproject-build-system) + ;; Tests require JAX, but JAX can't be packaged because it uses the Bazel + ;; build system. + (arguments (list #:tests? #f)) + (native-inputs (list python-hatchling)) + (propagated-inputs (list python-numpy python-typeguard + python-typing-extensions)) + (home-page "https://github.com/google/jaxtyping") + (synopsis + "Type annotations and runtime checking for JAX arrays and others") + (description "@code{jaxtyping} provides type annotations and runtime +checking for shape and dtype of JAX arrays, PyTorch, NumPy, TensorFlow, and +PyTrees.") + (license license:expat))) + ;; There have been no proper releases yet. (define-public kaldi (let ((commit "be22248e3a166d9ec52c78dac945f471e7c3a8aa") From c7bd5811da38509762609eb8dcae90ed9b610421 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 20 May 2023 21:46:03 -0300 Subject: [PATCH 268/440] gnu: Add python-linear-operator. * gnu/packages/machine-learning.scm (python-linear-operator): New variable. --- gnu/packages/machine-learning.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 92a60d1616..717c52345c 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -4571,6 +4571,32 @@ and Numpy.") inference.") (license license:asl2.0))) +(define-public python-linear-operator + (package + (name "python-linear-operator") + (version "0.5.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "linear_operator" version)) + (sha256 + (base32 + "03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-jaxtyping + python-pytorch + python-scipy + python-typeguard)) + (native-inputs (list python-flake8 + python-flake8-print + python-pytest + python-setuptools-scm + python-twine)) + (home-page "https://github.com/cornellius-gp/linear_operator/") + (synopsis "Linear operator implementation") + (description "LinearOperator is a PyTorch package for abstracting away the +linear algebra routines needed for structured matrices (or operators).") + (license license:expat))) + (define-public vosk-api (let* ((openfst openfst-for-vosk) (kaldi kaldi-for-vosk)) From 9b78699744b0c4c8af28820cc4f0d59b9d317ead Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 20 May 2023 21:48:47 -0300 Subject: [PATCH 269/440] gnu: Add python-gpytorch. * gnu/packages/machine-learning.scm (python-gpytorch): New variable. --- gnu/packages/machine-learning.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 717c52345c..f351586214 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -4597,6 +4597,37 @@ inference.") linear algebra routines needed for structured matrices (or operators).") (license license:expat))) +(define-public python-gpytorch + (package + (name "python-gpytorch") + (version "1.11") + (source (origin + (method url-fetch) + (uri (pypi-uri "gpytorch" version)) + (sha256 + (base32 + "0q17bml53vixk3cwj3p893809927hz81fprwsmxpxqv5i4mvgyvj")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags + ;; The error message in test_t_matmul_matrix suggests the error may + ;; be due to a bug in gpytorch. test_deprecated_methods fails with + ;; an AssertionError. + #~(list "-k" (string-append "not test_deprecated_methods" + " and not test_t_matmul_matrix")))) + (propagated-inputs (list python-linear-operator python-scikit-learn)) + (native-inputs (list python-coverage + python-flake8 + python-flake8-print + python-nbval + python-pytest + python-twine)) + (home-page "https://gpytorch.ai") + (synopsis "Implementation of Gaussian Processes in PyTorch") + (description + "GPyTorch is a Gaussian process library implemented using PyTorch.") + (license license:expat))) + (define-public vosk-api (let* ((openfst openfst-for-vosk) (kaldi kaldi-for-vosk)) From ed566a51de63c424bfee8ed1c8a8956d158ddccb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 270/440] gnu: dovecot: Update to 2.3.21. * gnu/packages/mail.scm (dovecot): Update to 2.3.21. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index ecaab1c7cd..c03b07ebf8 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1989,7 +1989,7 @@ facilities for checking incoming mail.") (package (name "dovecot") ;; Also update dovecot-pigeonhole when updating to a new minor version. - (version "2.3.20") + (version "2.3.21") (source (origin (method url-fetch) @@ -1997,7 +1997,7 @@ facilities for checking incoming mail.") (version-major+minor version) "/" "dovecot-" version ".tar.gz")) (sha256 - (base32 "0ll546dldhxqk8yr2jnfq0rag7vp9d9hz7gf6pgsnj41jvmk5a6a")) + (base32 "0bah6rn5ihczai8q50p6pqxwj73j21smib89ycp7q8qwly9i1c85")) (patches (search-patches "dovecot-opensslv3.patch")))) (build-system gnu-build-system) From 23f6e86bf2f953a4d500c3e88c29f10a228e656d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 271/440] gnu: dovecot-pigeonhole: Update to 0.5.21. * gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.21. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index c03b07ebf8..1562dde866 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -2059,7 +2059,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.") (let ((dovecot-version (version-major+minor (package-version dovecot)))) (package (name "dovecot-pigeonhole") - (version "0.5.20") + (version "0.5.21") (source (origin (method url-fetch) @@ -2067,7 +2067,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.") "https://pigeonhole.dovecot.org/releases/" dovecot-version "/" "dovecot-" dovecot-version "-pigeonhole-" version ".tar.gz")) (sha256 - (base32 "163wc5spzvy9pcpsbz3adl22h8f1krp21fh9mql16b7af14bscmf")) + (base32 "09zd7n6ljqaj3i3m6r1hn1vb1cjhy64040vji82i4rq7b4k1v9qw")) (modules '((guix build utils))) (snippet '(begin From 87fc604c2e2e0d461f56c8645d64e1425f016b38 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 272/440] gnu: mbuffer: Update to 20230301. * gnu/packages/networking.scm (mbuffer): Update to 20230301. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 1eb464673d..0726e4b808 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1194,7 +1194,7 @@ or server shell scripts with network connections.") (define-public mbuffer (package (name "mbuffer") - (version "20220418") + (version "20230301") (source (origin (method url-fetch) (uri (string-append @@ -1202,7 +1202,7 @@ or server shell scripts with network connections.") version ".tgz")) (sha256 (base32 - "1iq0lcl350r7qja7yyv911aay26d0dd8n0h33mfl84gzypwh2n3f")))) + "009d4m48yjidb91vdnrfv84nnd76n0i57g607llan3y0vq4n5xsk")))) (build-system gnu-build-system) (native-inputs (list which)) From 609de77184beedc0fffb3d31d8bb6cea87afea9e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 273/440] gnu: lldpd: Update to 1.0.17. * gnu/packages/networking.scm (lldpd): Update to 1.0.17. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 0726e4b808..383f28e793 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -4252,14 +4252,14 @@ cables.") (define-public lldpd (package (name "lldpd") - (version "1.0.16") + (version "1.0.17") (source (origin (method url-fetch) (uri (string-append "https://media.luffy.cx/files/lldpd/lldpd-" version ".tar.gz")) (sha256 - (base32 "1ab5hkgi2iwqpfw6xy2wxjhqmz6pnkynfkg85zm7r9kv1ijr3cz3")) + (base32 "1ki7c7ffys42s2wy5c94qriicgwx0wl9bm83xxkclasx2izifhwk")) (modules '((guix build utils))) (snippet '(begin From ef27d1cd1ee701cd61c76b76299d4138476f9e91 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 274/440] gnu: musl: Update to 1.2.4. * gnu/packages/musl.scm (musl): Update to 1.2.4. --- gnu/packages/musl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/musl.scm b/gnu/packages/musl.scm index d61d6b2461..dfd0e12186 100644 --- a/gnu/packages/musl.scm +++ b/gnu/packages/musl.scm @@ -28,14 +28,14 @@ (define-public musl (package (name "musl") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (string-append "https://www.musl-libc.org/releases/" "musl-" version ".tar.gz")) (sha256 (base32 - "196lrzw0qy5axiz9p5ay50q2mls8hbfckr4rw0klc7jjc9h0nnvx")))) + "0fgh2hhsbaksx7my6yiva4jqixi6hxwxx20ivb0afwjk7piyldbs")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; musl has no tests From 4d026e48702aa8e2c74b8ae1030dc9e4b75e57ca Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 275/440] gnu: synthv1: Update to 0.9.32. * gnu/packages/music.scm (synthv1): Update to 0.9.32. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 3f17a054ca..4482975487 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2371,7 +2371,7 @@ perform creative live mixes with digital music files.") (define-public synthv1 (package (name "synthv1") - (version "0.9.31") + (version "0.9.32") (source (origin (method url-fetch) (uri @@ -2379,7 +2379,7 @@ perform creative live mixes with digital music files.") "/synthv1-" version ".tar.gz")) (sha256 (base32 - "06yfiwnxdawyby63zqm1jv4ihi4fxzabpkba7v4d8lgwvhxa014k")))) + "1i76d4w2anccyp70vylxxrmqgf1i3znl98ag82wz8lxb5sh34i4x")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; there are no tests From 15fdb77682f52de622fe8050fbfe8e5ff0c5e191 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 276/440] gnu: drumkv1: Update to 0.9.32. * gnu/packages/music.scm (drumkv1): Update to 0.9.32. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 4482975487..8470468c60 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2403,7 +2403,7 @@ oscillators and stereo effects.") (define-public drumkv1 (package (name "drumkv1") - (version "0.9.31") + (version "0.9.32") (source (origin (method url-fetch) (uri @@ -2411,7 +2411,7 @@ oscillators and stereo effects.") "/drumkv1-" version ".tar.gz")) (sha256 (base32 - "0cw0lqxd4igkb25vlivbi0hamn33d26nl96mzm59cda158r0jayl")))) + "15csm09wjgzdkvy2wqq1jzq7b1m8zzchl5s8fb4ir5rg395jkxai")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; there are no tests From 575abe5f3f9f09501a4fbb9357452f338e20b628 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 277/440] gnu: samplv1: Update to 0.9.32. * gnu/packages/music.scm (samplv1): Update to 0.9.32. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 8470468c60..f4ae38aec0 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2436,7 +2436,7 @@ effects.") (define-public samplv1 (package (name "samplv1") - (version "0.9.31") + (version "0.9.32") (source (origin (method url-fetch) (uri @@ -2444,7 +2444,7 @@ effects.") "/samplv1-" version ".tar.gz")) (sha256 (base32 - "1jqblmb24vbnpm4a4wlvasz45h3zy00rrpf850yxaplyf0qb8klx")))) + "17w5m5sk8fcnnph1njz9sz031kk0aid8mhs64myc2jvpvwm5snlb")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; there are no tests From c2dff1f05e87c74c78d48925b900a3f546f89b0f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 278/440] gnu: padthv1: Update to 0.9.32. * gnu/packages/music.scm (padthv1): Update to 0.9.32. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index f4ae38aec0..c978392a1b 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2469,7 +2469,7 @@ effects.") (define-public padthv1 (package (name "padthv1") - (version "0.9.31") + (version "0.9.32") (source (origin (method url-fetch) (uri @@ -2477,7 +2477,7 @@ effects.") "/padthv1-" version ".tar.gz")) (sha256 (base32 - "1iqmjdxihil039c8g9kywd5dx3rd47ph2fs6f6kcyfwj9jz4aprh")))) + "0qpdyczgqblf3sxjkvxn2g8qyx1hm0pmiqhncncrijbaalazsp7m")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; there are no tests From fbc1be7705565c89b337520902c173852fe3f8d7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 279/440] gnu: qtractor: Update to 0.9.35. * gnu/packages/music.scm (qtractor): Update to 0.9.35. --- gnu/packages/music.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index c978392a1b..cfa37d69af 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3482,14 +3482,14 @@ from the command line.") (define-public qtractor (package (name "qtractor") - (version "0.9.34") + (version "0.9.35") (source (origin (method url-fetch) (uri (string-append "https://downloads.sourceforge.net/qtractor/" "qtractor-" version ".tar.gz")) (sha256 (base32 - "0w6g51jhj9c72j6qjjkjhiq0vwklb6q4cr3xgj4mzp0iw279hbjz")))) + "1v3w8x9dfqldfa8gjxxszzclnhqlgyanpr7b4dhva68qyxmp4m7v")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no "check" target From 8c833d0bc7be456ca20038af50f53a684ca7c5b4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 280/440] gnu: libdiscid: Update to 0.6.4. * gnu/packages/music.scm (libdiscid): Update to 0.6.4. --- gnu/packages/music.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index cfa37d69af..a26719aec2 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5517,7 +5517,7 @@ for the DSSI Soft Synth Interface. A brief list of features: (define-public libdiscid (package (name "libdiscid") - (version "0.6.2") + (version "0.6.4") (source (origin (method url-fetch) @@ -5525,8 +5525,7 @@ for the DSSI Soft Synth Interface. A brief list of features: "http://ftp.musicbrainz.org/pub/musicbrainz/libdiscid/libdiscid-" version ".tar.gz")) (sha256 - (base32 - "1f9irlj3dpb5gyfdnb1m4skbjvx4d4hwiz2152f83m0d9jn47r7r")))) + (base32 "10mj1hwv1598nsi7jw5di0pfcwk36g4rr6kl7gi45m7ak8f8ypnx")))) (arguments `(#:test-target "check")) (build-system cmake-build-system) (home-page "https://musicbrainz.org/doc/libdiscid") From b2a2d922801deb58221dfdb691ddb6eec131caff Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 281/440] gnu: fuse-overlayfs: Update to 1.13. * gnu/packages/file-systems.scm (fuse-overlayfs): Update to 1.13. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 0d98e23e93..33cea9176a 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -1922,7 +1922,7 @@ and rewritable media that wears out (DVD/CD-RW).") (define-public fuse-overlayfs (package (name "fuse-overlayfs") - (version "1.10") + (version "1.13") (source (origin (method git-fetch) (uri (git-reference @@ -1930,7 +1930,7 @@ and rewritable media that wears out (DVD/CD-RW).") (commit (string-append "v" version)))) (sha256 (base32 - "085hrz0nrdsjfjci0z2qfyqrydn8wwdp790dx2x67hwdw1kib3wp")) + "03gqb4czswqhx6zrv9jj88mf3mczk4m7azcjgr785c2lmga442ly")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs From b9efcd5a5d6ff0286504152b371d4f8acfca70ed Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 282/440] gnu: fsarchiver: Update to 0.8.7. * gnu/packages/file-systems.scm (fsarchiver): Update to 0.8.7. --- gnu/packages/file-systems.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 33cea9176a..e97013dce3 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -394,7 +394,7 @@ ones.") (define-public fsarchiver (package (name "fsarchiver") - (version "0.8.6") + (version "0.8.7") (source (origin (method git-fetch) @@ -404,7 +404,7 @@ ones.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1ry2sdkfbg4bwcldk42g1i3wa3z4pr9yh9dil6ilhwcvhqiw41zc")))) + (base32 "1vy8ay0fn32i298bx9scqghi7xm9z2101zxk5xshbrkl00b2m4nm")))) (build-system gnu-build-system) (native-inputs (list autoconf automake pkg-config)) From 655686a2bdb8f5880f1239e8a8267442f73363c0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 283/440] gnu: dstask: Update to 0.26. * gnu/packages/task-management.scm (dstask): Update to 0.26. --- gnu/packages/task-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/task-management.scm b/gnu/packages/task-management.scm index e4dd488cb6..f9221f8483 100644 --- a/gnu/packages/task-management.scm +++ b/gnu/packages/task-management.scm @@ -271,7 +271,7 @@ time to a logfile.") (define-public dstask (package (name "dstask") - (version "0.25") + (version "0.26") (source (origin (method git-fetch) @@ -280,7 +280,7 @@ time to a logfile.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1m83zc2zqvpcbjng92jvlnk0biw4krv12wjvjas66jbbk3sjghcy")))) + (base32 "10q0524gfc76k0v9cy0j60cbgmmwkpnkbvl6w0pn1j5y690514f5")))) (build-system go-build-system) (arguments `(#:import-path "github.com/naggie/dstask" From 2749c21588239926635b35542a9c8f5e1ee5c070 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 284/440] gnu: foot: Update to 1.15.3. * gnu/packages/terminals.scm (foot): Update to 1.15.3. --- gnu/packages/terminals.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index a67ec97859..ee18326204 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -833,7 +833,7 @@ eye-candy, customizable, and reasonably lightweight.") (define-public foot (package (name "foot") - (version "1.15.2") + (version "1.15.3") (home-page "https://codeberg.org/dnkl/foot") (source (origin (method git-fetch) @@ -841,7 +841,7 @@ eye-candy, customizable, and reasonably lightweight.") (file-name (git-file-name name version)) (sha256 (base32 - "1iz9l01fpryc335pb0c3qi67fmmfplizv5pbc9s578mxl5j9dxg4")))) + "1a224i2i7qk170kf2rzyxqcv3lnx9f548lwa37jgjr7i339x4zwf")))) (build-system meson-build-system) (arguments `(;; Using a "release" build is recommended both for performance, and From 1a7d730fe68b5b845ba412f4f7ee64fce727ecba Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 285/440] gnu: boxes: Update to 2.2.1. * gnu/packages/shellutils.scm (boxes): Update to 2.2.1. --- gnu/packages/shellutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index abcb7c2f2a..15e911a619 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -104,7 +104,7 @@ chart.") (define-public boxes (package (name "boxes") - (version "2.2.0") + (version "2.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -113,7 +113,7 @@ chart.") (file-name (git-file-name name version)) (sha256 (base32 - "0vv2gaav1m4z2xdk0k3ragmv4kcnzv7p3v97lkjl1wbfmk5nhz07")))) + "1blni7kjskg6y9ycvhwq3srfvh891xhfnjbh5h2zl0pb5szpllqi")))) (build-system gnu-build-system) (arguments `(#:test-target "test" From a8e3858c9e7fdb3407cddfe664eb784ac07b62b0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 286/440] gnu: conflict: Update to 20221002. * gnu/packages/shellutils.scm (conflict): Update to 20221002. --- gnu/packages/shellutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm index 15e911a619..671848fd27 100644 --- a/gnu/packages/shellutils.scm +++ b/gnu/packages/shellutils.scm @@ -685,7 +685,7 @@ city, state, zip, or area code, it will check out.") (define-public conflict (package (name "conflict") - (version "20210108") + (version "20221002") (source (origin (method url-fetch) (uri (string-append @@ -693,7 +693,7 @@ city, state, zip, or area code, it will check out.") version ".tgz")) (sha256 (base32 - "0mls4climvp7v9hnc3zh01mh270kqcj797ng0xslwb027lipis4h")))) + "1z6z61yiss9m45m3agqs92l569r55w9nsqaap56kh568mcy3y64c")))) (build-system gnu-build-system) (arguments `(#:phases From 6ba1f8db6db9bac832be39201febcf4ac44965aa Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 287/440] gnu: eid-mw: Update to 5.1.11. * gnu/packages/security-token.scm (eid-mw): Update to 5.1.11. --- gnu/packages/security-token.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index b03c3b8080..a1fc058db8 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -130,7 +130,7 @@ readers and is needed to communicate with such devices through the (define-public eid-mw (package (name "eid-mw") - (version "5.1.10") + (version "5.1.11") (source (origin (method git-fetch) @@ -139,7 +139,7 @@ readers and is needed to communicate with such devices through the (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "14nx0hdpv0w5wwsg3894g8pzxlzgp9ryd38k4djhcsyarvzfwynr")))) + (base32 "09mhpwvqsr3pd2by3jm5jzjhyfx0f80bii35zd81vbzy85z26igg")))) (build-system glib-or-gtk-build-system) (native-inputs (list autoconf From efaeb605adeb70edbc40e8258feaed6d69eef70c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 288/440] gnu: plocate: Update to 1.1.19. * gnu/packages/search.scm (plocate): Update to 1.1.19. --- gnu/packages/search.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm index 3e3e8e00c6..f035389d11 100644 --- a/gnu/packages/search.scm +++ b/gnu/packages/search.scm @@ -568,14 +568,14 @@ conflict with slocate compatibility.") (define-public plocate (package (name "plocate") - (version "1.1.18") + (version "1.1.19") (source (origin (method url-fetch) (uri (string-append "https://plocate.sesse.net/download/" "plocate-" version ".tar.gz")) (sha256 - (base32 "0b71chcnl0xymwpcg8ixsnh64017cj5irz04rq0rnwbh1c2mg5lk")))) + (base32 "0rb15sifsmcm756bifs3y8wj282vp0zzagg6kkvbjyczibpchnyr")))) (build-system meson-build-system) (arguments `(#:configure-flags From 93f8124c5e4f6a703ea0d20ca2a09aeeb48695d3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 289/440] gnu: fsearch: Update to 0.2.3. * gnu/packages/search.scm (fsearch): Update to 0.2.3. --- gnu/packages/search.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm index f035389d11..5e86d1a76c 100644 --- a/gnu/packages/search.scm +++ b/gnu/packages/search.scm @@ -390,7 +390,7 @@ queries. A subset of VQL (Verity Query Language) is supported.") (define-public fsearch (package (name "fsearch") - (version "0.2.2") + (version "0.2.3") (source (origin (method git-fetch) @@ -399,7 +399,7 @@ queries. A subset of VQL (Verity Query Language) is supported.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "126sg0fa96vxwinih120riqhj42jlxs2h1bp373r6ml7jwkvlyyn")))) + (base32 "12vj1ymvg561594vdq852ianbkgnvrq585qp5jrrv2kq307jh5sl")))) (build-system meson-build-system) (native-inputs (list autoconf From 22fc2f9ab27f3a7f246e06105df0b8679c44d019 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 290/440] gnu: mu: Update to 1.10.7. * gnu/packages/mail.scm (mu): Update to 1.10.7. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 1562dde866..aac87d4eea 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1202,14 +1202,14 @@ security functionality including PGP, S/MIME, SSH, and SSL.") (define-public mu (package (name "mu") - (version "1.10.5") + (version "1.10.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/djcb/mu/releases/download/v" version "/mu-" version ".tar.xz")) (sha256 - (base32 "0bfclmffcqpb7hsgzvg7ailnnrcpvfv4ljcq7ds0z66n37f97xhs")))) + (base32 "089w1m6sd0nk9l9j40d357fjym8kxmz7kwh3bclk58jxa6xckapa")))) (build-system meson-build-system) (native-inputs (list pkg-config From 521147d04c218186548b176ddd47a678ccf62d1d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 291/440] gnu: drpm: Update to 0.5.2. * gnu/packages/rpm.scm (drpm): Update to 0.5.2. --- gnu/packages/rpm.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/rpm.scm b/gnu/packages/rpm.scm index b7802e3ecd..2c0d971377 100644 --- a/gnu/packages/rpm.scm +++ b/gnu/packages/rpm.scm @@ -44,7 +44,7 @@ (define-public drpm (package (name "drpm") - (version "0.5.1") + (version "0.5.2") (source (origin (method git-fetch) (uri (git-reference @@ -53,7 +53,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0czg69crs2idnd8zsr7p01cd02f981gb5hq15m3qkwd25zxxd1l0")))) + "0jnbj5c9yf46bpbkq6gax4lfpq54c3xjyl0sa8psya7c1kzn44fx")))) (build-system cmake-build-system) (native-inputs (list cmocka pkg-config)) From 477600f818d37e7fab99386370d36a67c962573e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 292/440] gnu: httping: Update to 2.9. * gnu/packages/networking.scm (httping): Update to 2.9. [source]: Use GIT-FETCH and GIT-FILE-NAME. --- gnu/packages/networking.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 383f28e793..a36f8c3f65 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1928,15 +1928,16 @@ transmission protocol (SCTP) in a Go application.") (define-public httping (package (name "httping") - (version "2.5") + (version "2.9") (source (origin - (method url-fetch) - (uri (string-append "https://www.vanheusden.com/httping/httping-" - version ".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/folkertvanheusden/HTTPing") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 - "1y7sbgkhgadmd93x1zafqc4yp26ssiv16ni5bbi9vmvvdl55m29y")))) + (base32 "1gbpirzih0zr93fm71scqjji9wwkfp64q8z36857blsngdfm6k38")))) (build-system gnu-build-system) (arguments (list #:make-flags From 681965861229357186ee947af22a183219d1ee38 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 293/440] gnu: iperf: Update to 3.15. * gnu/packages/networking.scm (iperf): Update to 3.15. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index a36f8c3f65..239afbb0ae 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2655,7 +2655,7 @@ that block port 22.") (define-public iperf (package (name "iperf") - (version "3.14") + (version "3.15") (source (origin (method git-fetch) @@ -2664,7 +2664,7 @@ that block port 22.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0xy7q508yrraa8q3bxdsc2fwacc6qm7l6p44a07jp7ki8bwdcs8z")))) + (base32 "10fzz3j2kx36yhqd0mvwlawvhdbcm0qc41i3f6jf6a5whm70177q")))) (build-system gnu-build-system) (arguments `(#:configure-flags From e5d88e82b441523eccd9917b096bba6d5627edf9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 294/440] gnu: putty: Update to 0.79. * gnu/packages/networking.scm (putty): Update to 0.79. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 239afbb0ae..815f07971b 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -4525,7 +4525,7 @@ Further information on the usage could be found on the Wikibooks page (define-public putty (package (name "putty") - (version "0.77") + (version "0.79") (source (origin (method url-fetch) @@ -4534,7 +4534,7 @@ Further information on the usage could be found on the Wikibooks page (string-append "http://www.putty.be/" version "/putty-" version ".tar.gz"))) (sha256 - (base32 "1rgabc447a5aa9h16krpg3x78vh5jf4l6hkbqzr4bz9qabs7d6j1")))) + (base32 "1n7h1vprayfgjr21ccsv77g71k8dk10n69y99azqx4xvdxkci322")))) (build-system cmake-build-system) (arguments `(#:phases From bdbaf2c2ff54f493df5ed9e65ee6b4d416628b6e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 295/440] gnu: Add glirc-lua. * gnu/packages/irc.scm (glirc-lua): New public variable. --- gnu/packages/irc.scm | 94 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 93 insertions(+), 1 deletion(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 9fc0943db1..107c4d0d19 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -103,7 +103,7 @@ (define-public glirc (package (name "glirc") - (version "2.39.0.1") + (version "2.39.0.1") ; inherited by glirc-* extensions below (source (origin (method url-fetch) @@ -159,6 +159,98 @@ line-editing features including syntax-highlighting, multi-line buffering, and argument placeholders.") (license license:isc))) +(define-public glirc-lua + (package + (name "glirc-lua") + (version (package-version glirc)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/glguy/irc-core") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hadxsahl30jhgk8vvcg7lwndzc282iybcjam87xx5c0lh0mfzan")))) + (build-system meson-build-system) + (arguments + (list + #:modules + '((guix build meson-build-system) + (guix build utils) + (ice-9 match)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'enter-subdirectory + (lambda _ + (chdir "lua-extension"))) + (replace 'install + (lambda _ + (install-file "glirc-lua.so" (string-append #$output "/lib")))) + (add-after 'install 'set-lua-paths + (lambda _ + (let ((x.y #$(version-major+minor + (package-version + (this-package-native-input "lua")))) + (libraries (filter (match-lambda + ((label . _) + (string-prefix? "lua-" label))) + '#$(package-native-inputs + this-package)))) + (setenv "LUA_PATH" + (string-join + (map (match-lambda + ((_ dir) + (string-append + dir "/share/lua/" x.y "/?.lua;" + dir "/share/lua/" x.y "/?/?.lua"))) + libraries) + ";")) + (setenv "LUA_CPATH" + (string-join + (map (match-lambda + ((_ dir) + (string-append + dir "/lib/lua/" x.y "/?.so;" + dir "/lib/lua/" x.y "/?/?.so"))) + libraries) + ";"))))) + (add-after 'set-lua-paths 'document + (lambda _ + (with-directory-excursion "../lua-extension/doc" + ;; Guix's ldoc command is a shell script without a shebang. + (invoke "sh" "ldoc" ".") + (let ((doc (string-append #$output "/share/doc/" #$name))) + (mkdir-p doc) + (copy-recursively "api" doc))))) + (add-after 'document 'leave-subdirectory + ;; Let default phases like 'install-license-files do their thing. + (lambda _ + (chdir "..")))))) + (native-inputs + (list pkg-config + ;; For building the API documentation. + lua lua-filesystem lua-ldoc lua-penlight)) + (inputs + (list lua)) + (home-page (package-home-page glirc)) + (synopsis "Lua scripting extension to the glirc IRC client") + (description + "This extension lets you script the glirc IRC client using Lua. +To use it, you must tell @command{glirc} exactly where to find +@file{glirc-lua.so} by adding something like this to your +@file{~/.config/glirc/config}: + +@example +extensions: + * path: \"../../.guix-profile/lib/glirc-lua.so\" + args: [\"example.lua\", @dots{}] +@end example + +Also ensure that @file{example.lua} finds any Lua libraries it needs, e.g., by +setting @env{LUA_PATH} and @env{LUA_CPATH} in glirc's run-time environment.") + (license (package-license glirc)))) + (define-public quassel (package (name "quassel") From 51670ff0289406d7f5651c7c663d239ccdd68fd8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 296/440] gnu: glirc: Re-indent. No functional change. * gnu/packages/irc.scm (glirc): C-M-q. --- gnu/packages/irc.scm | 104 +++++++++++++++++++++---------------------- 1 file changed, 52 insertions(+), 52 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 107c4d0d19..9e6cb3d001 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -102,62 +102,62 @@ (define-public glirc (package - (name "glirc") - (version "2.39.0.1") ; inherited by glirc-* extensions below - (source - (origin - (method url-fetch) - (uri (hackage-uri "glirc" version)) - (sha256 - (base32 "0jaywb43jfv6kzyz540k02mxdgw1shc6hn7kia21alssszkilh4r")))) - (build-system haskell-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'install 'install-extra-documentation - (lambda _ - (install-file "glirc.1" - (string-append #$output "/share/man/man1")) - ;; The man page is very terse and punts to the GitHub wiki for real - ;; information. Some of that is also in the README, so install it. - (install-file "README.md" - (string-append #$output "/share/doc/" - #$name "-" #$version))))))) - (native-inputs - (list ghc-hunit)) - (inputs - (list ghc-async - ghc-attoparsec - ghc-base64-bytestring - ghc-config-schema - ghc-config-value - ghc-curve25519 - ghc-free - ghc-githash - ghc-hashable - ghc-hookup - ghc-hsopenssl - ghc-irc-core - ghc-kan-extensions - ghc-lens - ghc-network - ghc-psqueues - ghc-random - ghc-regex-tdfa - ghc-split - ghc-unordered-containers - ghc-vector - ghc-vty)) - (home-page "https://github.com/glguy/irc-core") - (synopsis "Console IRC client") - (description - "Glirc is a console IRC client that focuses on providing both high-detail + (name "glirc") + (version "2.39.0.1") ; inherited by glirc-* extensions below + (source + (origin + (method url-fetch) + (uri (hackage-uri "glirc" version)) + (sha256 + (base32 "0jaywb43jfv6kzyz540k02mxdgw1shc6hn7kia21alssszkilh4r")))) + (build-system haskell-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'install-extra-documentation + (lambda _ + (install-file "glirc.1" + (string-append #$output "/share/man/man1")) + ;; The man page is very terse and punts to the GitHub wiki for real + ;; information. Some of that is also in the README, so install it. + (install-file "README.md" + (string-append #$output "/share/doc/" + #$name "-" #$version))))))) + (native-inputs + (list ghc-hunit)) + (inputs + (list ghc-async + ghc-attoparsec + ghc-base64-bytestring + ghc-config-schema + ghc-config-value + ghc-curve25519 + ghc-free + ghc-githash + ghc-hashable + ghc-hookup + ghc-hsopenssl + ghc-irc-core + ghc-kan-extensions + ghc-lens + ghc-network + ghc-psqueues + ghc-random + ghc-regex-tdfa + ghc-split + ghc-unordered-containers + ghc-vector + ghc-vty)) + (home-page "https://github.com/glguy/irc-core") + (synopsis "Console IRC client") + (description + "Glirc is a console IRC client that focuses on providing both high-detail and concise views of an IRC connection. All views and transformation are dynamic and don't change the underlying model. It also provides advanced line-editing features including syntax-highlighting, multi-line buffering, and argument placeholders.") - (license license:isc))) + (license license:isc))) (define-public glirc-lua (package From d6e4ad32b809d5fe467e3625891dae3bf3b53597 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 297/440] gnu: net-snmp: Update to 5.9.4. * gnu/packages/networking.scm (net-snmp): Update to 5.9.4. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 815f07971b..74a279e2d1 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3427,14 +3427,14 @@ Features: (define-public net-snmp (package (name "net-snmp") - (version "5.9.3") + (version "5.9.4") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/net-snmp/net-snmp/" version "/net-snmp-" version ".tar.gz")) (sha256 (base32 - "02pgl89s8qll5zhdp61rbn6vpl084gx55bjb1cqg3wqvgsdz55r0")) + "0i05bds30jazb2wq0hn3mh1zmmnnl9hkkd5y2iq3qkp7j49y0kcb")) (modules '((guix build utils))) (snippet '(begin From af08de2b2d8bee54bd2664e3da3c8470a046e352 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Batista?= Date: Mon, 11 Sep 2023 18:33:00 -0300 Subject: [PATCH 298/440] gnu: mutt: Update to 2.2.12 [security fixes]. Fixes CVE-2023-4874 and CVE-2023-4875. See http://lists.mutt.org/pipermail/mutt-announce/Week-of-Mon-20230904/000056.html * gnu/packages/mail.scm (mutt): Update to 2.2.12 Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index aac87d4eea..e0c185ceb5 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -600,7 +600,7 @@ aliasing facilities to work just as they would on normal mail.") (define-public mutt (package (name "mutt") - (version "2.2.10") + (version "2.2.12") (source (origin (method url-fetch) (uri (list @@ -610,7 +610,7 @@ aliasing facilities to work just as they would on normal mail.") version ".tar.gz"))) (sha256 (base32 - "121xrns9b0n5cdjb7nv5a6idjjk58pp7pdclgdphjy9g88i3yxsd")) + "0f6f32xlfp36axj5in8b0fcc9m05la27zxqbzpvmd3jbyq9g6fh4")) (patches (search-patches "mutt-store-references.patch")))) (build-system gnu-build-system) (inputs From db014e394e4fe256d2413d8316c85119828dc2f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 16 Sep 2023 23:02:37 +0200 Subject: [PATCH 299/440] tests: childhurd: Add missing module imports. Fixes a regression introduced in a09c7da8f8d8e732f969cf0a09aaa78f87032ab1. * gnu/tests/virtualization.scm (run-childhurd-test)[test]: Import (ice-9 textual-ports) and (ice-9 match) in the marionette when needed. --- gnu/tests/virtualization.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/tests/virtualization.scm b/gnu/tests/virtualization.scm index effdeb4cfa..73c8099b79 100644 --- a/gnu/tests/virtualization.scm +++ b/gnu/tests/virtualization.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Christopher Baines -;;; Copyright © 2020-2022 Ludovic Courtès +;;; Copyright © 2020-2023 Ludovic Courtès ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen ;;; Copyright © 2021 Pierre Langlois ;;; Copyright © 2022 Marius Bakke @@ -301,7 +301,9 @@ (test-assert "service running" (marionette-eval '(begin - (use-modules (gnu services herd)) + (use-modules (gnu services herd) + (ice-9 match)) + (match (start-service 'childhurd) (#f #f) (('service response-parts ...) @@ -316,7 +318,8 @@ ;; to the host won't work because QEMU listens on 127.0.0.1. (marionette-eval '(begin - (use-modules (ice-9 match)) + (use-modules (ice-9 match) + (ice-9 textual-ports)) (let loop ((n 60)) (if (zero? n) From 944c1b62a1b36d6383b8e902f1a4abbee0165e34 Mon Sep 17 00:00:00 2001 From: Adam Maleszka Date: Mon, 4 Sep 2023 14:25:23 +0200 Subject: [PATCH 300/440] services: syncthing: Ensure that service runs after mounting home directories. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Sometimes `syncthing-service-type' fails during startup because it tries to read configuration files from the user's home directory: Failure on home directory: mkdir /home/xyz/.config: permission denied This patch adds `user-processes' to the shepherd service requirements to ensure that `user-homes' is fired before `syncthing' tries to read data from the home directory. * gnu/services/syncthing.scm (syncthing-shepherd-service): add `user-processes' to requirements Signed-off-by: Ludovic Courtès --- gnu/services/syncthing.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/syncthing.scm b/gnu/services/syncthing.scm index 2f7c822827..9bb623186b 100644 --- a/gnu/services/syncthing.scm +++ b/gnu/services/syncthing.scm @@ -63,7 +63,7 @@ (list (string->symbol (string-append "syncthing-" user))))) (documentation "Run syncthing.") - (requirement (if home-service? '() '(loopback))) + (requirement (if home-service? '() '(loopback user-processes))) (start #~(make-forkexec-constructor (append (list (string-append #$syncthing "/bin/syncthing") "--no-browser" From 04f71edb73205d0bb82404de28a70ae17b897429 Mon Sep 17 00:00:00 2001 From: Alexey Abramov Date: Tue, 25 Jul 2023 12:59:56 +0200 Subject: [PATCH 301/440] services: dhcp-client-configuration: Allow provision override. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/networking.scm ()[shepherd-provision]: New field. (dhcp-client-shepherd-service): Honor it. * doc/guix.texi (Networking Setup): Document it. Co-authored-by: Ludovic Courtès --- doc/guix.texi | 6 ++++++ gnu/services/networking.scm | 11 +++++++---- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 46cc8e1b80..983b471fd8 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -20461,10 +20461,16 @@ non-loopback interfaces that can be activated. Otherwise the DHCP client listens only on the specified interfaces. @item @code{shepherd-requirement} (default: @code{'()}) +@itemx @code{shepherd-provision} (default: @code{'(networking)}) This option can be used to provide a list of symbols naming Shepherd services that this service will depend on, such as @code{'wpa-supplicant} or @code{'iwd} if you require authenticated access for encrypted WiFi or Ethernet networks. + +Likewise, @code{shepherd-provision} is a list of Shepherd service names +(symbols) provided by this service. You might want to change the +default value if you intend to run several DHCP clients, only one of +which provides the @code{networking} Shepherd service. @end table @end deftp diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index e2f6e6c0ca..ec34137d39 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -89,6 +89,7 @@ dhcp-client-configuration? dhcp-client-configuration-package dhcp-client-configuration-interfaces + dhcp-client-configuration-shepherd-provision dhcp-client-configuration-shepherd-requirement dhcpd-service-type @@ -303,6 +304,8 @@ (default isc-dhcp)) (shepherd-requirement dhcp-client-configuration-shepherd-requirement (default '())) + (shepherd-provision dhcp-client-configuration-provision + (default '(networking))) (interfaces dhcp-client-configuration-interfaces (default 'all))) ;'all | list of strings @@ -310,19 +313,19 @@ (match-lambda ((? dhcp-client-configuration? config) (let ((package (dhcp-client-configuration-package config)) - (shepherd-requirement (dhcp-client-configuration-shepherd-requirement config)) + (requirement (dhcp-client-configuration-shepherd-requirement config)) + (provision (dhcp-client-configuration-shepherd-provision config)) (interfaces (dhcp-client-configuration-interfaces config)) (pid-file "/var/run/dhclient.pid")) (list (shepherd-service (documentation "Set up networking via DHCP.") - (requirement `(user-processes udev ,@shepherd-requirement)) + (requirement `(user-processes udev ,@requirement)) + (provision provision) ;; XXX: Running with '-nw' ("no wait") avoids blocking for a minute when ;; networking is unavailable, but also means that the interface is not up ;; yet when 'start' completes. To wait for the interface to be ready, one ;; should instead monitor udev events. - (provision '(networking)) - (start #~(lambda _ (define dhclient (string-append #$package "/sbin/dhclient")) From 19b617370844ad48eab68e6fc4b9e47665f71710 Mon Sep 17 00:00:00 2001 From: Jean-Pierre De Jesus DIAZ Date: Wed, 26 Jul 2023 17:37:29 +0200 Subject: [PATCH 302/440] transformations: tuned-package: Use target on cross-compile. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/transformations.scm (tuned-package): Use either bag-target if available or bag-system to select the CPU architecture of the package that is going to be tuned. This enables the tuning of cross-compiled packages. Signed-off-by: Ludovic Courtès --- guix/transformations.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/transformations.scm b/guix/transformations.scm index ede914456f..9cba6bedab 100644 --- a/guix/transformations.scm +++ b/guix/transformations.scm @@ -529,8 +529,9 @@ system that builds code for MICRO-ARCHITECTURE; otherwise raise an error." ;; leading to an obscure build error, check whether the compiler is known ;; to support MICRO-ARCHITECTURE. If not, bail out. (let* ((lowered (apply lower args)) - (architecture (match (string-tokenize (bag-system lowered) - %not-hyphen) + (target (or (bag-target lowered) + (bag-system lowered))) + (architecture (match (string-tokenize target %not-hyphen) ((arch _ ...) arch))) (compiler (any (match-lambda ((label (? package? p) . _) From c69dc48da684c338fb8fc991a5d95a238df7573a Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Tue, 18 Jul 2023 17:46:16 +0000 Subject: [PATCH 303/440] gnu: spdlog: Update to 1.12.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/logging.scm (spdlog): Update to 1.12.0. [native-inputs]: Add catch2-3.3. Signed-off-by: Ludovic Courtès --- gnu/packages/logging.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm index dbaf9fa7aa..c204a013b4 100644 --- a/gnu/packages/logging.scm +++ b/gnu/packages/logging.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages bison) #:use-module (gnu packages c) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) @@ -212,7 +213,7 @@ output in multiple windows in a terminal.") (define-public spdlog (package (name "spdlog") - (version "1.11.0") + (version "1.12.0") (source (origin (method git-fetch) @@ -222,7 +223,7 @@ output in multiple windows in a terminal.") (file-name (git-file-name name version)) (patches (search-patches "spdlog-fix-tests.patch")) (sha256 - (base32 "0i3a1cqrg1sz0w50g7zz9x73rf838igqri12q8ijh4rzpq0qq3ch")))) + (base32 "0yyncv6wjs5rqm76rkqyxpfbsingk1dq5zfcqhy1a7fpw8xdl53k")))) (build-system cmake-build-system) ;; TODO run benchmark. Currently not possible, as adding ;; (gnu packages benchmark) forms a dependency cycle @@ -231,6 +232,7 @@ output in multiple windows in a terminal.") (list "-DSPDLOG_BUILD_BENCH=OFF" "-DSPDLOG_BUILD_SHARED=ON" "-DSPDLOG_BUILD_TESTS=ON"))) + (native-inputs (list catch2-3.3)) (home-page "https://github.com/gabime/spdlog") (synopsis "Fast C++ logging library") (description "Spdlog is a very fast header-only/compiled C++ logging From d2a751c14eac664e32c79613f09cf146504d433f Mon Sep 17 00:00:00 2001 From: Saku Laesvuori Date: Thu, 17 Aug 2023 10:38:48 +0300 Subject: [PATCH 304/440] gnu: home: zsh: Load environment when running via ssh MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/home/services/shells.scm (zsh-file-zshenv): Add snippet to source /etc/profile when running via ssh. (zsh-get-configuration-files): Always add .zshenv as it is never empty. Signed-off-by: Ludovic Courtès --- gnu/home/services/shells.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/home/services/shells.scm b/gnu/home/services/shells.scm index 7960590e7c..9dd56f634a 100644 --- a/gnu/home/services/shells.scm +++ b/gnu/home/services/shells.scm @@ -183,7 +183,8 @@ another process for example).")) (mixed-text-file "zshenv" (zsh-serialize-field config 'zshenv) - (zsh-serialize-field config 'environment-variables))) + (zsh-serialize-field config 'environment-variables) + "[ -n \"$SSH_CLIENT\" ] && source /etc/profile")) (define (zsh-file-zprofile config) (mixed-text-file @@ -209,9 +210,7 @@ source ~/.profile (define (zsh-get-configuration-files config) `((".zprofile" ,(zsh-file-by-field config 'zprofile)) ;; Always non-empty - ,@(if (or (zsh-field-not-empty? config 'zshenv) - (zsh-field-not-empty? config 'environment-variables)) - `((".zshenv" ,(zsh-file-by-field config 'zshenv))) '()) + (".zshenv" ,(zsh-file-by-field config 'zshenv)) ;; Always non-empty ,@(if (zsh-field-not-empty? config 'zshrc) `((".zshrc" ,(zsh-file-by-field config 'zshrc))) '()) ,@(if (zsh-field-not-empty? config 'zlogin) From d4da1f26e1c3fdb2b5d1d8f67ebd195d119fa964 Mon Sep 17 00:00:00 2001 From: Nicolas Graves Date: Thu, 27 Jul 2023 13:59:08 +0200 Subject: [PATCH 305/440] gnu: file-systems: Add variable %base-live-file-systems. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/system/file-systems.scm (%base-live-file-systems): New variable. * gnu/system/install.scm (installation-os): Use %base-live-file-systems. Signed-off-by: Ludovic Courtès --- gnu/system/file-systems.scm | 21 +++++++++++++++++++++ gnu/system/install.scm | 17 +---------------- 2 files changed, 22 insertions(+), 16 deletions(-) diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm index 95b757a698..529f1536de 100644 --- a/gnu/system/file-systems.scm +++ b/gnu/system/file-systems.scm @@ -85,6 +85,7 @@ %elogind-file-systems %base-file-systems + %base-live-file-systems %container-file-systems @@ -495,6 +496,26 @@ TARGET in the other system." %efivars-file-system %immutable-store)) +(define %base-live-file-systems + ;; This is the bare minimum to use live file-systems. + ;; Used in installation-os. + (list (file-system + (mount-point "/") + (device (file-system-label "Guix_image")) + (type "ext4")) + + ;; Make /tmp a tmpfs instead of keeping the overlayfs. This + ;; originally was used for unionfs because FUSE creates + ;; '.fuse_hiddenXYZ' files for each open file, and this confuses + ;; Guix's test suite, for instance (see + ;; ). We keep this for overlayfs to be + ;; on the safe side. + (file-system + (mount-point "/tmp") + (device "none") + (type "tmpfs") + (check? #f)))) + ;; File systems for Linux containers differ from %base-file-systems in that ;; they impose additional restrictions such as no-exec or need different ;; options to function properly. diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 7a68c19606..28161de153 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -517,22 +517,7 @@ Access documentation at any time by pressing Alt-F2.\x1b[0m (file-systems ;; Note: the disk image build code overrides this root file system with ;; the appropriate one. - (cons* (file-system - (mount-point "/") - (device (file-system-label "Guix_image")) - (type "ext4")) - - ;; Make /tmp a tmpfs instead of keeping the overlayfs. This - ;; originally was used for unionfs because FUSE creates - ;; '.fuse_hiddenXYZ' files for each open file, and this confuses - ;; Guix's test suite, for instance (see - ;; ). We keep this for overlayfs to be - ;; on the safe side. - (file-system - (mount-point "/tmp") - (device "none") - (type "tmpfs") - (check? #f)) + (append %base-live-file-systems ;; XXX: This should be %BASE-FILE-SYSTEMS but we don't need ;; elogind's cgroup file systems. From 5abc40d7f740bb36c4b6eea649db198d950ca402 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Pastor=20P=C3=A9rez?= Date: Sat, 29 Jul 2023 18:33:26 +0200 Subject: [PATCH 306/440] gnu: cockatrice: add wayland dependency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/games.scm (cockatrice): add wayland dependency Signed-off-by: Ludovic Courtès --- gnu/packages/games.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1167443825..db157f30e1 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1146,6 +1146,7 @@ want what you have.") qtsvg-5 qttools-5 qtwebsockets-5 + qtwayland-5 xz zlib)) (home-page "https://cockatrice.github.io") From fc3a53525ab3dcaf7c22eec8d62294017f9760fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 17 Sep 2023 16:29:19 +0200 Subject: [PATCH 307/440] services: dhcp-client: Fix name of the provision accessor. This is a followup to 04f71edb73205d0bb82404de28a70ae17b897429. * gnu/services/networking.scm ()[shepherd-provision]: Fix accessor name. --- gnu/services/networking.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index ec34137d39..befaca0aca 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -304,7 +304,7 @@ (default isc-dhcp)) (shepherd-requirement dhcp-client-configuration-shepherd-requirement (default '())) - (shepherd-provision dhcp-client-configuration-provision + (shepherd-provision dhcp-client-configuration-shepherd-provision (default '(networking))) (interfaces dhcp-client-configuration-interfaces (default 'all))) ;'all | list of strings From 3c4e890fccb2f21a8dc35728329932e4ef14fc14 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 308/440] gnu: lkrg: Update to 0.9.7. This fixes the build with Linux-Libre >= 6.4. * gnu/packages/linux.scm (lkrg): Update to 0.9.7. --- 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 9a49c090aa..86580c29cc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1636,7 +1636,7 @@ registers of the @acronym{EC, Embedded Controller} supported by the (define-public lkrg (package (name "lkrg") - (version "0.9.3") + (version "0.9.7") (source (origin (method git-fetch) (uri (git-reference @@ -1645,7 +1645,7 @@ registers of the @acronym{EC, Embedded Controller} supported by the (file-name (git-file-name name version)) (sha256 (base32 - "0yirb7n4mqv8cn0gziz1m7ymq00dhhy79j59jdgrx00b8rj57cfw")))) + "0k0z9caj48nqjwk3bapgfcdzi1lkizxcjj4r1dvkvwsk38mbk1c4")))) (build-system linux-module-build-system) (arguments (list #:linux linux-libre From 4d16fd8829e9d4ff31f226ccabd1e88ffbf425c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 309/440] gnu: libnftnl: Update to 1.2.6. * gnu/packages/linux.scm (libnftnl): Update to 1.2.6. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 86580c29cc..4152e93e05 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7837,14 +7837,14 @@ re-use code and to avoid re-inventing the wheel.") (define-public libnftnl (package (name "libnftnl") - (version "1.2.4") + (version "1.2.6") (source (origin (method url-fetch) (uri (string-append "mirror://netfilter.org/libnftnl/" - "libnftnl-" version ".tar.bz2")) + "libnftnl-" version ".tar.xz")) (sha256 - (base32 "0zs7c8swlirxnbhl8q1b0p8g3jrzns7fyxsrglz71zfdwhxj7zn0")))) + (base32 "1x3pqxclpxcw8x5qx0vyi7znf9xwlkqsfd9sy4cxlir1v4nfmsnf")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) From 9770dd00d1cf2cb557c9def8e289b895940dfdfe Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 310/440] gnu: nftables: Update to 1.0.8. * gnu/packages/linux.scm (nftables): Update to 1.0.8. --- 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 4152e93e05..f5d777390e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7883,7 +7883,7 @@ used by nftables.") (define-public nftables (package (name "nftables") - (version "1.0.6") + (version "1.0.8") (source (origin (method url-fetch) @@ -7892,7 +7892,7 @@ used by nftables.") (string-append "https://www.nftables.org/projects/nftables" "/files/nftables-" version ".tar.xz"))) (sha256 - (base32 "0k2y03dz77b0inqlmh5yg8qaifl0walzvhldwiq7d642vl6l61r4")))) + (base32 "0l1xpwr9qfbl3bxa97v8s2lbibiz0xma9q0qi34xp0hswh6p8wwk")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-static" From 1d70205ad79fc1330de6cad71abbdfc93a52d9d7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 311/440] gnu: cpuid: Update to 20230614. * gnu/packages/linux.scm (cpuid): Update to 20230614. --- 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 f5d777390e..3d94282d59 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8394,14 +8394,14 @@ available in the kernel Linux.") (define-public cpuid (package (name "cpuid") - (version "20221201") + (version "20230614") (source (origin (method url-fetch) (uri (string-append "http://www.etallen.com/cpuid/cpuid-" version ".src.tar.gz")) (sha256 (base32 - "0vlg5zc0dayyn9bzyb25fcaxid9svrsjjza11afplrhh50wdrzh8")))) + "1s54qc1j10d765r05kw9pzwzaxq2b0nndq2ifwq7cq62xx2k1j5i")))) (build-system gnu-build-system) (arguments (list #:make-flags From 02e7d6057624a8410ba473460b9fb33682b7af3d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 312/440] gnu: lua: Update to 5.4.6. * gnu/packages/lua.scm (lua): Update to 5.4.6. --- gnu/packages/lua.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 3b58952911..65cab6511c 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -119,13 +119,13 @@ for configuration, scripting, and rapid prototyping.") (define-public lua-5.4 (package (inherit lua) - (version "5.4.3") + (version "5.4.6") (source (origin (method url-fetch) (uri (string-append "https://www.lua.org/ftp/lua-" version ".tar.gz")) (sha256 - (base32 "1yxvjvnbg4nyrdv10bq42gz6dr66pyan28lgzfygqfwy2rv24qgq")) + (base32 "125dncwz8syhxk034m4fpahq7vsprfnwdqfxlffbb83arfws2pkx")) (patches (search-patches "lua-5.4-pkgconfig.patch" "lua-5.4-liblua-so.patch")))))) From 4cb885947313c97f8e621bd646158a946cd372b3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 313/440] gnu: mcelog: Update to 195. * gnu/packages/linux.scm (mcelog): Update to 195. --- 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 3d94282d59..7150673f4b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7156,7 +7156,7 @@ the @code{mce-inject} module loaded if it exists.") (define-public mcelog (package (name "mcelog") - (version "191") + (version "195") (source (origin (method git-fetch) @@ -7165,7 +7165,7 @@ the @code{mce-inject} module loaded if it exists.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0vx0lziw6g20vh42ngs66fiq2bm714llx5xx6f0m1hbjcihi1afy")) + (base32 "1bg2bj8flybd8kzmmaaslisc6lc1fs9nbv09im6r32dq48skx5aj")) (modules '((guix build utils))) (snippet `(begin From 56790b9dbca9add9a66d2c9e38969031a880c2b6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 314/440] gnu: ddcci-driver-linux: Update to 0.4.4. * gnu/packages/linux.scm (ddcci-driver-linux): Update to 0.4.4. --- 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 7150673f4b..b1ebad276a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1720,7 +1720,7 @@ graphics card on Optimus laptops.") (define-public ddcci-driver-linux (package (name "ddcci-driver-linux") - (version "0.4.2") + (version "0.4.4") (source (origin (method git-fetch) @@ -1730,7 +1730,7 @@ graphics card on Optimus laptops.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1lww3mnqhxqzj0qbxzbwbq93v9zw49myp7p9ib873a5izbq8nadi")))) + (base32 "19vi7dk4jv5wm18cznz4lj2fb1c7m7j3ig62x4a6qy9djxf9z472")))) (build-system linux-module-build-system) (arguments (list #:tests? #f ; no tests From b2d5a491442bcfc6a7d74d582087126ad7846af0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 315/440] gnu: bpftrace: Update to 0.18.1. * gnu/packages/linux.scm (bpftrace): Update to 0.18.1. --- 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 b1ebad276a..85e3d9845d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -9611,7 +9611,7 @@ modification of BPF objects on the system.") (define-public bpftrace (package (name "bpftrace") - (version "0.18.0") + (version "0.18.1") (source (origin (method git-fetch) @@ -9620,7 +9620,7 @@ modification of BPF objects on the system.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0n0mm5vlaildilq5nmjymmq8ijif1lcyfin76wcmhzwfriq4n87r")) + (base32 "0j8ba2j98d3j8lilgx3z2n162r26ryg7zw5ldwd9m36xnjp40347")) (patches (search-patches "bpftrace-disable-bfd-disasm.patch")))) (build-system cmake-build-system) (native-inputs From 38c2c076e24ee1f6c0e2c4fcf9a5143ce8d0cdc2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 316/440] gnu: feh: Update to 3.10. * gnu/packages/image-viewers.scm (feh): Update to 3.10. --- gnu/packages/image-viewers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 0ce3a27b01..206b91c878 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -177,7 +177,7 @@ YouTube videos without requiring API and opens/downloads them using mpv/ytdl.") (define-public feh (package (name "feh") - (version "3.9") + (version "3.10") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -185,7 +185,7 @@ YouTube videos without requiring API and opens/downloads them using mpv/ytdl.") name "-" version ".tar.bz2")) (sha256 (base32 - "185wwqd60r2rk6lzcvd6sl58589qfqrfnf7lqd6friyj84n9cjc6")))) + "166cayf1zh84y5bfaykxmi7ypxvq36hnjsbnwbjzx7zyvkvd2w8x")))) (build-system gnu-build-system) (arguments (list #:phases From 6eaae8a96518f12d52d3393f72740844bbe5b0dd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 317/440] gnu: angband: Update to 4.2.5. * gnu/packages/games.scm (angband): Update to 4.2.5. --- 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 db157f30e1..0b7518c2c2 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3313,7 +3313,7 @@ that beneath its ruins lay buried an ancient evil.") (define-public angband (package (name "angband") - (version "4.2.4") + (version "4.2.5") (source (origin (method git-fetch) @@ -3322,7 +3322,7 @@ that beneath its ruins lay buried an ancient evil.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1x0qqsv7xa3figcl4v35sin64ffgz32652vk541d8qaq4qcc378n")) + (base32 "0kg6npbfy42mhggsqvs04khc8198i980z52xm59pws29698qazaw")) (modules '((guix build utils))) (snippet ;; So, some of the sounds/graphics/tilesets are under different From ad051b038eec422ee9bfc4f5e77ff84a11c27666 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 318/440] gnu: memcached: Update to 1.6.21. * gnu/packages/databases.scm (memcached): Update to 1.6.21. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2b8e80e1b0..8a2063ee29 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -488,14 +488,14 @@ mapping from string keys to string values.") (define-public memcached (package (name "memcached") - (version "1.6.18") + (version "1.6.21") (source (origin (method url-fetch) (uri (string-append "https://memcached.org/files/memcached-" version ".tar.gz")) (sha256 - (base32 "0n21svnjw8j7bdbwrn0apnfql7ckraqgrl7wj9fsqj86h6w6mpfb")))) + (base32 "1vm27la2yanjhwwdwabci4c21yv9hy5iqas47kcxaza1zh79i267")))) (build-system gnu-build-system) (inputs (list libevent cyrus-sasl)) From a426d92fe8f88faa1b7b2c2d7e75be27e553137f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 319/440] gnu: nnn: Update to 4.9. * gnu/packages/admin.scm (nnn): Update to 4.9. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 0cf38bed9a..99b60263d4 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4250,14 +4250,14 @@ information tool.") (define-public nnn (package (name "nnn") - (version "4.7") + (version "4.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/jarun/nnn/releases/download/v" version "/nnn-v" version ".tar.gz")) (sha256 - (base32 "0dbm54m3iv8hzar38dsfxh77z4mlpjj649ga82s0wwms4vlrm5pg")))) + (base32 "0d8apcichwbmsqgbs0kay3k63898x6xdxpb9hn1nvv5qwxxdq59b")))) (build-system gnu-build-system) (inputs (list ncurses readline)) From 059d604ddf2a6bd40b21be842752157c27a16eb0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 320/440] gnu: lightning: Update to 2.2.2. * gnu/packages/assembly.scm (lightning): Update to 2.2.2. --- gnu/packages/assembly.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index 81e38c3f41..fef2181e6e 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -134,14 +134,14 @@ debugging information in STABS, DWARF 2, and CodeView 8 formats.") (define-public lightning (package (name "lightning") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/lightning/lightning-" version ".tar.gz")) (sha256 (base32 - "1aiwx9cl9c7swqcgrsjnvd5laah3iwxzl1van3670iv8sn0icrwq")))) + "1qmkfg7br543kqy82hhpr1n8bsm9wrwb1z5w2whxc5xdvr185jha")))) (build-system gnu-build-system) (native-inputs (list zlib)) (arguments From a6170fcd2ba1b4b677399f048bdcd7a5701775af Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Sun, 10 Sep 2023 15:27:39 -0400 Subject: [PATCH 321/440] gnu: Remove extraneous imports. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Found by running 'guild compile -W3 gnu/packages/$module.scm', using guild from the upcoming Guile. * gnu/packages/admin.scm: Remove extraneous imports. * gnu/packages/avr.scm: Likewise. * gnu/packages/base.scm: Likewise. * gnu/packages/bootloaders.scm: Likewise. * gnu/packages/firmware.scm: Likewise. * gnu/packages/linphone.scm: Likewise. * gnu/packages/telephony.scm: Likewise. * gnu/packages/cran.scm: Likewise. * gnu/packages/kde.scm: Likewise. * gnu/packages/libcanberra.scm: Likewise. * gnu/packages/libreoffice.scm: Likewise. * gnu/packages/mes.scm: Likewise. * gnu/packages/mingw.scm: Likewise. * gnu/packages/serialization.scm: Likewise. * gnu/packages/sync.scm: Likewise. * gnu/packages/syncthing.scm: Likewise. * gnu/packages/terminals.scm: Likewise. * gnu/packages/version-control.scm: Likewise. * gnu/packages/video.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/emulators.scm: Likewise. Reviewed-by: Ludovic Courtès --- gnu/packages/admin.scm | 5 ----- gnu/packages/avr.scm | 1 - gnu/packages/base.scm | 1 - gnu/packages/bootloaders.scm | 2 -- gnu/packages/cran.scm | 2 -- gnu/packages/emulators.scm | 3 --- gnu/packages/firmware.scm | 4 ---- gnu/packages/kde.scm | 3 --- gnu/packages/libcanberra.scm | 6 +----- gnu/packages/libreoffice.scm | 4 ---- gnu/packages/linphone.scm | 4 ---- gnu/packages/mes.scm | 5 ----- gnu/packages/mingw.scm | 6 ------ gnu/packages/serialization.scm | 5 +---- gnu/packages/sync.scm | 2 -- gnu/packages/syncthing.scm | 2 -- gnu/packages/telephony.scm | 12 ------------ gnu/packages/terminals.scm | 1 - gnu/packages/version-control.scm | 2 -- gnu/packages/video.scm | 7 ------- gnu/packages/wm.scm | 3 --- 21 files changed, 2 insertions(+), 78 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 99b60263d4..c6b62834f1 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -101,7 +101,6 @@ #:use-module (gnu packages acl) #:use-module (gnu packages algebra) #:use-module (gnu packages attr) - #:use-module (gnu packages autogen) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bash) @@ -112,7 +111,6 @@ #:use-module (gnu packages compression) #:use-module (gnu packages crates-graphics) #:use-module (gnu packages crates-io) - #:use-module (gnu packages cross-base) #:use-module (gnu packages crypto) #:use-module (gnu packages cryptsetup) #:use-module (gnu packages curl) @@ -140,7 +138,6 @@ #:use-module (gnu packages inkscape) #:use-module (gnu packages kerberos) #:use-module (gnu packages libbsd) - #:use-module (gnu packages libftdi) #:use-module (gnu packages libunwind) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) @@ -161,11 +158,9 @@ #:use-module (gnu packages perl-check) #:use-module (gnu packages pkg-config) #:use-module (gnu packages polkit) - #:use-module (gnu packages popt) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-crypto) - #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages readline) diff --git a/gnu/packages/avr.scm b/gnu/packages/avr.scm index 9c623a9626..b9bee5e624 100644 --- a/gnu/packages/avr.scm +++ b/gnu/packages/avr.scm @@ -31,7 +31,6 @@ #:use-module (guix packages) #:use-module (guix build-system gnu) #:use-module (guix build-system trivial) - #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cross-base) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 786b080ae4..0b6cb2ddc5 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -49,7 +49,6 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages ed) - #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages guile) #:use-module (gnu packages multiprecision) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 1c47636341..1124eca837 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -36,8 +36,6 @@ (define-module (gnu packages bootloaders) #:use-module (gnu packages) - #:use-module (gnu packages admin) - #:use-module (gnu packages algebra) #:use-module (gnu packages assembly) #:use-module (gnu packages base) #:use-module (gnu packages disk) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6166b0d006..612524e2f7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -62,7 +62,6 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system r) - #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) @@ -79,7 +78,6 @@ #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) - #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 1d50c9ef01..ce61f935fb 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -56,7 +56,6 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) - #:use-module (gnu packages build-tools) #:use-module (gnu packages cdrom) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -72,7 +71,6 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages fribidi) #:use-module (gnu packages game-development) - #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -102,7 +100,6 @@ #:use-module (gnu packages upnp) #:use-module (gnu packages video) #:use-module (gnu packages vulkan) - #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xiph) #:use-module (gnu packages xml) diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 2e2c4af796..cbb24230de 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -40,7 +40,6 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages admin) - #:use-module (gnu packages autotools) #:use-module (gnu packages assembly) #:use-module (gnu packages backup) #:use-module (gnu packages base) @@ -58,7 +57,6 @@ #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) - #:use-module (gnu packages gnupg) #:use-module (gnu packages gtk) #:use-module (gnu packages hardware) #:use-module (gnu packages libusb) @@ -71,13 +69,11 @@ #:use-module (gnu packages polkit) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) - #:use-module (gnu packages python-build) #:use-module (gnu packages python-xyz) #:use-module (gnu packages shells) #:use-module (gnu packages sqlite) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) - #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (ice-9 match)) diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 9e5ac767b8..20fbb41d73 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -36,13 +36,11 @@ (define-module (gnu packages kde) #:use-module (guix build-system cmake) #:use-module (guix build-system qt) - #:use-module (guix deprecation) #:use-module (guix download) #:use-module (guix gexp) #: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 algebra) #:use-module (gnu packages apr) @@ -69,7 +67,6 @@ #:use-module (gnu packages gettext) #: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 gperf) diff --git a/gnu/packages/libcanberra.scm b/gnu/packages/libcanberra.scm index c0ec47a445..cf38ac113e 100644 --- a/gnu/packages/libcanberra.scm +++ b/gnu/packages/libcanberra.scm @@ -25,10 +25,8 @@ #:use-module (gnu packages) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system python) - #:use-module (guix utils) #:use-module (gnu packages autotools) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) @@ -36,9 +34,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages python) - #:use-module (gnu packages xiph) - #:use-module ((srfi srfi-1) #:select (alist-delete))) + #:use-module (gnu packages xiph)) (define-public libcanberra (package diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index d06166e64a..71131ca1f3 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -44,7 +44,6 @@ #:use-module (ice-9 match) #:use-module (gnu packages) #:use-module (gnu packages aidc) - #:use-module (gnu packages aspell) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bison) @@ -73,10 +72,8 @@ #:use-module (gnu packages hunspell) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) - #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages logging) - #:use-module (gnu packages m4) #:use-module (gnu packages maths) #:use-module (gnu packages nss) #:use-module (gnu packages openldap) @@ -87,7 +84,6 @@ #:use-module (gnu packages python) #:use-module (gnu packages rdf) #:use-module (gnu packages scanner) - #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages xml) diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm index 7d87ee602c..48a30f32d0 100644 --- a/gnu/packages/linphone.scm +++ b/gnu/packages/linphone.scm @@ -34,11 +34,8 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages gettext) #:use-module (gnu packages gl) - #:use-module (gnu packages glib) #:use-module (gnu packages gnome) - #:use-module (gnu packages gnome-xyz) #:use-module (gnu packages graphviz) - #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages linux) #:use-module (gnu packages ncurses) @@ -49,7 +46,6 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) - #:use-module (gnu packages java) #:use-module (gnu packages sqlite) #:use-module (gnu packages telephony) #:use-module (gnu packages tls) diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index 4176977375..a7924d943d 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -24,15 +24,10 @@ (define-module (gnu packages mes) #:use-module (gnu packages) #:use-module (gnu packages base) - #:use-module (gnu packages bash) - #:use-module (gnu packages bootstrap) - #:use-module (gnu packages compression) #:use-module (gnu packages cross-base) - #:use-module (gnu packages gcc) #:use-module (gnu packages graphviz) #:use-module (gnu packages guile) #:use-module (gnu packages man) - #:use-module (gnu packages package-management) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages texinfo) diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm index 4eeefe1490..0ac6f0e767 100644 --- a/gnu/packages/mingw.scm +++ b/gnu/packages/mingw.scm @@ -22,16 +22,10 @@ (define-module (gnu packages mingw) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) - #:use-module (gnu packages base) #:use-module (gnu packages cross-base) - #:use-module (gnu packages gcc) - #:use-module (gnu packages compression) - #:use-module (gnu packages multiprecision) #:use-module (guix build-system gnu) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix utils) - #:use-module (ice-9 match) #:export (make-mingw-w64)) (define* (make-mingw-w64 machine diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index c17d417d5e..d0b4bd2735 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -52,8 +52,6 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) - #:use-module (gnu packages cmake) - #:use-module (gnu packages cpp) #:use-module (gnu packages databases) #:use-module (gnu packages documentation) #:use-module (gnu packages gcc) @@ -64,8 +62,7 @@ #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-science) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages perl)) + #:use-module (gnu packages python-xyz)) (define-public avro-cpp-1.9 (package diff --git a/gnu/packages/sync.scm b/gnu/packages/sync.scm index 8235332cb0..c4410c67fd 100644 --- a/gnu/packages/sync.scm +++ b/gnu/packages/sync.scm @@ -50,7 +50,6 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) - #:use-module (gnu packages golang) #:use-module (gnu packages graphviz) #:use-module (gnu packages image) #:use-module (gnu packages kde-frameworks) @@ -62,7 +61,6 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) - #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages readline) #:use-module (gnu packages rsync) diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index fd30360006..5570aa9361 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -38,9 +38,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages linux) - #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) - #:use-module (gnu packages python-xyz) #:use-module (gnu packages time)) (define-public syncthing diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index aa65c4eaad..42158784ca 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -44,7 +44,6 @@ #:use-module (guix gexp) #:use-module (gnu packages) #:use-module (gnu packages admin) - #:use-module (gnu packages aidc) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages avahi) @@ -52,23 +51,17 @@ #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages check) - #:use-module (gnu packages compression) #:use-module (gnu packages cpp) - #:use-module (gnu packages crypto) #:use-module (gnu packages databases) #:use-module (gnu packages sqlite) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages file) #:use-module (gnu packages protobuf) - #:use-module (gnu packages gettext) #:use-module (gnu packages gl) #:use-module (gnu packages glib) - #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) - #:use-module (gnu packages gtk) #:use-module (gnu packages image) - #:use-module (gnu packages libcanberra) #:use-module (gnu packages libusb) #:use-module (gnu packages linphone) #:use-module (gnu packages linux) @@ -77,7 +70,6 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages netpbm) #:use-module (gnu packages networking) - #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) @@ -85,12 +77,8 @@ #:use-module (gnu packages qt) #:use-module (gnu packages samba) #:use-module (gnu packages security-token) - #:use-module (gnu packages serialization) #:use-module (gnu packages speech) #:use-module (gnu packages tls) - #:use-module (gnu packages upnp) - #:use-module (gnu packages video) - #:use-module (gnu packages webkit) #:use-module (gnu packages xiph) #:use-module (gnu packages xorg) #:use-module (gnu packages xml) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index ee18326204..add4cedc26 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -103,7 +103,6 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-check) - #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) #:use-module (gnu packages serialization) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 86dcea908c..cf3c4d4e19 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -115,7 +115,6 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages ssh) #:use-module (gnu packages web) - #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -128,7 +127,6 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) - #:use-module (gnu packages rsync) #:use-module (gnu packages ruby) #:use-module (gnu packages sqlite) #:use-module (gnu packages texinfo) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index e8cee27382..c2f5b52042 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -117,10 +117,8 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) - #:use-module (gnu packages build-tools) #:use-module (gnu packages cdrom) #:use-module (gnu packages check) - #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cpp) #:use-module (gnu packages crates-io) @@ -131,7 +129,6 @@ #:use-module (gnu packages dns) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) - #:use-module (gnu packages elf) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages fonts) @@ -157,9 +154,7 @@ #:use-module (gnu packages libidn) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) - #:use-module (gnu packages llvm) #:use-module (gnu packages lua) - #:use-module (gnu packages m4) #:use-module (gnu packages man) #:use-module (gnu packages markup) #:use-module (gnu packages maths) @@ -188,7 +183,6 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) - #:use-module (gnu packages rdesktop) #:use-module (gnu packages re2c) #:use-module (gnu packages ruby) #:use-module (gnu packages rust-apps) @@ -208,7 +202,6 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages vulkan) #:use-module (gnu packages web) - #:use-module (gnu packages webkit) #:use-module (gnu packages wget) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xdisorg) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 9ef60ec668..e26a032267 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -131,9 +131,7 @@ #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages logging) #:use-module (gnu packages lua) - #:use-module (gnu packages m4) #:use-module (gnu packages man) - #:use-module (gnu packages maths) #:use-module (gnu packages mpd) #:use-module (gnu packages pciutils) #:use-module (gnu packages music) @@ -153,7 +151,6 @@ #:use-module (gnu packages texinfo) #:use-module (gnu packages textutils) #:use-module (gnu packages time) - #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xml) From 8202adbceeba6c43dd5af5ffaa35e780cc9c5429 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Sat, 16 Sep 2023 17:49:27 +0100 Subject: [PATCH 322/440] gnu: enblend-enfuse: Backport upstream fixes. Backport changes for reproducible builds & missing include. * gnu/packages/patches/enblend-enfuse-reproducible.patch: New file. * gnu/local.mk: Register it. * gnu/packages/photo.scm (enblend-enfuse)[source]: Use newly added patch. Add snippet to fix missing header. [arguments]<#:phases>: Remove 'add-missing-include. Signed-off-by: Maxim Cournoyer --- gnu/local.mk | 1 + .../patches/enblend-enfuse-reproducible.patch | 44 +++++++++++++++++++ gnu/packages/photo.scm | 25 ++++++----- 3 files changed, 59 insertions(+), 11 deletions(-) create mode 100644 gnu/packages/patches/enblend-enfuse-reproducible.patch diff --git a/gnu/local.mk b/gnu/local.mk index 672050723f..54217fbd5a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1113,6 +1113,7 @@ dist_patch_DATA = \ %D%/packages/patches/emacs-kv-fix-tests.patch \ %D%/packages/patches/emacs-pgtk-super-key-fix.patch \ %D%/packages/patches/emacs-xelb-ignore-length-element.patch \ + %D%/packages/patches/enblend-enfuse-reproducible.patch \ %D%/packages/patches/enjarify-setup-py.patch \ %D%/packages/patches/enlightenment-fix-setuid-path.patch \ %D%/packages/patches/erlang-man-path.patch \ diff --git a/gnu/packages/patches/enblend-enfuse-reproducible.patch b/gnu/packages/patches/enblend-enfuse-reproducible.patch new file mode 100644 index 0000000000..8bd6a3aeda --- /dev/null +++ b/gnu/packages/patches/enblend-enfuse-reproducible.patch @@ -0,0 +1,44 @@ +# HG changeset patch +# User Bernhard M. Wiedemann +# Date 1502609999 -7200 +# Sun Aug 13 09:39:59 2017 +0200 +# Node ID a98e00eed893f62dd8349fc2894abca3aff4b33a +# Parent 41ce01b7d413b3654211da0147857e7d6a1495de +Facilitate reproducible builds +by allowing to externally hold constant the build date and time. +See + https://reproducible-builds.org/specs/source-date-epoch/ + +Backport asap. + +diff -r 41ce01b7d413 -r a98e00eed893 NEWS +--- a/NEWS Sun Aug 13 09:39:56 2017 +0200 ++++ b/NEWS Sun Aug 13 09:39:59 2017 +0200 +@@ -48,6 +48,12 @@ + https://github.com/akrzemi1/Optional + where only "optional.hpp" is needed. + ++- The environment variable SOURCE_DATE_EPOCH overrides the build ++ timestamp as recorded by the signatures. See ++ https://reproducible-builds.org/specs/source-date-epoch/ ++ for details. ++ ++ + + * Version 4.2 "Compressor Road" + +diff -r 41ce01b7d413 -r a98e00eed893 src/DefaultSig.pm +--- a/src/DefaultSig.pm Sun Aug 13 09:39:56 2017 +0200 ++++ b/src/DefaultSig.pm Sun Aug 13 09:39:59 2017 +0200 +@@ -109,9 +109,10 @@ + sub update_date_and_time { + my $self = shift; + ++ my $now = $ENV{SOURCE_DATE_EPOCH} || time; + my ($second, $minute, $hour, + $day_of_month, $month, $year, +- $day_of_week) = $self->is_using_gmt() ? gmtime : localtime; ++ $day_of_week) = $self->is_using_gmt() ? gmtime($now) : localtime($now); + + $self->{DATE} = $self->format_date($day_of_month, $month, $year + 1900, $day_of_week, + $self->weekdays->[$day_of_week], diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index b290e2b29a..39f4ce10d6 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -370,7 +370,18 @@ overlapping images, as well as some command line tools.") name "-" version ".tar.gz")) (sha256 (base32 - "0j5x011ilalb47ssah50ag0a4phgh1b0wdgxdbbp1gcyjcjf60w7")))) + "0j5x011ilalb47ssah50ag0a4phgh1b0wdgxdbbp1gcyjcjf60w7")) + (patches + ;; TODO: Remove when updating. + ;; Fixed upstream with a98e00eed893f62dd8349fc2894abca3aff4b33a. + (search-patches "enblend-enfuse-reproducible.patch")) + (modules '((guix build utils))) + (snippet + ;; TODO: Remove when updating. + ;; Fixed upstream with 81e25afe71146aaaf5058c604034f35d57e3be9d. + #~(substitute* "src/minimizer.cc" + (("^#include " all) + (string-append all "\n#include ")))))) (build-system gnu-build-system) (native-inputs (list pkg-config @@ -395,16 +406,8 @@ overlapping images, as well as some command line tools.") vigra zlib)) (arguments - (list #:configure-flags - #~(list "--enable-openmp") - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'add-missing-include - (lambda _ - (substitute* "src/minimizer.h" - ;; Fix error: ‘numeric_limits’ is not a member of ‘std’. - (("#include " line) - (string-append line "\n#include ")))))))) + (list + #:configure-flags #~(list "--enable-openmp"))) (home-page "https://enblend.sourceforge.net/") (synopsis "Tools for combining and blending images") (description From 33e300508947d831b1d63c018e92325ae4c4f959 Mon Sep 17 00:00:00 2001 From: Bruno Victal Date: Sat, 16 Sep 2023 17:49:28 +0100 Subject: [PATCH 323/440] gnu: enblend-enfuse: Build documentation. Notes: * transfig is not needed according to the NEWS since 4.2. * help2man is not optional. * gnu/packages/photo.scm (enblend-enfuse)[native-inputs]: Remove libxml2, tidy-html and transfig. Replace imagemagick with imagemagick/stable. Add graphviz-minimal, font-ghostscript, librsvg, m4, perl-readonly, texlive-texloganalyser, texlive-bold-extra, texlive-cm-mf-extra-bold, texlive-comment, texlive-float, texlive-enumitem, texlive-mdwtools, texlive-hyphenat, texlive-index, texlive-listings, texlive-microtype, texlive-etoolbox, texlive-nag, texlive-ragged2e, texlive-shorttoc, texlive-bigfoot, texlive-xstring and hevea. [arguments]<#:phases>: Add 'fontconfig-cache, 'exclude-doc-from-check and 'install-doc. Replace 'build and 'install. [outputs]: Add 'doc. Signed-off-by: Maxim Cournoyer --- gnu/packages/photo.scm | 82 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 74 insertions(+), 8 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 39f4ce10d6..78ae61c799 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020. 2021, 2022 Vinicius Monego ;;; Copyright © 2022, 2023 John Kehayias ;;; Copyright © 2022 Sharlatan Hellseher +;;; Copyright © 2023 Bruno Victal ;;; ;;; This file is part of GNU Guix. ;;; @@ -60,6 +61,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages glib) #: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) @@ -70,8 +72,10 @@ #:use-module (gnu packages libusb) #:use-module (gnu packages llvm) #:use-module (gnu packages lua) + #:use-module (gnu packages m4) #:use-module (gnu packages man) #:use-module (gnu packages maths) + #:use-module (gnu packages ocaml) #:use-module (gnu packages opencl) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -89,7 +93,6 @@ #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages wxwidgets) - #:use-module (gnu packages xfig) #:use-module (gnu packages xorg) #:use-module (gnu packages xml) #:use-module ((srfi srfi-1) #:hide (zip)) @@ -387,14 +390,34 @@ overlapping images, as well as some command line tools.") (list pkg-config perl perl-timedate + help2man ;; For building the documentation. gnuplot - help2man - imagemagick - libxml2 - (texlive-updmap.cfg) - tidy-html - transfig)) + graphviz-minimal ; for 'dot' + font-ghostscript + imagemagick/stable + librsvg + m4 + perl-readonly + texlive-texloganalyser + (texlive-updmap.cfg + (list texlive-bold-extra + texlive-cm-mf-extra-bold + texlive-comment + texlive-float + texlive-enumitem + texlive-mdwtools + texlive-hyphenat + texlive-index + texlive-listings + texlive-microtype + texlive-etoolbox ;used but not propagated by microtype + texlive-nag + texlive-ragged2e + texlive-shorttoc + texlive-bigfoot + texlive-xstring)) + hevea)) (inputs (list boost gsl @@ -407,7 +430,50 @@ overlapping images, as well as some command line tools.") zlib)) (arguments (list - #:configure-flags #~(list "--enable-openmp"))) + #:configure-flags #~(list "--enable-openmp") + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'fontconfig-cache + (lambda _ + (setenv "XDG_CACHE_HOME" (mkdtemp "/tmp/cache-XXXXXX")))) + ;; XXX: There's some extreme sillyness when building the + ;; documentation. It gets rebuilt thrice, during build, check and + ;; install, possibly due to the effects of the invocation of + ;; UPDATED_ON in doc/Makefile. + ;; Reported: + (add-after 'configure 'exclude-doc-from-check + (lambda _ + (substitute* "doc/Makefile" + (("^(check:).+$" _ rule) + (string-append rule "\n"))))) + ;; XXX: Skip building the docs since they're rebuilt again + ;; during install. + (replace 'build + (lambda args + (with-directory-excursion "src" + (apply (assoc-ref %standard-phases 'build) args)))) + ;; XXX: Save another doc rebuild when installing. + (replace 'install + ;; Intercept and insert a make-flag for this phase only. + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "install" + (cons "MAYBE_DOC=" make-flags)))) + ;; XXX: 'make install' doesn't install the docs. + (add-after 'install 'install-doc + (lambda* (#:key make-flags #:allow-other-keys) + ;; Install examples first, for which the 'install' rule works. + (with-directory-excursion "doc/examples" + (apply invoke "make" "install" make-flags)) + ;; The docs have to be installed with specific rules. + (with-directory-excursion "doc" + (apply invoke "make" + "install-ps-local" + "install-html-local" + "install-dvi-local" + ;; Do not overwhelm the console by printing the source + ;; to stdout. + (cons "V=0" make-flags)))))))) + (outputs '("out" "doc")) (home-page "https://enblend.sourceforge.net/") (synopsis "Tools for combining and blending images") (description From f1df78959a18aa1aed07e885051514938bd1fa92 Mon Sep 17 00:00:00 2001 From: Sughosha Date: Fri, 18 Aug 2023 16:52:46 +0200 Subject: [PATCH 324/440] gnu: Add qgit. * gnu/packages/version-control.scm (qgit): New variable. Signed-off-by: Maxim Cournoyer --- gnu/packages/version-control.scm | 37 +++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index cf3c4d4e19..248dc33171 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -79,6 +79,7 @@ #:use-module (guix build-system go) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module (guix build-system trivial) #:use-module (gnu packages apr) #:use-module (gnu packages autotools) @@ -1295,7 +1296,7 @@ and additionally allows you to access the Git repository more directly using either a pure Python implementation, or the faster, but more resource intensive @command{git} command implementation.") (license license:bsd-3))) - + (define-public savane (package (name "savane") @@ -3552,6 +3553,40 @@ has tools for tagging, merging, checking in/out, and other user operations. TkDiff is included for browsing and merging your changes.") (license license:gpl2+))) +(define-public qgit + (package + (name "qgit") + (version "2.10") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tibirna/qgit") + (commit (string-append "qgit-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10j5xll7ai1rb2ybyblbgqm762bqspffpf33fdr61qdchnp2gkf4")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f)) ;no tests + (propagated-inputs + (list git)) + (home-page "https://github.com/tibirna/qgit") + (synopsis "Graphical front-end for git") + (description + "Qgit is a graphical front-end for git, with features to: +@itemize +@item view revisions, diffs, files history, files annotation and archive tree, +@item commit changes visually cherry picking modified files, +@item apply or save patch series from selected commits, drag and drop commits, +@item associate commands sequences, scripts and anything else executable to a + custom action, +@item push/pop commits, +@item apply/save/create patches +@item and cherry pick single modified files. +@end itemize") + (license license:gpl3+))) + (define-public git-filter-repo (package (name "git-filter-repo") From fc1b4756e36857e66986a30a6652ee988f8f30fd Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Mon, 11 Sep 2023 22:31:56 -0400 Subject: [PATCH 325/440] .dir-locals.el: Update bug-reference configuration and document it. (nil) : Update URL. Add comment. * doc/contributing.texi (The Perfect Setup): New "Viewing bugs within Emacs" subsection. Co-authored-by: Brian Cully --- .dir-locals.el | 6 ++-- doc/contributing.texi | 64 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 68 insertions(+), 2 deletions(-) diff --git a/.dir-locals.el b/.dir-locals.el index 36714c1aa4..c63262848c 100644 --- a/.dir-locals.el +++ b/.dir-locals.el @@ -5,10 +5,12 @@ (tab-width . 8) (sentence-end-double-space . t) - ;; For use with 'bug-reference-prog-mode'. + ;; For use with 'bug-reference-prog-mode'. Extra bug-reference + ;; configuration should be done in your Emacs user configuration file; + ;; refer to (info (guix) The Perfect Setup). (bug-reference-bug-regexp . "\\(\\)") - (bug-reference-url-format . "https://bugs.gnu.org/%s") + (bug-reference-url-format . "https://issues.guix.gnu.org/%s") (eval . (add-to-list 'completion-ignored-extensions ".go")) diff --git a/doc/contributing.texi b/doc/contributing.texi index a0da871f1a..156a6cb19e 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -379,6 +379,70 @@ copyright-update}. If you want to do it automatically after each buffer save then add @code{(add-hook 'after-save-hook 'copyright-update)} in Emacs. +@subsection Viewing Bugs within Emacs + +Emacs has a nice minor mode called @code{bug-reference}, which, when +combined with @samp{emacs-debbugs} (the Emacs package), can be used to +open links such as @samp{} or +@samp{} as bug report buffers. From +there you can easily consult the email thread via the Gnus interface, +reply or modify the bug status, all without leaving the comfort of +Emacs! Below is a sample configuration to add to your @file{~/.emacs} +configuration file: + +@lisp +;;; Bug references. +(add-hook 'prog-mode-hook #'bug-reference-prog-mode) +(add-hook 'gnus-mode-hook #'bug-reference-mode) +(add-hook 'erc-mode-hook #'bug-reference-mode) +(add-hook 'bug-reference-mode-hook 'debbugs-browse-mode) +(add-hook 'bug-reference-prog-mode-hook 'debbugs-browse-mode) +(add-hook 'gnus-summary-mode-hook 'bug-reference-mode) +(add-hook 'gnus-article-mode-hook 'bug-reference-mode) + +;;; This extends the default expression (the top-most, first expression +;;; provided to 'or') to also match URLs such as +;;; or . +;;; It is also extended to detect "Fixes: #NNNNN" git trailers. +(setq bug-reference-bug-regexp + (rx (group (or (seq word-boundary + (or (seq (char "Bb") "ug" + (zero-or-one " ") + (zero-or-one "#")) + (seq (char "Pp") "atch" + (zero-or-one " ") + "#") + (seq (char "Ff") "ixes" + (zero-or-one ":") + (zero-or-one " ") "#") + (seq "RFE" + (zero-or-one " ") "#") + (seq "PR " + (one-or-more (char "a-z+-")) "/")) + (group (one-or-more (char "0-9")) + (zero-or-one + (seq "#" (one-or-more + (char "0-9")))))) + (seq ""))))) + +;; The following allows Emacs Debbugs user to open the issue directly within +;; Emacs. +(setq debbugs-browse-url-regexp + (rx line-start + "http" (zero-or-one "s") "://" + (or "debbugs" "issues.guix" "bugs") + ".gnu.org" (one-or-more "/") + (group (zero-or-one "cgi/bugreport.cgi?bug=")) + (group-n 3 (one-or-more digit)) + line-end)) +@end lisp + +For more information, refer to @ref{Bug Reference,,, emacs, The GNU +Emacs Manual} and @ref{Minor Mode,,, debbugs-ug, The Debbugs User +Guide}. + @node Packaging Guidelines @section Packaging Guidelines From 7075551d082a5b1d80832c15bb306de760bcdff4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 326/440] gnu: borg: Update to 1.2.6. * gnu/packages/backup.scm (borg): Update to 1.2.6. --- gnu/packages/backup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index bd5e2e463f..40655acd79 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -635,13 +635,13 @@ detection, and lossless compression.") (define-public borg (package (name "borg") - (version "1.2.4") + (version "1.2.6") (source (origin (method url-fetch) (uri (pypi-uri "borgbackup" version)) (sha256 - (base32 "1a2d6z2ln476l0fcnkl4rpciij5b2lql44b71aivg0cy8vlm9gd4")) + (base32 "178klb3pglhhz553frf928v7zvaiqvri9fbhj33yx7h3hvqgi9mp")) (modules '((guix build utils))) (snippet #~(begin From 591dbeb124596f032675993caad720f4e9f71cae Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 327/440] gnu: qpwgraph: Update to 0.5.3. * gnu/packages/audio.scm (qpwgraph): Update to 0.5.3. --- gnu/packages/audio.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 48a4f8d536..3ab496bcdf 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -6287,7 +6287,7 @@ and DSD streams.") (define-public qpwgraph (package (name "qpwgraph") - (version "0.5.2") + (version "0.5.3") (source (origin (method git-fetch) (uri (git-reference @@ -6296,9 +6296,10 @@ and DSD streams.") (file-name (git-file-name name version)) (sha256 (base32 - "186c3s56py8xjasbp4380m9sqdba9mf7mppqz8hkli1nhbspbix9")))) + "1i9p8gqm9swa2szr7i8rf3dhqxlaqjslb6yd5s9z1rs1jdb9lhp7")))) (build-system cmake-build-system) - (arguments (list #:tests? #f)) ;; no tests + (arguments + (list #:tests? #f)) ; no tests (inputs (list alsa-lib libxkbcommon pipewire From 1d30ec935126f316187dfc26446347bc7de9868b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 10 Sep 2023 02:00:00 +0200 Subject: [PATCH 328/440] gnu: rdiff-backup: Update to 2.2.6. * gnu/packages/backup.scm (rdiff-backup): Update to 2.2.6. --- gnu/packages/backup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 40655acd79..12c4a45b9d 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -481,14 +481,14 @@ errors.") (define-public rdiff-backup (package (name "rdiff-backup") - (version "2.2.5") + (version "2.2.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/rdiff-backup/rdiff-backup/releases/" "download/v" version "/rdiff-backup-" version ".tar.gz")) (sha256 - (base32 "13m0kq9y6rzgaq0zlzh7qhi789qmbzp3dnc7y57fmhsfg1mq5ql6")))) + (base32 "1ksqjkqadhxzp83zdfs80dvb494vn9q4anppnwxm3ikb4rbq6xyh")))) (build-system python-build-system) (native-inputs (list python-setuptools-scm)) From 658de25e990a56265e2398a3737e9cf1eb57af68 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 22 Jun 2023 08:30:25 +0200 Subject: [PATCH 329/440] self: Build directories in chunks of max 25 files at a time. This increases the chances of a successful `guix pull' on the Hurd, see . * guix/self.scm (compiled-modules)[process-directory]: Split building of directories into chunks of max 25 files. Also call gc. --- guix/self.scm | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/guix/self.scm b/guix/self.scm index 81a36e007f..d2300052d8 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017-2023 Ludovic Courtès ;;; Copyright © 2020 Martin Becze +;;; Copyright © 2023 Janneke Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -1210,7 +1211,8 @@ containing MODULE-FILES and possibly other files as well." '((guix build compile) (guix build utils))) #~(begin - (use-modules (srfi srfi-26) + (use-modules (srfi srfi-1) + (srfi srfi-26) (ice-9 match) (ice-9 format) (ice-9 threads) @@ -1244,12 +1246,23 @@ containing MODULE-FILES and possibly other files as well." (force-output)) (define (process-directory directory files output) - ;; Hide compilation warnings. - (parameterize ((current-warning-port (%make-void-port "w"))) - (compile-files directory #$output files - #:workers (parallel-job-count) - #:report-load report-load - #:report-compilation report-compilation))) + (let* ((size 25) ;compile max 25 files a time + (chunks (unfold + (lambda (seed) (< (length seed) size)) ;p + (cute take <> size) ;f + (cute drop <> size) ;g + files ;seed + list))) ;tail + (for-each + (lambda (chunk) + ;; Hide compilation warnings. + (parameterize ((current-warning-port (%make-void-port "w"))) + (compile-files directory output chunk + #:workers (parallel-job-count) + #:report-load report-load + #:report-compilation report-compilation) + (gc))) + chunks))) (setvbuf (current-output-port) 'line) (setvbuf (current-error-port) 'line) From 1a0c7f71f0d74167f04377773791305260871b26 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Mon, 18 Sep 2023 06:49:46 +0200 Subject: [PATCH 330/440] gnu: guix: Update to 1.4.0-11.658de25e99. * gnu/packages/package-management.scm (guix): Update to 1.4.0-11.658de25e99. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index cbda40f78b..9db928dea0 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -174,8 +174,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "1.4.0") - (commit "4dfdd822102690b5687acf28365ab707b68d9476") - (revision 10)) + (commit "658de25e990a56265e2398a3737e9cf1eb57af68") + (revision 11)) (package (name "guix") @@ -191,7 +191,7 @@ (commit commit))) (sha256 (base32 - "1p21gz2lr7iqvma1m83k2r04w201rzvk31d5kfn2qkr9l0gds4cx")) + "039hmqbfkhscjyzrydvz5c8dvddwqdwlxrrl8l60prz0bfhshda9")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments From 30e5484f35cfb0f6b00ca317c1fc360002ffb8c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 18 Sep 2023 10:12:40 +0200 Subject: [PATCH 331/440] gnu: swineherd: Propagate inputs. Swineherd does not wrap its inputs, so it needs to drag along all its Guile inputs when installed. * gnu/packages/admin.scm (swineherd)[inputs]: Move all from here... [propagated-inputs]: ...to here. --- gnu/packages/admin.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index c6b62834f1..741d4758f6 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -422,7 +422,7 @@ interface and is based on GNU Guile.") #:make-flags '("GUILE_AUTO_COMPILE=0"))) (native-inputs (list autoconf automake guile-3.0 pkg-config texinfo)) - (inputs + (propagated-inputs (list btrfs-progs guile-config guile-fibers-1.3 From 1c8e159335c3723194cd0e5357c89abb8d4edf13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 18 Sep 2023 05:39:20 +0200 Subject: [PATCH 332/440] gnu: python-plastid: Patch it for python 3.10. * gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase 'patch-for-python-3.10. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c78f017a24..b909cd5ee0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3787,6 +3787,13 @@ UCSC genome browser.") "-xf" (assoc-ref inputs "test-data")) ;; This one requires bowtie-build (delete-file "plastid/test/functional/test_crossmap.py"))) + (add-after 'unpack 'patch-for-python-3.10 + (lambda _ + ;; Some classes were moved from collections to collections.abc + ;; in Python 3.10. + (substitute* "plastid/readers/bigbed.pyx" + ((", Iterable") + "\nfrom collections.abc import Iterable")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. From 83598dafb971fda9206f14cf46d072e04e27fd43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= Date: Mon, 18 Sep 2023 06:35:33 +0200 Subject: [PATCH 333/440] gnu: python-fit-nbinom: Remove syntax error in setup.py. * gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Add phase 'remove-invalid-syntax. Signed-off-by: Ricardo Wurmus --- gnu/packages/python-xyz.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index dd3f987475..e96f4a2d0d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -582,6 +582,14 @@ and variables you'll need already imported and created. (base32 "12v8l5i35vjbpvh5i4lw29ys6vpr3z7pysyrx33hxaq09zr015mx")))) (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'remove-invalid-syntax + (lambda _ + (substitute* "setup.py" + ((".\\*\"") "\""))))))) (propagated-inputs (list python-numpy python-scipy)) (home-page "https://github.com/joachimwolff/fit_nbinom") (synopsis "Negative binomial maximum likelihood estimator") From 9c98e144ff3ba2038b21c7d44edabc786bb99f8d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 18 Sep 2023 10:53:12 +0300 Subject: [PATCH 334/440] gnu: font-gnu-unifont: Update to 15.1.01. * gnu/packages/fonts.scm (font-gnu-unifont): Update to 15.1.01. [source]: Adjust snippet to not remove non-existent precompiled files. [arguments]: Disable parallel build. Adjust custom 'install phase to not duplicate actions from the Makefile. --- gnu/packages/fonts.scm | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index c51679c273..404495f6e3 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -933,7 +933,7 @@ for use at smaller text sizes"))) (define-public font-gnu-unifont (package (name "font-gnu-unifont") - (version "15.0.01") + (version "15.1.01") (source (origin (method url-fetch) @@ -943,12 +943,11 @@ for use at smaller text sizes"))) (string-append "mirror://gnu/unifont/unifont-" version "/unifont-" version ".tar.gz"))) (sha256 - (base32 "1m9lfss6sbmcr0b6h7pxxmdl71j9dmnvk8idvxzylqrwpwjaj4bx")) + (base32 "1dydcqa2nvmnij5jzj10carrzssd3ar24i8zd18pk4zpl84l4pz1")) (snippet '(begin (use-modules (guix build utils)) - (delete-file-recursively "font/precompiled") - (delete-file-recursively "hangul/precompiled"))))) + (delete-file-recursively "font/precompiled"))))) (build-system gnu-build-system) (outputs '("out" ; TrueType/OpenType version "pcf" ; PCF (bitmap) version @@ -956,6 +955,7 @@ for use at smaller text sizes"))) "bin")) ; Utilities to manipulate '.hex' format (arguments `(#:tests? #f ; no check target + #:parallel-build? #f ; Race condition in the font Makefile #:make-flags (list (string-append "CC=" ,(cc-for-target)) "BUILDFONT=TRUE") @@ -977,20 +977,13 @@ for use at smaller text sizes"))) (psf (string-append (assoc-ref outputs "psf") "/share/consolefonts")) (bin (assoc-ref outputs "bin"))) - ;; This directory isn't created in fonts/Makefile. - (mkdir-p otf) (apply invoke "make" "install" (string-append "PREFIX=" bin) (string-append "TTFDEST=" ttf) (string-append "OTFDEST=" otf) (string-append "PCFDEST=" pcf) (string-append "CONSOLEDEST=" psf) - make-flags) - ;; Move Texinfo file to the right place. - (mkdir (string-append bin "/share/info")) - (invoke "gzip" "-9n" "doc/unifont.info") - (install-file "doc/unifont.info.gz" - (string-append bin "/share/info")))))))) + make-flags))))))) (native-inputs (list bdftopcf console-setup fontforge)) (inputs From c46fe3ed743dde2fb4b15e578e6985d888ce87e4 Mon Sep 17 00:00:00 2001 From: "Andre A. Gomes" Date: Fri, 15 Sep 2023 20:44:18 +0300 Subject: [PATCH 335/440] gnu: cl-nkeymaps: Update to 1.1.0. * gnu/packages/lisp-xyz.scm (sbcl-nkeymaps): Update to 1.1.0. [inputs]: Add sbcl-cl-str. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 1d88654962..c6f66db840 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -26528,7 +26528,7 @@ in a native template application).") (define-public sbcl-nkeymaps (package (name "sbcl-nkeymaps") - (version "1.0.0") + (version "1.1.0") (source (origin (method git-fetch) @@ -26537,11 +26537,12 @@ in a native template application).") (commit version))) (file-name (git-file-name "cl-nkeymaps" version)) (sha256 - (base32 "1f7s9g5s9riyyrbj8lyvzlvymdbh9x9sknxmjzfrkbz3iqlpanc3")))) + (base32 "08q3bmb3i7mjpm83msp1qgpifpzf019ggikbxwc2dk04i3c2w0vv")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-alexandria sbcl-fset + sbcl-cl-str sbcl-trivial-package-local-nicknames)) (native-inputs (list sbcl-lisp-unit2)) From 273709932fa47f6ae56c96564a9415fdbff4a169 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Mon, 18 Sep 2023 12:31:50 +0200 Subject: [PATCH 336/440] Revert "gnu: guix: Update to 1.4.0-11.658de25e99." Several people on IRC report that "rewrite-url, to-version specified" fails. This reverts commit 1a0c7f71f0d74167f04377773791305260871b26. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 9db928dea0..cbda40f78b 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -174,8 +174,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "1.4.0") - (commit "658de25e990a56265e2398a3737e9cf1eb57af68") - (revision 11)) + (commit "4dfdd822102690b5687acf28365ab707b68d9476") + (revision 10)) (package (name "guix") @@ -191,7 +191,7 @@ (commit commit))) (sha256 (base32 - "039hmqbfkhscjyzrydvz5c8dvddwqdwlxrrl8l60prz0bfhshda9")) + "1p21gz2lr7iqvma1m83k2r04w201rzvk31d5kfn2qkr9l0gds4cx")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments From a749ae387d308d998c5b44dc03a95ef87f66ebc3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 18 Sep 2023 13:05:01 +0300 Subject: [PATCH 337/440] gnu: julia-forwarddiff: Update to 0.10.36. * gnu/packages/julia-xyz.scm (julia-forwarddiff): Update to 0.10.36. [propagated-inputs]: Add julia-logexpfunctions. --- gnu/packages/julia-xyz.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index a1e65332fa..11feea7d46 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2353,7 +2353,7 @@ c-style numerical formatting.") (define-public julia-forwarddiff (package (name "julia-forwarddiff") - (version "0.10.34") + (version "0.10.36") (source (origin (method git-fetch) @@ -2362,7 +2362,7 @@ c-style numerical formatting.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1lwjw2jzkffwk06hfc30vxhv36ng3gf12qjc43swmqiakkd3m5jx")))) + (base32 "0mg9b5p3farc05wdxzciykrlx9hy7ivm0dq50hwp0dgd600hdjxy")))) (build-system julia-build-system) (arguments ;; XXXX: Unexpected and non-deterministic failures for i686, e.g., @@ -2380,6 +2380,7 @@ c-style numerical formatting.") julia-diffresults julia-diffrules julia-difftests + julia-logexpfunctions julia-nanmath julia-specialfunctions julia-staticarrays)) From 3d9ebc7b2ed24312fd6a0916c203f7b86d57753d Mon Sep 17 00:00:00 2001 From: "Dr. Arne Babenhauserheide" Date: Mon, 18 Sep 2023 12:58:26 +0200 Subject: [PATCH 338/440] gnu: icecat: Update to 102.15.1 [security fixes]. This fixes fix mfsa2023-40, a critical webp vulnerability. See https://www.mozilla.org/en-US/security/advisories/mfsa2023-40/ * gnu/packages/gnuzilla.scm (%icecat-base-version, icecat-source): Update to 102.15.1. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/gnuzilla.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 6e2f9729cf..e700931d28 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -518,7 +518,7 @@ variable defined below. It requires guile-json to be installed." ;; XXXX: Workaround 'snippet' limitations. (define computed-origin-method (@@ (guix packages) computed-origin-method)) -(define %icecat-base-version "102.15.0") +(define %icecat-base-version "102.15.1") (define %icecat-version (string-append %icecat-base-version "-guix0-preview1")) (define %icecat-build-id "20230829000000") ;must be of the form YYYYMMDDhhmmss @@ -540,7 +540,7 @@ variable defined below. It requires guile-json to be installed." "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "1bs6hxfsb77cbi238wvizq2iw4mlgz29m0sd027sz8zm1025kyl1")))) + "04q1fjninm9lw721xgv0c2fknicc24s8iaimkabwcfwmcnvly689")))) ;; The upstream-icecat-base-version may be older than the ;; %icecat-base-version. From 71ec12d8bacd3901e8c7853d3c9403f3d09dfb31 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 339/440] gnu: ocl-icd: Delete dubiously deprecated duplicate definition. This follows up on commit 3341b22f594398b3aa3ff930d99b74a78abd1a30 which re-added ocl-icd. opencl-icd-loader is a different, incompatible package. * gnu/packages/opencl.scm (ocl-icd): Remove duplicate variable. --- gnu/packages/opencl.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm index 74b250cb9d..036834f567 100644 --- a/gnu/packages/opencl.scm +++ b/gnu/packages/opencl.scm @@ -161,9 +161,6 @@ implementation. The ICD Loader is responsible for: This package contains the Khronos official OpenCL ICD Loader.") (license license:asl2.0))) -(define-public ocl-icd - (deprecated-package "ocl-icd" opencl-icd-loader)) - (define-public clinfo (package (name "clinfo") From 926a79a86aa89d3b743fd3405b49e37493f7792d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 18 Sep 2023 17:43:53 +0300 Subject: [PATCH 340/440] gnu: julia-deepdiffs: Skip tests. * gnu/packages/julia-xyz.scm (julia-deepdiffs)[arguments]: Skip the test suite. --- gnu/packages/julia-xyz.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 11feea7d46..144574857e 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1591,6 +1591,8 @@ to represent missing data.") (sha256 (base32 "1gsbxb1d67g05h5bvzz3swdfih6404jrydy724a8dvbdgqvm3sds")))) (build-system julia-build-system) + ;; This package seems unmaintained but still has dependant packages. + (arguments (list #:tests? #f)) (home-page "https://github.com/ssfrr/DeepDiffs.jl") (synopsis "Compute and pretty-print diffs for data structures") (description "@code{DeepDiffs.jl} provides the @code{deepdiff} function, From a515f8b1d8fbda4ea791762fc3987bd5411de077 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 18 Sep 2023 22:30:44 +0300 Subject: [PATCH 341/440] gnu: tor: Update to 0.4.8.6. * gnu/packages/tor.scm (tor): Update to 0.4.8.6. [source]: Remove patch. * gnu/packages/patches/tor-remove-defensive-assert.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../patches/tor-remove-defensive-assert.patch | 28 ------------------- gnu/packages/tor.scm | 7 ++--- 3 files changed, 3 insertions(+), 33 deletions(-) delete mode 100644 gnu/packages/patches/tor-remove-defensive-assert.patch diff --git a/gnu/local.mk b/gnu/local.mk index 54217fbd5a..13e7d1af72 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -2023,7 +2023,6 @@ dist_patch_DATA = \ %D%/packages/patches/tofi-32bit-compat.patch \ %D%/packages/patches/tootle-glib-object-naming.patch \ %D%/packages/patches/tootle-reason-phrase.patch \ - %D%/packages/patches/tor-remove-defensive-assert.patch \ %D%/packages/patches/transcode-ffmpeg.patch \ %D%/packages/patches/transfig-gcc10-fno-common.patch \ %D%/packages/patches/trytond-add-egg-modules-to-path.patch \ diff --git a/gnu/packages/patches/tor-remove-defensive-assert.patch b/gnu/packages/patches/tor-remove-defensive-assert.patch deleted file mode 100644 index 7207ec867a..0000000000 --- a/gnu/packages/patches/tor-remove-defensive-assert.patch +++ /dev/null @@ -1,28 +0,0 @@ -This patch removes a call to `tor_assert_nonfatal_unreached()` in -`relay_key_is_unavailable_()` that is only called when Tor is compiled -without relay support. - -Unfortunately, the non-fatal assertion causes a BUG log -message to appear for clients when they start up without relay support -for each CPU worker we spawn. This makes it spotting issues during -bootstrap harder particularly for our iOS developers. - -Since the call sites to `get_master_identity_key()` handles `NULL` -values already, we do not think this will be an issue later on. - -Reported by Benjamin Erhart (@tla) from Guardian Project. - -Fixes tpo/core/tor#40848. - -diff --git a/src/feature/relay/routerkeys.h b/src/feature/relay/routerkeys.h -index 7b6d80773c..b97615a9c9 100644 ---- a/src/feature/relay/routerkeys.h -+++ b/src/feature/relay/routerkeys.h -@@ -53,7 +53,6 @@ void routerkeys_free_all(void); - static inline void * - relay_key_is_unavailable_(void) - { -- tor_assert_nonfatal_unreached(); - return NULL; - } - #define relay_key_is_unavailable(type) \ diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 44e62b63cc..1eb62a950e 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2021 Ludovic Courtès ;;; Copyright © 2014, 2015 Mark H Weaver -;;; Copyright © 2016, 2017, 2018, 2020, 2021, 2022 Efraim Flashner +;;; Copyright © 2016-2018, 2020-2023 Efraim Flashner ;;; Copyright © 2016, 2017 Nikita ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice ;;; Copyright © 2017, 2018, 2019, 2021, 2023 Eric Bavier @@ -63,15 +63,14 @@ (define-public tor (package (name "tor") - (version "0.4.8.5") + (version "0.4.8.6") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "06g1awb4piqvgxa97pyswxgjzkpj8rx3iy2jbiaygvi99b8wymv9")) - (patches (search-patches "tor-remove-defensive-assert.patch")))) + "122h6l3nh8xrpzkmn4alsbz30jw8nxivwnhgnp97qv7nr9gqjbam")))) (build-system gnu-build-system) (arguments (list #:configure-flags From 7bf12820f61179900f9d1f753acf91fd33724976 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Mon, 21 Aug 2023 20:57:12 +0200 Subject: [PATCH 342/440] maint: Support `guix shell' in Guix's git archive with manifest.scm. * manifest.scm: New file. * Makefile.am (EXTRA_DIST): Add it. * doc/contributing.texi (Building from Git): Mention using it. --- Makefile.am | 1 + doc/contributing.texi | 6 ++++++ manifest.scm | 30 ++++++++++++++++++++++++++++++ 3 files changed, 37 insertions(+) create mode 100644 manifest.scm diff --git a/Makefile.am b/Makefile.am index 922913355c..8924974e8a 100644 --- a/Makefile.am +++ b/Makefile.am @@ -692,6 +692,7 @@ EXTRA_DIST += \ ROADMAP \ TODO \ bootstrap \ + manifest.scm \ build-aux/build-self.scm \ build-aux/check-channel-news.scm \ build-aux/check-final-inputs-self-contained.scm \ diff --git a/doc/contributing.texi b/doc/contributing.texi index 156a6cb19e..4de659c7ed 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -77,6 +77,12 @@ hack on Guix: guix shell -D guix --pure @end example +or even, from within a Git worktree for Guix: + +@example +guix shell --pure +@end example + @xref{Invoking guix shell}, for more information on that command. If you are unable to use Guix when building Guix from a checkout, the diff --git a/manifest.scm b/manifest.scm new file mode 100644 index 0000000000..bcd94b68c5 --- /dev/null +++ b/manifest.scm @@ -0,0 +1,30 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2022 Janneke Nieuwenhuizen +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +;; GNU Guix development manifest. To create development environment, run +;; +;; guix shell +;; +;; or something like +;; +;; guix shell --pure git git:send-email openssh + +(use-modules (guix profiles) + (gnu packages package-management)) + +(package->development-manifest guix) From a839bb9777ac2686c41c48b7499123c7e8f9c281 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 17 Sep 2023 17:34:17 +0200 Subject: [PATCH 343/440] doc: Fix typo. * doc/guix.texi (Specifying Channel Authorizations): Remove extra hyphen. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 983b471fd8..50c4984d71 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -6114,7 +6114,7 @@ the fingerprint of the OpenPGP used to sign it. @end enumerate Before pushing to your public Git repository, you can run @command{guix -git-authenticate} to verify that you did sign all the commits you are +git authenticate} to verify that you did sign all the commits you are about to push with an authorized key: @example From 5e0ae2684615b6d10751390420e7db296785112b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 17 Sep 2023 17:56:27 +0200 Subject: [PATCH 344/440] =?UTF-8?q?services:=20hurd-vm:=20Use=20=E2=80=98q?= =?UTF-8?q?emu-system-x86=5F64=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/services/virtualization.scm (hurd-vm-shepherd-service)[vm-command]: Use ‘qemu-system-x86_64’. --- gnu/services/virtualization.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/services/virtualization.scm b/gnu/services/virtualization.scm index eef7ffd1c7..e1a206e0eb 100644 --- a/gnu/services/virtualization.scm +++ b/gnu/services/virtualization.scm @@ -1163,7 +1163,9 @@ is added to the OS specified in CONFIG." (provisions '(hurd-vm childhurd))) (define vm-command - #~(append (list #$(file-append qemu "/bin/qemu-system-i386") + ;; XXX: Use the x86_64 emulator instead of the i386 one to work around + ;; "Bad ram pointer" issues: . + #~(append (list #$(file-append qemu "/bin/qemu-system-x86_64") "-m" (number->string #$memory-size) #$@net-options #$@options From 9f0c9f9049a7190ff2167da2f455354b41744ffa Mon Sep 17 00:00:00 2001 From: Kjartan Oli Agustsson Date: Sun, 3 Sep 2023 20:59:33 +0000 Subject: [PATCH 345/440] gnu: Add commit-patch. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/version-control.scm (commit-patch): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/version-control.scm | 33 ++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 248dc33171..9716a6f27a 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -48,6 +48,7 @@ ;;; Copyright © 2022 Dhruvin Gandhi ;;; Copyright © 2015, 2022 David Thompson ;;; Copyright © 2023 Nicolas Graves +;;; Copyright © 2023 Kjartan Oli Agustsson ;;; ;;; This file is part of GNU Guix. ;;; @@ -116,6 +117,7 @@ #:use-module (gnu packages ncurses) #:use-module (gnu packages ssh) #:use-module (gnu packages web) + #:use-module (gnu packages patchutils) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -3722,3 +3724,34 @@ create and manage trackers, tickets interact with GraphQL APIs directly @end table") (license license:agpl3))) + +(define-public commit-patch + (package + (name "commit-patch") + (version "2.6.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/caldwell/commit-patch/releases/download/" + version "/commit-patch-" version ".tar.gz")) + (sha256 + (base32 + "0v11vjyisk243zi0ym90bnqb229j7iaqx1lwqdkszxzn1yxwq4ck")))) + (build-system copy-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (patch-shebang "commit-patch")))) + #:install-plan ''(("commit-patch" "bin/") + ("commit-patch-buffer.el" + "share/emacs/site-lisp/")))) + (inputs (list perl)) + (propagated-inputs (list patchutils)) + (synopsis "Commit parts of changes to VCS repositories") + (description + "commit-patch is a utility that lets you check in select portions of a +file into Darcs, Git, Mercurial, Bazaar, Subversion, or CVS repositories. It +comes as a command line app and also an Emacs interface.") + (home-page "https://porkrind.org/commit-patch/") + (license license:gpl2+))) From 429a543d2222b12ffd014e1a8dc072c7ece8ad9e Mon Sep 17 00:00:00 2001 From: Andy Tai Date: Thu, 14 Sep 2023 22:20:55 -0700 Subject: [PATCH 346/440] gnu: tensorflow-lite: Update to 2.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/machine-learning.scm: (tensorflow-lite): Update to 2.13.0 [inputs]: Add gemmlowp [native-inputs]: Remove gemmlowp-src * gnu/packages/patches/tensorflow-lite-unbundle.patch: New file * gnu/local.mk (dist_patch_DATA): Add it. Co-authored-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/machine-learning.scm | 31 +++++-------------- .../patches/tensorflow-lite-unbundle.patch | 27 ++++++++++++++++ 3 files changed, 36 insertions(+), 23 deletions(-) create mode 100644 gnu/packages/patches/tensorflow-lite-unbundle.patch diff --git a/gnu/local.mk b/gnu/local.mk index 13e7d1af72..de3cb0332c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -2003,6 +2003,7 @@ dist_patch_DATA = \ %D%/packages/patches/tcsh-fix-autotest.patch \ %D%/packages/patches/teensy-loader-cli-help.patch \ %D%/packages/patches/tensorflow-c-api-fix.patch \ + %D%/packages/patches/tensorflow-lite-unbundle.patch \ %D%/packages/patches/texinfo-headings-single.patch \ %D%/packages/patches/texinfo-5-perl-compat.patch \ %D%/packages/patches/telegram-desktop-allow-disable-libtgvoip.patch \ diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f351586214..abba41626d 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -2997,7 +2997,7 @@ advanced research.") (define-public tensorflow-lite (package (name "tensorflow-lite") - (version "2.12.1") + (version "2.13.0") (source (origin (method git-fetch) @@ -3007,7 +3007,8 @@ advanced research.") (file-name (git-file-name name version)) (sha256 (base32 - "0jkgljdagdqllnxygl35r5bh3f9qmbczymfj357gm9krh59g2kmd")))) + "07g6vlrs0aayrg2mfdl15gxg5dy103wx2xlqkran15dib40nkbj6")) + (patches (search-patches "tensorflow-lite-unbundle.patch")))) (build-system cmake-build-system) (arguments (list @@ -3050,6 +3051,7 @@ advanced research.") "-DTFLITE_ENABLE_XNNPACK=OFF" ;; Don't fetch the sources. We have these already + "-Dgemmlowp_POPULATED=TRUE" "-Degl_headers_POPULATED=TRUE" "-Dfp16_headers_POPULATED=TRUE" "-Dopencl_headers_POPULATED=TRUE" @@ -3062,7 +3064,7 @@ advanced research.") "-DFFT2D_SOURCE_DIR=/tmp/fft2d" "-DFARMHASH_SOURCE_DIR=/tmp/farmhash" - "-Dgemmlowp_SOURCE_DIR=/tmp/gemmlowp") + (string-append "-Dgemmlowp_ROOT=" #$(this-package-input "gemmlowp"))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'chdir @@ -3092,11 +3094,7 @@ advanced research.") (mkdir-p "/tmp/fft2d") (with-directory-excursion "/tmp/fft2d" (invoke "tar" "--strip-components=1" - "-xf" (assoc-ref inputs "fft2d-src"))) - - (copy-recursively (assoc-ref inputs "gemmlowp-src") - "/tmp/gemmlowp/"))) - + "-xf" (assoc-ref inputs "fft2d-src"))))) (add-after 'build 'build-shared-library (lambda* (#:key configure-flags #:allow-other-keys) (mkdir-p "c") @@ -3126,7 +3124,7 @@ advanced research.") ("eigen" ,eigen) ("fp16" ,fp16) ("flatbuffers-shared" ,flatbuffers-next-shared) - ;;("gemmlowp" ,gemmlowp) ; TODO + ("gemmlowp" ,gemmlowp) ("mesa-headers" ,mesa-headers) ("neon2sse" ,neon2sse) ("nsync" ,nsync) @@ -3142,19 +3140,6 @@ advanced research.") (native-inputs `(("pkg-config" ,pkg-config) ("googletest" ,googletest) - ("gemmlowp-src" - ;; The commit hash is taken from - ;; "tensorflow/lite/tools/cmake/modules/gemmlowp.cmake". - ,(let ((commit "fda83bdc38b118cc6b56753bd540caa49e570745")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/google/gemmlowp") - (commit commit))) - (file-name (git-file-name "gemmlowp" (string-take commit 8))) - (sha256 - (base32 - "1sbp8kmr2azwlvfbzryy1frxi99jhsh1nc93bdbxdf8zdgpv0kxl"))))) ("farmhash-src" ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45")) (origin @@ -3176,7 +3161,7 @@ advanced research.") (sha256 (base32 "1jfflzi74fag9z4qmgwvp90aif4dpbr1657izmxlgvf4hy8fk9xd")))))) - (home-page "https://tensorflow.org") + (home-page "https://www.tensorflow.org") (synopsis "Machine learning framework") (description "TensorFlow is a flexible platform for building and training machine diff --git a/gnu/packages/patches/tensorflow-lite-unbundle.patch b/gnu/packages/patches/tensorflow-lite-unbundle.patch new file mode 100644 index 0000000000..efd7d5bbc6 --- /dev/null +++ b/gnu/packages/patches/tensorflow-lite-unbundle.patch @@ -0,0 +1,27 @@ +Disable local CMake build code for bundled 3rdparty components. + +diff --git a/tensorflow/lite/CMakeLists.txt b/tensorflow/lite/CMakeLists.txt +index 0476170e075..90abea00e8c 100644 +--- a/tensorflow/lite/CMakeLists.txt ++++ b/tensorflow/lite/CMakeLists.txt +@@ -564,7 +564,7 @@ set(_ALL_TFLITE_HDRS ${_ALL_TFLITE_SRCS}) + list(FILTER _ALL_TFLITE_HDRS INCLUDE REGEX ".*\\.h$") + target_include_directories(tensorflow-lite + PUBLIC $ $ +- ${CMAKE_BINARY_DIR}/gemmlowp ++ ${gemmlowp_ROOT}/include/gemmlowp + ) + target_link_libraries(tensorflow-lite + PUBLIC +diff --git a/tensorflow/lite/tools/cmake/modules/Findgemmlowp.cmake b/tensorflow/lite/tools/cmake/modules/Findgemmlowp.cmake +index 70331ad0a69..a9bd8a0f3bd 100644 +--- a/tensorflow/lite/tools/cmake/modules/Findgemmlowp.cmake ++++ b/tensorflow/lite/tools/cmake/modules/Findgemmlowp.cmake +@@ -18,7 +18,6 @@ + include(gemmlowp) + if(gemmlowp_POPULATED) + set(GEMMLOWP_FOUND TRUE) +- get_target_property(GEMMLOWP_INCLUDE_DIRS gemmlowp INTERFACE_DIRECTORIES) + set(GEMMLOWP_LIBRARIES + gemmlowp + gemmlowp_fixedpoint From 1fa438fd1caa7429b3a576b6beb6abaf85080df2 Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Fri, 8 Sep 2023 12:29:08 -0400 Subject: [PATCH 347/440] gnu: Add alure. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/audio.scm (alure): New variable. Co-authored-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/audio.scm | 32 +++++++++++++++++++++++++ gnu/packages/patches/alure-dumb-2.patch | 30 +++++++++++++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 gnu/packages/patches/alure-dumb-2.patch diff --git a/gnu/local.mk b/gnu/local.mk index de3cb0332c..e05f687467 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -902,6 +902,7 @@ dist_patch_DATA = \ %D%/packages/patches/akonadi-not-relocatable.patch \ %D%/packages/patches/akonadi-timestamps.patch \ %D%/packages/patches/allegro-mesa-18.2.5-and-later.patch \ + %D%/packages/patches/alure-dumb-2.patch \ %D%/packages/patches/ibus-anthy-fix-tests.patch \ %D%/packages/patches/ibus-table-paths.patch \ %D%/packages/patches/anki-mpv-args.patch \ diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3ab496bcdf..5136d5c9cf 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -3330,6 +3330,38 @@ buffers, and audio capture.") (home-page "https://kcat.strangesoft.net/openal.html") (license license:lgpl2.0))) +(define-public alure + (package + (name "alure") + (version "1.2") + (source (origin + (method url-fetch) + (uri (string-append "https://kcat.tomasu.net/alure-releases/" + "alure-" version ".tar.bz2")) + (sha256 + (base32 + "0w8gsyqki21s1qb2s5ac1kj08i6nc937c0rr08xbw9w9wvd6lpj6")) + (patches (search-patches "alure-dumb-2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;no tests + #:configure-flags '("-DMODPLUG=ON"))) + (native-inputs (list pkg-config)) + (inputs (list dumb + flac + mpg123 + libmodplug + libsndfile + libvorbis + openal)) + (home-page "https://kcat.tomasu.net/alure.html") + (synopsis "OpenAL utility library") + (description + "ALURE is a utility library to help manage common tasks with OpenAL applications. +This includes device enumeration and initialization, file loading, and +streaming.") + (license license:expat))) + (define-public patchage (package (name "patchage") diff --git a/gnu/packages/patches/alure-dumb-2.patch b/gnu/packages/patches/alure-dumb-2.patch new file mode 100644 index 0000000000..60d18f8570 --- /dev/null +++ b/gnu/packages/patches/alure-dumb-2.patch @@ -0,0 +1,30 @@ +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/alure/-/blob/main/dumb-2.patch + +diff -Naur a/src/codec_dumb.cpp b/src/codec_dumb.cpp +--- a/src/codec_dumb.cpp 2011-07-29 09:37:48.000000000 +0100 ++++ b/src/codec_dumb.cpp 2020-05-10 15:59:48.502632496 +0100 +@@ -272,7 +272,11 @@ + + private: + // DUMBFILE iostream callbacks ++#if DUMB_VERSION >= 2*10000 ++ static int skip(void *user_data, dumb_off_t offset) ++#else + static int skip(void *user_data, long offset) ++#endif + { + std::istream *stream = static_cast(user_data)->fstream; + stream->clear(); +@@ -282,7 +286,11 @@ + return -1; + } + ++#if DUMB_VERSION >= 2*10000 ++ static dumb_ssize_t read(char *ptr, size_t size, void *user_data) ++#else + static long read(char *ptr, long size, void *user_data) ++#endif + { + std::istream *stream = static_cast(user_data)->fstream; + stream->clear(); + From 90f65b5857c57b0db69b9380b4eec989fd7c05dd Mon Sep 17 00:00:00 2001 From: Attila Lendvai Date: Sat, 9 Sep 2023 23:49:01 +0200 Subject: [PATCH 348/440] gnu: Add netperf. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (netperf): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/networking.scm | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 74a279e2d1..c1cab1fe0d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -286,6 +286,44 @@ strict standards compliance. The code does, however, fairly closely follow the RFC.") (license (list license:gpl2 license:gpl3)))) +(define-public netperf + (let ((version "2.7.0") + (revision "1") + (commit "3bc455b23f901dae377ca0a558e1e32aa56b31c4")) + (package + (name "netperf") + (version (git-version version revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/HewlettPackard/netperf") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1msbhbvf39r1a0c9b9myla5i6235fvnp7r6021fl8b5svxjbb0dk")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + ;; Without -fcommon the build fails on newer gcc. + ;; See: https://gcc.gnu.org/gcc-10/porting_to.html + (list "CFLAGS=-fcommon" + ;; --enable-demo is needed for flent (not yet packaged). + "--enable-demo"))) + (native-inputs + (list autoconf + automake)) + (home-page "https://hewlettpackard.github.io/netperf/") + (synopsis "Benchmarking tool to measure network performance") + (description + "Netperf is a benchmark that can be used to measure the performance of +many different types of networking. It provides tests for both unidirectional +throughput, and end-to-end latency. The environments currently measureable +by netperf include: TCP and UDP via BSD Sockets for both IPv4 and IPv6, DLPI, +Unix Domain Sockets, SCTP for both IPv4 and IPv6.") + (license license:expat)))) + (define-public lcsync (package (name "lcsync") From 3d8d67ef6928f5d81118c97f03372cd341eab8b0 Mon Sep 17 00:00:00 2001 From: Simon South Date: Sat, 9 Sep 2023 19:07:37 -0400 Subject: [PATCH 349/440] gnu: Add asl. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/assembly.scm (asl): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/assembly.scm | 61 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index fef2181e6e..37b5712d81 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Guillaume Le Vaillant ;;; Copyright © 2022 Felix Gruber ;;; Copyright © 2022 Andy Tai +;;; Copyright © 2023 Simon South ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,6 +34,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module ((guix build utils) #:select (parallel-job-count)) #:use-module (guix download) #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) @@ -55,10 +57,69 @@ #:use-module (gnu packages python) #:use-module (gnu packages sphinx) #:use-module (gnu packages shells) + #:use-module (gnu packages tex) #:use-module (gnu packages xml) #:use-module ((guix utils) #:select (%current-system cc-for-target))) +(define-public asl + (let ((build "247")) + (package + (name "asl") + (version (string-append "1.42-beta-" build)) + (source + (origin + (method url-fetch) + (uri (string-append + "http://john.ccac.rwth-aachen.de:8000/ftp/as/source/c_version/" + "asl-current-142-bld" build ".tar.bz2")) + (sha256 + (base32 "1qgz5yzg50vpwzrjqvw8bgnvm67dqhfb8ldxyqwaqmrj3icshp5s")))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags #~(list "V=1") ; ensures output during "check" phase + #:phases + #~(modify-phases %standard-phases + (delete 'bootstrap) + (replace 'configure + (lambda* (#:key target #:allow-other-keys) + (copy-file "Makefile.def-samples/Makefile.def-unknown-linux" + "Makefile.def") + + ;; Use the cross-compilation tools when cross-compiling. + (when #$(%current-target-system) + (substitute* "Makefile.def" + (("^(TARG_(CC|LD) = ).*" all prefix) + (string-append prefix target "-gcc\n")))) + + ;; Set the output directories appropriately. + (substitute* "Makefile.def" + (("^(DOCDIR = ).*" all prefix) + (string-append prefix #$output:doc "/share/doc/" #$name)) + (("/usr/local") + #$output)))) + (add-after 'check 'build-doc + (lambda* (#:key parallel-build? #:allow-other-keys) + (invoke "make" + "-j" (if parallel-build? + (number->string (parallel-job-count)) + "1") + "docs")))) + #:test-target "test")) + (native-inputs + (list (texlive-updmap.cfg (list texlive-german texlive-hyperref)))) + (outputs '("out" "doc")) + (home-page "http://john.ccac.rwth-aachen.de:8000/as/") + (synopsis + "AS macro cross-assembler for microprocessors and microcontrollers") + (description + "AS is a portable macro cross-assembler targeting a wide range of +microprocessors and microcontrollers, including devices from Intel, Motorola, +MOS Technology, Hitachi, Fujitsu, NEC, Texas Instruments, Zilog and many other +manufacturers.") + (license (list license:gpl2 license:gpl3))))) + (define-public nasm (package (name "nasm") From 7841a624f0c94efbfeb48a5209dbd92575eacc09 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Tue, 19 Sep 2023 07:23:28 +0200 Subject: [PATCH 350/440] maint: Add gdk-pixbuf to native Hurd manifest. Gdk-pixbuf is a dependency for `guix system reconfigure' and currently also needs an unreleased glibc patch in order to build. * etc/hurd-manifest.scm: Add gdk-pixbuf to manifest. --- etc/hurd-manifest.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/etc/hurd-manifest.scm b/etc/hurd-manifest.scm index 1b1d0a53b4..8132da7d08 100644 --- a/etc/hurd-manifest.scm +++ b/etc/hurd-manifest.scm @@ -31,7 +31,7 @@ (srfi srfi-1)) (use-package-modules - base bootloaders commencement compression file gawk gdb gettext guile + base bootloaders commencement compression file gawk gdb gettext gtk guile hurd less m4 package-management python ssh version-control) (define (input->package input) @@ -72,6 +72,9 @@ ;; system grub-minimal grub + ;; system reconfigure + gdk-pixbuf + (append guix-dependencies %base-packages/hurd))) From 15c5f1a2c20b21de0f19f42db1ccab4c42117ebb Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Mon, 18 Sep 2023 08:09:50 +0200 Subject: [PATCH 351/440] self: Compile guix-packages-base in chunks of 10 files. This fixes or greatly increases the chances for `guix pull' to succeed on the Hurd, see . * guix/self.scm (compiled-modules)[process-directory]: Move hardcoded size to keyword parameter #:size. Set it to 10 when compiling "guix-packages-base". --- guix/self.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/guix/self.scm b/guix/self.scm index d2300052d8..b8b9b9fe37 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -1245,14 +1245,13 @@ containing MODULE-FILES and possibly other files as well." (* 100. (/ completed total)) total) (force-output)) - (define (process-directory directory files output) - (let* ((size 25) ;compile max 25 files a time - (chunks (unfold - (lambda (seed) (< (length seed) size)) ;p - (cute take <> size) ;f - (cute drop <> size) ;g - files ;seed - list))) ;tail + (define* (process-directory directory files output #:key (size 25)) + (let ((chunks (unfold + (lambda (seed) (< (length seed) size)) ;p + (cute take <> size) ;f + (cute drop <> size) ;g + files ;seed + list))) ;tail (for-each (lambda (chunk) ;; Hide compilation warnings. @@ -1290,7 +1289,8 @@ containing MODULE-FILES and possibly other files as well." (mkdir #$output) (chdir #+module-tree) - (process-directory "." '#+module-files #$output) + (let ((size (if (equal? #$name "guix-packages-base") 10 25))) + (process-directory "." '#+module-files #$output #:size size)) (newline)))) (computed-file name build From 695df753b9c8860e604e3609744cbbaad6f7e71a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 17:32:01 +0300 Subject: [PATCH 352/440] gnu: wl-clipboard: Update to 2.2.1. * gnu/packages/xdisorg.scm (wl-clipboard): Update to 2.2.1. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index ee6e00f518..f86608497d 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -2751,7 +2751,7 @@ Wayland and @code{wlroots} by leveraging @command{grim} and @command{slurp}.") (define-public wl-clipboard (package (name "wl-clipboard") - (version "2.2.0") + (version "2.2.1") (source (origin (method git-fetch) @@ -2760,7 +2760,7 @@ Wayland and @code{wlroots} by leveraging @command{grim} and @command{slurp}.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0r45k6fk9k26qs88s2sjlgjjamhj2jqghdivlh2xjqknws63d29g")))) + (base32 "09l6dv3qsqscbr98vxi4wg4rkx0wlhnsc40n21mx3ds6balmg105")))) (build-system meson-build-system) (arguments (list #:configure-flags From 6f30e5b3bf3a84ecdd8a78b4b22971a803360f99 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 17:32:25 +0300 Subject: [PATCH 353/440] gnu: git-annex: Update to 10.20230828. * gnu/packages/haskell-apps.scm (git-annex): Update to 10.20230828. --- gnu/packages/haskell-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index 4286ce206d..ac22082088 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -294,13 +294,13 @@ to @code{cabal repl}).") (define-public git-annex (package (name "git-annex") - (version "10.20230626") + (version "10.20230828") (source (origin (method url-fetch) (uri (hackage-uri "git-annex" version)) (sha256 - (base32 "1z16alb5193y4m70rq0bcxx1rn6lnlgswigdnv5lqybjq1fw1z99")))) + (base32 "0pb6834dwjs9kdki977rfkdyg58dfzy8wfwvswrz3n7h6bcnjd0b")))) (build-system haskell-build-system) (properties '((upstream-name . "git-annex"))) (arguments From 7083f2cf87f01b60c36ae82e42d5fe92a7a6336a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 17:32:25 +0300 Subject: [PATCH 354/440] gnu: keepassxc: Update to 2.7.6. * gnu/packages/password-utils.scm (keepassxc): Update to 2.7.6. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 753a29dcca..be85898c41 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -145,7 +145,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.7.5") + (version "2.7.6") (source (origin (method url-fetch) @@ -153,7 +153,7 @@ human.") "/releases/download/" version "/keepassxc-" version "-src.tar.xz")) (sha256 - (base32 "03002fncllr658mgl5s6an5wnh0a333qnkxad6aw85hqj004iqpd")))) + (base32 "0w6nh2lnzfqcxasfsppmh4q309p1flzgfiv25hahzsd8kx879055")))) (build-system cmake-build-system) (arguments (list From b37925ecddb4af2965220064a8a603d2fd3a77c5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 18:33:12 +0300 Subject: [PATCH 355/440] gnu: xterm: Update to 384. * gnu/packages/xorg.scm (xterm): Update to 384. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 08cbd8d757..cd1335661b 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5912,7 +5912,7 @@ to answer a question. Xmessage can also exit after a specified time.") (define-public xterm (package (name "xterm") - (version "377") + (version "384") (source (origin (method url-fetch) @@ -5922,7 +5922,7 @@ to answer a question. Xmessage can also exit after a specified time.") (string-append "ftp://ftp.invisible-island.net/xterm/" "xterm-" version ".tgz"))) (sha256 - (base32 "1clhm4c8d7vmz0dn6qz2c6g68wxl8f2ba8a7c1zdk3jxlkkqy46v")) + (base32 "0wy3rdj5smis44nsy6iccx3gsyzlqw0rcjjb7h605bnf803qgvri")) (patches (search-patches "xterm-370-explicit-xcursor.patch")))) (build-system gnu-build-system) From 8c56ab99d93c2d37fcc08d3fcff44c64b12ed443 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Sep 2023 23:27:19 +0200 Subject: [PATCH 356/440] gnu: Add python-benchmark-4dn. * gnu/packages/python-xyz.scm (python-benchmark-4dn): New variable. --- gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e96f4a2d0d..1b6291f12d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17319,6 +17319,27 @@ It is maintained by the Celery project, and used by kombu as a pure python alternative when librabbitmq is not available.") (license license:lgpl2.1+))) +(define-public python-benchmark-4dn + (package + (name "python-benchmark-4dn") + (version "0.5.23") + (source (origin + (method url-fetch) + (uri (pypi-uri "Benchmark-4dn" version)) + (sha256 + (base32 + "0z3vxrkap59sk394ynvp0457mdvb201idcswlrpgjscnrp2h4ypi")))) + (properties '(("upstream-name" . "Benchmark-4dn"))) + (build-system pyproject-build-system) + (native-inputs + (list python-poetry-core)) + (home-page "https://github.com/SooLee/Benchmark/") + (synopsis "Benchmark functions for CWL workflows") + (description + "This package provides benchmark functions that return total space, memory, +CPUs required per given input size, and parameters for CWL workflows.") + (license license:expat))) + (define-public python-beniget (package (name "python-beniget") From c5cf47ccffd9343c30a4a957aa8cb27e218acfe4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Sep 2023 23:27:34 +0200 Subject: [PATCH 357/440] gnu: Add python-lambda-4dn. * gnu/packages/web.scm (python-lambda-4dn): New variable. --- gnu/packages/web.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 1b4eafeab8..e9c6f1443c 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -98,6 +98,7 @@ #:use-module (guix build-system go) #:use-module (guix build-system meson) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) @@ -4807,6 +4808,31 @@ http://opensearch.a9.com} compatible search engines.") their web site.") (home-page "https://metacpan.org/release/WWW-RobotRules"))) +(define-public python-lambda-4dn + (package + (name "python-lambda-4dn") + (version "0.12.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "python-lambda-4dn" version)) + (sha256 + (base32 + "1p5i8wsi8q5fpq63i7n7ri1w1lnh4gpn17f88vhkbh14aah5wxj1")))) + (properties '(("upstream-name" . "python-lambda-4dn"))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-boto3 python-botocore python-docutils + python-six)) + (home-page "https://github.com/4dn-dcic/python-lambda") + (synopsis + "Toolkit for developing and deploying Python code in AWS Lambda") + (description + "This is a toolset for developing and deploying serverless Python code in +AWS Lambda. This is a fork of Nick Ficano's Python-lambda package. It is +frozen for the needs of projects at the 4D Nucleome Data Coordination and +Integration Center (4DN-DCIC).") + (license (list license:isc license:expat)))) + (define-public python-feedparser (package (name "python-feedparser") From 4b3b2e63007acee9e3a8c2ea728190480d092c3c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Sep 2023 23:27:45 +0200 Subject: [PATCH 358/440] gnu: Add python-tibanna. * gnu/packages/web.scm (python-tibanna): New variable. --- gnu/packages/web.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e9c6f1443c..980663fae9 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4863,6 +4863,36 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (license (list license:bsd-2 ; source code license:freebsd-doc)))) ; documentation +(define-public python-tibanna + (package + (name "python-tibanna") + (version "4.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "tibanna" version)) + (sha256 + (base32 + "185jr5b1dfgh82xcjal0y9wbzds37s0yhx0hp8awlvw26v72awv2")))) + (build-system pyproject-build-system) + (arguments + ;; Tests require AWS credentials and access to the internet. + (list #:tests? #false)) + (propagated-inputs + (list python-benchmark-4dn + python-boto3 python-botocore + python-lambda-4dn python-tomlkit)) + (native-inputs + (list python-poetry-core + python-pytest + python-pytest-cov + python-pytest-mock)) + (home-page "https://github.com/4dn-dcic/tibanna") + (synopsis "Tibanna runs portable workflows on the AWS Cloud") + (description + "Tibanna runs portable pipelines (in CWL/WDL and Snakemake) on the AWS +Cloud.") + (license license:expat))) + (define-public guix-data-service (let ((commit "1c7539418743e0dfe3a9cad22c414fd732daef8f") (revision "42")) From 7a2ee8524ab83fd3f22deda388f2fd0628cd7271 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Sep 2023 22:11:45 +0300 Subject: [PATCH 359/440] gnu: wfmash: Update to 0.10.5. * gnu/packages/bioinformatics.scm (wfmash): Update to 0.10.5. [source]: Update to changes in source code. [arguments]: Add configure-flag to enable more features. [native-inputs]: Add pkg-config. --- gnu/packages/bioinformatics.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b909cd5ee0..6acf37b312 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20463,7 +20463,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") (define-public wfmash (package (name "wfmash") - (version "0.8.1") + (version "0.10.5") (source (origin (method url-fetch) @@ -20471,7 +20471,7 @@ based on the pairwise alignment of hidden Markov models (HMMs).") version "/wfmash-v" version ".tar.gz")) (sha256 (base32 - "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + "1jsvnnh14h3ir4l13qhmglhd25kzwvni9apgvr1lbikqwgrpkiq4")) (snippet #~(begin (use-modules (guix build utils)) @@ -20482,14 +20482,12 @@ based on the pairwise alignment of hidden Markov models (HMMs).") "")) ;; Remove compiler optimizations. (substitute* (find-files "." "CMakeLists\\.txt") - (("-mcx16 ") "") - (("-march=native ") "")) - ;; Allow building on architectures other than x86_64. - (substitute* "src/common/dset64.hpp" - (("!__x86_64__") "0")))))) + (("-march=native ") "")))))) (build-system cmake-build-system) (arguments (list + #:configure-flags + #~(list "-DWFA_PNG_AND_TSV=ON") #:phases #~(modify-phases %standard-phases (replace 'check @@ -20602,7 +20600,8 @@ based on the pairwise alignment of hidden Markov models (HMMs).") jemalloc zlib)) (native-inputs - (list samtools)) + (list pkg-config + samtools)) (synopsis "Base-accurate DNA sequence aligner") (description "@code{wfmash} is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that From 00a1ee15cdc046708d2df35d3854156da14fcbb9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 20 Sep 2023 08:11:24 +0300 Subject: [PATCH 360/440] gnu: %gcc-11-x86_64-micro-architectures: Correct some values. * gnu/packages/gcc.scm (%gcc-11-x86_64-micro-architectures): Correct the values for the psABI micro-architectures. --- gnu/packages/gcc.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 862fdd79c3..c3a2d6256c 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -617,7 +617,7 @@ Go. It also includes runtime support libraries for these languages.") "btver1" "btver2" ;AMD ;; psABI micro-architecture levels - "x86_64-v1" "x86_64-v2" "x86_64-v3" "x86_64-v4"))) + "x86-64-v1" "x86-64-v2" "x86-64-v3" "x86-64-v4"))) ;; Suitable '-march' values for GCC 12. (define %gcc-12-aarch64-micro-architectures From e5ed1712da049b1c3dcf01e0a7e02e48a8aff012 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 9 Sep 2023 17:57:25 +0200 Subject: [PATCH 361/440] image: Introduce the mbr-hybrid-raw image type. Until 209204e23b39af09e0ea92540b6fa00a60e6a0ae and d57cab764122af69d52d8cc9c843456044e5d7bc, the default image type used by "guix system image" was an MBR image with an ESP partition. Having both an MBR image and an ESP partition is handy because the image will boot on most x86 based systems using legacy BIOS and/or UEFI. We now have a distinction between MBR images and EFI images. Introduce a new MBR hybrid image type and default to it to restore the default behaviour. This also fixes the images section of (gnu ci) that was trying to install a BIOS bootloader on an EFI, GPT image and failing to do so. Signed-off-by: Mathieu Othacehe --- doc/guix.texi | 34 +++++++++++++++++++++++++++------- gnu/ci.scm | 2 +- gnu/system/image.scm | 14 ++++++++++++++ guix/scripts/system.scm | 2 +- 4 files changed, 43 insertions(+), 9 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 50c4984d71..617b8463e3 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -40982,8 +40982,8 @@ QEMU monitor and the VM. @cindex image, creating disk images The @code{image} command can produce various image types. The image type can be selected using the @option{--image-type} option. It -defaults to @code{mbr-raw}. When its value is @code{iso9660}, the -@option{--label} option can be used to specify a volume ID with +defaults to @code{mbr-hybrid-raw}. When its value is @code{iso9660}, +the @option{--label} option can be used to specify a volume ID with @code{image}. By default, the root file system of a disk image is mounted non-volatile; the @option{--volatile} option can be provided to make it volatile instead. When using @code{image}, the bootloader @@ -41001,8 +41001,8 @@ qemu-system-x86_64 -enable-kvm -hda /tmp/my-image.qcow2 -m 1000 \ -bios $(guix build ovmf)/share/firmware/ovmf_x64.bin @end example -When using the @code{mbr-raw} image type, a raw disk image is produced; -it can be copied as is to a USB stick, for instance. Assuming +When using the @code{mbr-hybrid-raw} image type, a raw disk image is +produced; it can be copied as is to a USB stick, for instance. Assuming @code{/dev/sdc} is the device corresponding to a USB stick, one can copy the image to it using the following command: @@ -41139,7 +41139,7 @@ of the image. For the @code{image} action, create an image with given @var{type}. When this option is omitted, @command{guix system} uses the -@code{mbr-raw} image type. +@code{mbr-hybrid-raw} image type. @cindex ISO-9660 format @cindex CD image format @@ -45347,7 +45347,7 @@ then directly boot from it, without any kind of installation procedure. The @command{guix system image} command is able to turn an operating system definition into a bootable image. This command supports -different image types, such as @code{mbr-raw}, @code{iso9660} and +different image types, such as @code{mbr-hybrid-raw}, @code{iso9660} and @code{docker}. Any modern @code{x86_64} machine will probably be able to boot from an @code{iso9660} image. However, there are a few machines out there that require specific image types. Those machines, in general @@ -45611,8 +45611,24 @@ from them to simplify the @code{image} definition. The @code{(gnu system image)} module provides the following @code{image} definition variables. +@defvar mbr-disk-image +An MBR disk-image composed of a single ROOT partition. The ROOT +partition starts at a 1@tie{}MiB offset so that the bootloader can +install itself in the post-MBR gap. +@end defvar + +@defvar mbr-hybrid-disk-image +An MBR disk-image composed of two partitions: a 64 bits ESP partition +and a ROOT boot partition. The ESP partition starts at a 1@tie{}MiB +offset so that a BIOS compatible bootloader can install itself in the +post-MBR gap. The image can be used by @code{x86_64} and @code{i686} +machines supporting only legacy BIOS booting. The ESP partition ensures +that it can also be used by newer machines relying on UEFI booting, +hence the @emph{hybrid} denomination. +@end defvar + @defvar efi-disk-image -A MBR disk-image composed of two partitions: a 64 bits ESP partition and +A GPT disk-image composed of two partitions: a 64 bits ESP partition and a ROOT boot partition. This image can be used on most @code{x86_64} and @code{i686} machines, supporting BIOS or UEFI booting. @end defvar @@ -45703,6 +45719,10 @@ system image)} and the @code{(gnu system images @dots{})} modules. Build an image based on the @code{mbr-disk-image} image. @end defvar +@defvar mbr-hybrid-raw-image-type +Build an image based on the @code{mbr-hybrid-disk-image} image. +@end defvar + @defvar efi-raw-image-type Build an image based on the @code{efi-disk-image} image. @end defvar diff --git a/gnu/ci.scm b/gnu/ci.scm index 520ac28110..279dd4d910 100644 --- a/gnu/ci.scm +++ b/gnu/ci.scm @@ -268,7 +268,7 @@ otherwise use the IMAGE name." (if (member system %guix-system-supported-systems) `(,(image->job store (image - (inherit efi-disk-image) + (inherit mbr-hybrid-disk-image) (operating-system installation-os)) #:name "usb-image" #:system system) diff --git a/gnu/system/image.scm b/gnu/system/image.scm index 5b8da2f896..b1b928b222 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -77,6 +77,7 @@ root-partition mbr-disk-image + mbr-hybrid-disk-image efi-disk-image iso9660-image docker-image @@ -86,6 +87,7 @@ image-with-os mbr-raw-image-type + mbr-hybrid-raw-image-type efi-raw-image-type efi32-raw-image-type qcow2-image-type @@ -156,6 +158,13 @@ parent image record." (inherit root-partition) (offset root-offset)))))) +(define mbr-hybrid-disk-image + (image-without-os + (format 'disk-image) + (partition-table-type 'mbr) + (partitions + (list esp-partition root-partition)))) + (define efi-disk-image (image-without-os (format 'disk-image) @@ -217,6 +226,11 @@ set to the given OS." (name 'mbr-raw) (constructor (cut image-with-os mbr-disk-image <>)))) +(define mbr-hybrid-raw-image-type + (image-type + (name 'mbr-hybrid-raw) + (constructor (cut image-with-os mbr-hybrid-disk-image <>)))) + (define efi-raw-image-type (image-type (name 'efi-raw) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index ec331809ef..547387d5e1 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -1169,7 +1169,7 @@ Some ACTIONS support additional ARGS.\n")) (debug . 0) (verbosity . #f) ;default (validate-reconfigure . ,ensure-forward-reconfigure) - (image-type . mbr-raw) + (image-type . mbr-hybrid-raw) (image-size . guess) (install-bootloader? . #t) (label . #f) From 6bd17a0806ad32d1493ac51a7443276f719c4224 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Sat, 9 Sep 2023 17:57:26 +0200 Subject: [PATCH 362/440] image: Do not allow BIOS bootloader and GPT. When using grub-bootloader with a GPT image, GRUB will fail during installation with a cryptic error message. * gnu/system/image.scm (system-disk-image): Raise an error when trying to use a non-EFI compatible bootloader with a GPT image partitioning. Signed-off-by: Mathieu Othacehe --- gnu/system/image.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/system/image.scm b/gnu/system/image.scm index b1b928b222..fa4cab0b03 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -530,6 +530,13 @@ used in the image." (image-partition-table-type image))) (else ""))) + (when (and (gpt-image? image) + (not + (memq (bootloader-name bootloader) '(grub-efi grub-efi32)))) + (raise + (formatted-message + (G_ "EFI bootloader required with GPT partitioning")))) + (let* ((format (image-format image)) (image-type (format->image-type format)) (image-type-options (genimage-type-options image-type image)) From e05c225ffbc6decb8294d30dfb0776284025c19f Mon Sep 17 00:00:00 2001 From: Felix Lechner Date: Wed, 6 Sep 2023 14:23:50 -0700 Subject: [PATCH 363/440] gnu: Add wasm-micro-runtime. * gnu/packages/web.scm (wasm-micro-runtime): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/web.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 980663fae9..631106028d 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -63,6 +63,7 @@ ;;; Copyright © 2022 Bruno Victal ;;; Copyright © 2023 David Thompson ;;; Copyright © 2023 Christopher Howard +;;; Copyright © 2023 Felix Lechner ;;; ;;; This file is part of GNU Guix. ;;; @@ -1710,6 +1711,42 @@ other systems that want to manipulate WebAssembly files.") (description "WASM3 is a fast WebAssembly interpreter.") (license license:expat))) +(define-public wasm-micro-runtime + (package + (name "wasm-micro-runtime") + (version "1.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bytecodealliance/wasm-micro-runtime") + (commit (string-append "WAMR-" version)))) + (file-name (git-file-name "WAMR" version)) + (sha256 + (base32 + "1s7r8vfxixf737jp12cf7as68fd63lrmqdxj7fiqdla2wk89ly3f")))) + (build-system cmake-build-system) + (arguments + (list + ;; Running the tests is difficult. The test script in + ;; tests/wamr-test-suites insists on downloading and building wabt (even + ;; if we provide it) and it has a hard time accepting a separately + ;; provided clone of the https://github.com/WebAssembly/spec repository. + ;; Future releases provide unit tests which may be easier to run. + #:tests? #false + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "product-mini/platforms/linux")))))) + (home-page "https://bytecodealliance.github.io/wamr.dev") + (synopsis "WebAssembly Micro Runtime") + (description "WebAssembly Micro Runtime (WAMR) is a lightweight standalone +WebAssembly (Wasm) runtime with small footprint, high performance and highly +configurable features for applications cross from embedded, IoT, edge to +Trusted Execution Environment (TEE), smart contract, cloud native and other +features.") + (license license:asl2.0))) + (define-public websocketpp (package (name "websocketpp") From e82a2337b97a5bad96a8a38d26ddf4a05ad9d0e6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 364/440] gnu: pfetch: Update to 0.7.0-1.a906ff8. * gnu/packages/admin.scm (pfetch): Update to 0.7.0-1.a906ff8. [arguments]: Don't explicitly return #t from phases. --- gnu/packages/admin.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 741d4758f6..f9fffcec2b 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4204,8 +4204,8 @@ everyone's screenshots nowadays.") (license license:expat)))) (define-public pfetch - (let ((commit "e18a0959ab98b963744755ec4687e59dc11db3c5") - (revision "0")) + (let ((commit "a906ff89680c78cec9785f3ff49ca8b272a0f96b") + (revision "1")) (package (name "pfetch") (version (git-version "0.7.0" revision commit)) @@ -4217,7 +4217,7 @@ everyone's screenshots nowadays.") (file-name (git-file-name name version)) (sha256 (base32 - "1md40av6i3xvvwig5jzhy4kf3s5sgxxk35r0vcyrjd8qyndk927l")))) + "1yhf8mxjn58gjfdii3bpn8522gfaicd8jxjxvmwi2jz7fgvp0zpn")))) (build-system trivial-build-system) (inputs (list bash)) (arguments @@ -4234,8 +4234,7 @@ everyone's screenshots nowadays.") (install-file (source "pfetch") (string-append output "/bin")) (patch-shebang (string-append output "/bin/pfetch") - (list (string-append (assoc-ref %build-inputs "bash") "/bin"))) - #t)))) + (list (string-append (assoc-ref %build-inputs "bash") "/bin"))))))) (home-page "https://github.com/dylanaraps/pfetch") (synopsis "System information tool") (description "This package provides a simple, configurable system From 30ff8d169268a2be02525bb7f084ae36066ac2bb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 365/440] gnu: dolphin-emu: Remove input labels. * gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Remove input labels. --- gnu/packages/emulators.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index ce61f935fb..5fc8b8c9f2 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -316,8 +316,7 @@ console.") "/lib/libX11.so") "-DX11_FOUND=1"))) (native-inputs - `(("pkg-config" ,pkg-config) - ("gettext" ,gettext-minimal))) + (list gettext-minimal pkg-config)) (inputs (list alsa-lib ao From 4bdb8bd2674c2b630626be43a5cd3c2b65401b52 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 366/440] gnu: dolphin-emu: Update to 5.0-13669.f9deb68. * gnu/packages/emulators.scm (dolphin-emu): Update to 5.0-13669.f9deb68. [source]: Don't explicitly return #t from snippet. [arguments]: Nor from phases. --- gnu/packages/emulators.scm | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 5fc8b8c9f2..c5932a057c 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -250,8 +250,8 @@ console.") ;; Following commits and revision numbers of beta versions listed at ;; https://dolphin-emu.org/download/. (define-public dolphin-emu - (let ((commit "a34823df61df65168aa40ef5e82e44defd4a0138") - (revision "13178")) + (let ((commit "f9deb68aee962564b1495ff04c54c015e58d086f") + (revision "13669")) (package (name "dolphin-emu") (version (git-version "5.0" revision commit)) @@ -262,6 +262,8 @@ console.") (url "https://github.com/dolphin-emu/dolphin") (commit commit))) (file-name (git-file-name name version)) + (sha256 + (base32 "1p8qsxlabgmz3nic0a9ghh9d3lzl5f8i3kmdrrvx6w8kdlp33018")) (modules '((guix build utils))) (snippet '(begin @@ -273,11 +275,8 @@ console.") "gettext" "hidapi" "libpng" "libusb" "mbedtls" "miniupnpc" "MoltenVK" "zlib")) ;; Clean up source. - (for-each delete-file (find-files "." ".*\\.(bin|dsy|exe|jar|rar)$")) - #t)) - (sha256 - (base32 - "0j6hnj60iai366kl0kdbn1jkwc183l02g65mp2vq4qb2yd4399l1")))) + (for-each delete-file + (find-files "." ".*\\.(bin|dsy|exe|jar|rar)$")))))) (build-system cmake-build-system) (arguments '(#:tests? #f @@ -301,8 +300,7 @@ console.") (substitute* "Source/Core/VideoBackends/Vulkan/VulkanLoader.cpp" (("\"vulkan\", 1") (string-append "\"vulkan\"")) (("\"vulkan\"") (string-append "\"" libvulkan "\"")) - (("Common::DynamicLibrary::GetVersionedFilename") "")) - #t)))) + (("Common::DynamicLibrary::GetVersionedFilename") "")))))) ;; The FindGTK2 cmake script only checks hardcoded directories for ;; glib/gtk headers. From be9f749a29e30f78f81c3622d0668d19a472238a Mon Sep 17 00:00:00 2001 From: Artyom Bologov Date: Mon, 18 Sep 2023 19:38:55 +0400 Subject: [PATCH 367/440] gnu: cl-njson: Update to 1.2.1. * gnu/packages/lisp-xyz.scm (sbcl-njson): Update to 1.2.1. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/lisp-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index c6f66db840..752b777ed2 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -26603,7 +26603,7 @@ instead of #'FOO. (define-public sbcl-njson (package (name "sbcl-njson") - (version "1.2.0") + (version "1.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -26612,7 +26612,7 @@ instead of #'FOO. (file-name (git-file-name "cl-njson" version)) (sha256 (base32 - "1zsf7sm88wjrd4da5bvpxi8fvsx01cv51p8820fnj062x6hlhg38")))) + "0p3zvn3jfzcdzpvikdaw3g14wfsklq0msw0rjaxin3aa7vmqpyqk")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-cl-json sbcl-jzon)) (native-inputs (list sbcl-lisp-unit2)) From 84442d04235a615984667363c0f9b6b91d1ed0bf Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Sun, 17 Sep 2023 15:39:35 -0400 Subject: [PATCH 368/440] gnu: libosmium: Update to 2.19.0. * gnu/packages/geo.scm (libosmium): Update to 2.19.0. [inputs]: Replace proj with proj-7, the last version with PROJ API version 4 compatibility. Remove sparsehash and utfcpp. [native-inputs]: Add graphviz-minimal, to build documentation. Reviewed-by: Bruno Victal Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 48 +++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 25 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index d702046865..f41ef826fd 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -89,6 +89,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages gps) #:use-module (gnu packages graphics) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-apps) #:use-module (gnu packages haskell-xyz) @@ -1535,34 +1536,31 @@ visualizing and performing calculations with weather data.") (define-public libosmium (package (name "libosmium") - (version "2.18.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/osmcode/libosmium") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0fh57mpii1ksacwfx5rz213j896aklib53jbybld2i517q2mmxr0")))) + (version "2.19.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/osmcode/libosmium") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d69xzd29hk846g049y2g668mr8kaf05f6a26s3qn6az062hxfa7")))) (build-system cmake-build-system) - (propagated-inputs - (list boost - bzip2 - expat - gdal - geos - lz4 - proj - protozero - sparsehash - utfcpp - zlib)) - (native-inputs - (list doxygen)) + (propagated-inputs (list boost + bzip2 + expat + gdal + geos + lz4 + proj-7 + protozero + zlib)) + (native-inputs (list doxygen graphviz-minimal)) (home-page "https://osmcode.org/libosmium/") (synopsis "C++ library for working with OpenStreetMap data") - (description "Libosmium is a fast and flexible C++ library for working with + (description + "Libosmium is a fast and flexible C++ library for working with OpenStreetMap data.") (license license:boost1.0))) From ef18fd58b45b27898d2e97d5d6f580ad33bf571b Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Sun, 17 Sep 2023 15:39:36 -0400 Subject: [PATCH 369/440] gnu: osm2pgsql: Update to 1.9.2. * gnu/packages/geo.scm (osm2pgsql): Update to 1.9.2. [arguments]: Use G-expressions. <#:configure-flags>: Ensure compilation with LuaJIT, PROJ API version 4. [inputs]: Replace lua with luajit. Replace proj with proj-7. Add nlohmann-json. [native-inputs]: Add pandoc, python-argparse-manpage, for building documentation. Remove python-psycopg2, as it is only used for tests, and testing has been disabled. [home-page]: Update URL. Reviewed-by: Bruno Victal Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 71 ++++++++++++++++++++++---------------------- 1 file changed, 36 insertions(+), 35 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index f41ef826fd..c7ee877a1e 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1596,43 +1596,44 @@ based on the Osmium library.") (define-public osm2pgsql (package (name "osm2pgsql") - (version "1.8.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/openstreetmap/osm2pgsql") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0ssz7ny4wx8dzl3027p37xc5h7m1aj6bzxzdc6g8fbp7q57ykvxz")) - (modules '((guix build utils))) - (snippet - ;; Remove bundled libraries. - '(delete-file-recursively "contrib")))) + (version "1.9.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openstreetmap/osm2pgsql") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "198qcgl42pb8lk1bn41ncp8hc9gcg9k2p0ny42vak019w5l6jcj7")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled libraries. + '(delete-file-recursively "contrib")))) (build-system cmake-build-system) (arguments - `(#:tests? #f; tests fail because we need to setup a database - #:configure-flags - (list "-DEXTERNAL_LIBOSMIUM=ON" - "-DEXTERNAL_PROTOZERO=ON" - "-DEXTERNAL_FMT=ON"))) - (inputs - (list boost - bzip2 - expat - fmt-8 - libosmium - lua - postgresql - proj - protozero - zlib)) - (native-inputs - (list python python-psycopg2)) - (home-page "https://github.com/openstreetmap/osm2pgsql") - (synopsis "OSM data importer to postgresql") - (description "Osm2pgsql is a tool for loading OpenStreetMap data into a + (list #:tests? #f ;tests fail because we need to setup a database + #:configure-flags #~(list "-DUSE_PROJ_LIB=4" ;use API version 4 + "-DWITH_LUAJIT=ON" + "-DEXTERNAL_LIBOSMIUM=ON" + "-DEXTERNAL_PROTOZERO=ON" + "-DEXTERNAL_FMT=ON"))) + (inputs (list boost + bzip2 + expat + fmt-8 + libosmium + luajit + nlohmann-json + postgresql + proj-7 + protozero + zlib)) + (native-inputs (list pandoc python python-argparse-manpage)) + (home-page "https://osm2pgsql.org/") + (synopsis "OSM data importer to PostgreSQL") + (description + "Osm2pgsql is a tool for loading OpenStreetMap data into a PostgreSQL / PostGIS database suitable for applications like rendering into a map, geocoding with Nominatim, or general analysis.") (license license:gpl2+))) From f92bff51b4595bb61729328a3a149d4d02df8cd3 Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Sun, 17 Sep 2023 15:39:37 -0400 Subject: [PATCH 370/440] gnu: osmium-tool: Update to 1.15.0. * gnu/packages/geo.scm (osmium-tool): Update to 1.15.0. Reviewed-by: Bruno Victal Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 35 ++++++++++++++++------------------- 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index c7ee877a1e..8ee3b1a7ec 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1567,26 +1567,23 @@ OpenStreetMap data.") (define-public osmium-tool (package (name "osmium-tool") - (version "1.14.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/osmcode/osmium-tool") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0zgyqyrs89vch0qnkh9m5xq079sr2wmydy5zz4l8xbysbjf6xry5")) - (modules '((guix build utils))) - (snippet - ;; Remove bundled libraries. - '(delete-file-recursively "include/rapidjson")))) + (version "1.15.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/osmcode/osmium-tool") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d90vz316xdl3c416nicgdw7ybw17l2125wgxglbzl7jaqngapy5")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled libraries. + '(delete-file-recursively "include/rapidjson")))) (build-system cmake-build-system) - (inputs - (list libosmium - rapidjson)) - (native-inputs - (list pandoc)) + (inputs (list libosmium rapidjson)) + (native-inputs (list pandoc)) (home-page "https://osmcode.org/osmium-tool/") (synopsis "Osmium command-line tool") (description "Command line tool for working with OpenStreetMap data From 70fd6721f4921a5ccd0dcf6964458e74636c2c65 Mon Sep 17 00:00:00 2001 From: Hendursaga Date: Tue, 19 Sep 2023 11:56:00 -0400 Subject: [PATCH 371/440] gnu: routino: Update to 3.4.1. * gnu/packages/geo.scm (routino): Update to 3.4.1. [source]: Use HTTPS. [arguments]: Use G-expressions. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/geo.scm | 67 +++++++++++++++++++++----------------------- 1 file changed, 32 insertions(+), 35 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 8ee3b1a7ec..3c238cd62a 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -2157,43 +2157,40 @@ The API also works with MaxMind’s free GeoLite2 databases.") (define-public routino (package - (name "routino") - (version "3.3.3") - (source - (origin - (method url-fetch) - (uri (string-append "http://www.routino.org/download/routino-" - version ".tgz")) - (sha256 - (base32 "1xa7l2bjn832nk6bc7b481nv8hd2gj41jwhg0d2qy10lqdvjpn5b")))) - (build-system gnu-build-system) - (native-inputs - (list perl)) - (inputs - (list bzip2 xz zlib)) - (arguments - `(#:test-target "test" - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "Makefile.conf" - (("prefix=/usr/local") - (string-append "prefix=" (assoc-ref outputs "out"))) - (("LDFLAGS_LDSO=-Wl,-R\\.") - "LDFLAGS_LDSO=-Wl,-R$(libdir)") - (("#CFLAGS\\+=-DUSE_XZ") - "CFLAGS+=-DUSE_XZ") - (("#LDFLAGS\\+=-llzma") - "LDFLAGS+=-llzma")) - #t))))) - (synopsis "Routing application for OpenStreetMap data") - (description - "Routino is an application for finding a route between two points + (name "routino") + (version "3.4.1") + (source (origin + (method url-fetch) + (uri (string-append "https://www.routino.org/download/routino-" + version ".tgz")) + (sha256 + (base32 + "0aw5idqz7nv458llgwp5wcgikf34xcblpq46mq7msxfib0m8vahb")))) + (build-system gnu-build-system) + (native-inputs (list perl)) + (inputs (list bzip2 xz zlib)) + (arguments + (list #:test-target "test" + #:phases #~(modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile.conf" + (("prefix=/usr/local") + (string-append "prefix=" + (assoc-ref outputs "out"))) + (("LDFLAGS_LDSO=-Wl,-R\\.") + "LDFLAGS_LDSO=-Wl,-R$(libdir)") + (("#CFLAGS\\+=-DUSE_XZ") + "CFLAGS+=-DUSE_XZ") + (("#LDFLAGS\\+=-llzma") + "LDFLAGS+=-llzma"))))))) + (synopsis "Routing application for OpenStreetMap data") + (description + "Routino is an application for finding a route between two points using the dataset of topographical information collected by @url{https://www.OpenStreetMap.org}.") - (home-page "https://www.routino.org/") - (license license:agpl3+))) + (home-page "https://www.routino.org/") + (license license:agpl3+))) (define-public r-rnaturalearthhires (let ((commit "c3785a8c44738de6ae8f797080c0a337ebed929d") From ee7c9d254117fa470686210ad2ef5e7f1ba4fefc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= Date: Thu, 21 Sep 2023 17:35:57 +0200 Subject: [PATCH 372/440] gnu: python-bashlex: Update to 0.18. * gnu/packages/python-xyz.scm (python-bashlex): Update to 0.18. This fixes the build. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1b6291f12d..e90333cadf 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -51,7 +51,7 @@ ;;; Copyright © 2016, 2018 Tomáš Čech ;;; Copyright © 2018-2023 Nicolas Goaziou ;;; Copyright © 2018 Oleg Pykhalov -;;; Copyright © 2018, 2019, 2021 Clément Lassieur +;;; Copyright © 2018, 2019, 2021, 2023 Clément Lassieur ;;; Copyright © 2018, 2019, 2020, 2021, 2022, 2023 Maxim Cournoyer ;;; Copyright © 2018 Luther Thompson ;;; Copyright © 2018 Vagrant Cascadian @@ -28915,14 +28915,14 @@ at import time.") (define-public python-bashlex (package (name "python-bashlex") - (version "0.14") + (version "0.18") (source (origin (method url-fetch) (uri (pypi-uri "bashlex" version)) (sha256 (base32 - "1z9g96fgsfpdwawp4sb5x6hbdhmda7kgmcrqlf9xx4bs1f8f14js")))) + "1vln4zszzdqkypiir2hxsvkhgbf816005lbgqcw66rymqq0kmc2v")))) (build-system python-build-system) (arguments `(#:phases From a76ccdddaf70e0734b268f88cf7aa1dc6937a3e5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 8 Sep 2023 23:12:03 +0800 Subject: [PATCH 373/440] gnu: Add python-jwcrypto. * gnu/packages/python-web.scm (python-jwcrypto): New variable. --- gnu/packages/python-web.scm | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 12f0ce6208..e1c5412a93 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2017 Christopher Baines ;;; Copyright © 2016, 2017 Danny Milosavljevic ;;; Copyright © 2013, 2014, 2015, 2016, 2020 Andreas Enge -;;; Copyright © 2016, 2017, 2019-2022 Marius Bakke +;;; Copyright © 2016, 2017, 2019-2023 Marius Bakke ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2017, 2021 Roel Janssen ;;; Copyright © 2016, 2017, 2020 Julien Lepiller @@ -1250,6 +1250,25 @@ JSON Web Algorithms (JWA) - collectively can be used to encrypt and/or sign content using a variety of algorithms.") (license license:expat))) +(define-public python-jwcrypto + (package + (name "python-jwcrypto") + (version "1.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "jwcrypto" version)) + (sha256 + (base32 + "138bh6x1yy0qpk63bxa7mxnd97gfdm1fkpwm8wrdz3g3z0fca79c")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-cryptography python-deprecated)) + (home-page "https://github.com/latchset/jwcrypto") + (synopsis "Implementation of JOSE Web standards") + (description + "WCrypto is an implementation of the @dfn{Javascript Object Signing and +Encryption} (JOSE) Web Standards.") + (license license:lgpl3+))) + (define-public python-pyscss (package (name "python-pyscss") From 146cf4c306ac2d534a0b35af03112c883f160390 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 15:31:50 +0800 Subject: [PATCH 374/440] gnu: Add python-dirty-equals. * gnu/packages/python-xyz.scm (python-dirty-equals): New variable. --- gnu/packages/python-xyz.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e90333cadf..2c8a4c3019 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -26,7 +26,7 @@ ;;; Copyright © 2016, 2017 Nikita ;;; Copyright © 2016 Dylan Jeffers ;;; Copyright © 2016 David Craven -;;; Copyright © 2016-2022 Marius Bakke +;;; Copyright © 2016-2023 Marius Bakke ;;; Copyright © 2016, 2017, 2021, 2022 Stefan Reichör ;;; Copyright © 2016, 2017, 2019 Alex Vong ;;; Copyright © 2016–2018, 2021–2023 Arun Isaac @@ -8513,6 +8513,38 @@ by pycodestyle.") (license (license:non-copyleft "https://github.com/hhatto/autopep8/blob/master/LICENSE")))) +(define-public python-dirty-equals + (package + (name "python-dirty-equals") + (version "0.7.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samuelcolvin/dirty-equals") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hw044d6q0ij8hrrbp6wbdb49xbyjd22viansy817hpmd0yf85ja")))) + (build-system pyproject-build-system) + (arguments + ;; This test requires pytest-examples, which in turn requires + ;; python-ruff, which is difficult to package because it is + ;; written in Rust (TODO: Enable when Ruff is in Guix!). + (list #:test-flags #~'("--ignore" "tests/test_docs.py"))) + (native-inputs + (list python-hatchling + python-pydantic + python-pytest)) + (propagated-inputs (list python-pytz)) + (home-page "https://dirty-equals.helpmanual.io/") + (synopsis "Do dirty (but useful) things with equals") + (description + "@code{dirty-equals} is a Python library that (mis)uses the +@code{__eq__} method to make code (generally unit tests) more declarative +and therefore easier to read and write.") + (license license:expat))) + (define-public python-distlib (package (name "python-distlib") From e592513d394735730d925ee4be6486fc16bb22b1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 04:04:38 +0800 Subject: [PATCH 375/440] gnu: python-certauth: Fix test failure with newer PyOpenSSL. * gnu/packages/python-crypto.scm (python-certauth)[arguments]: New field. --- gnu/packages/python-crypto.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index e6483996fd..1ff742717c 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2015-2021, 2023 Efraim Flashner ;;; Copyright © 2015, 2016, 2017, 2019 Leo Famulari -;;; Copyright © 2016, 2017, 2020, 2022 Marius Bakke +;;; Copyright © 2016, 2017, 2020, 2022, 2023 Marius Bakke ;;; Copyright © 2017 Ben Sturmfels ;;; Copyright © 2016 Sou Bunnbu ;;; Copyright © 2015 Cyril Roelandt @@ -441,6 +441,16 @@ blake3, a cryptographic hash function.") (base32 "1yxqfb5131wahjyw9pxz03bq476rcfx62s6k53xx4cqbzzgdaqkq")))) (build-system python-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test + (lambda _ + ;; Newer PyOpenSSL no longer separates extensions with + ;; newline (this can be removed for >1.3.0). + (substitute* "test/test_certauth.py" + (("7334\\\\n, DNS") + "7334, DNS"))))))) (propagated-inputs (list python-pyopenssl python-tldextract)) (native-inputs From 1ddb081d6b266d555f9126db7b9e1a9a2e2c136e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 15:09:52 +0800 Subject: [PATCH 376/440] gnu: python-filelock: Update home page. * gnu/packages/python-xyz.scm (python-filelock)[home-page]: Follow redirect. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2c8a4c3019..b3a09db715 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2576,8 +2576,7 @@ Python's built-in @code{re} module with compatible interfaces.") (base32 "0ngzlvb5j8gqs2nxlp2b0jhzii792h66wsn694qm8kqixr225n0q")))) (build-system python-build-system) - (home-page - "https://github.com/benediktschmitt/py-filelock") + (home-page "https://github.com/tox-dev/py-filelock") (synopsis "Platform independent file lock") (description "@code{filelock} contains a single module implementing a platform independent file lock in Python, which provides a simple way of From 82ecaa1c569e9776db96874baaa98f09b51adff5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 16:31:00 +0800 Subject: [PATCH 377/440] gnu: python-deprecated: Remove unused inputs. * gnu/packages/python-xyz.scm (python-deprecated): Remove PYTHON-SPHINX and PYTHON-TOX. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b3a09db715..51196e71c7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6176,8 +6176,7 @@ software version simply.") (propagated-inputs (list python-wrapt)) (native-inputs - (list python-bumpversion python-pytest python-pytest-cov - python-sphinx python-tox)) + (list python-bumpversion python-pytest)) (home-page "https://github.com/tantale/deprecated") (synopsis "Python decorator to deprecate classes, functions or methods") (description "The @code{deprecated} decorator provides a convenient way to deprecate From 353f58db510ed5c37287c066449d701ec2092656 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 21:45:03 +0800 Subject: [PATCH 378/440] gnu: Add python-a2wsgi. * gnu/packages/python-web.scm (python-a2wsgi): New variable. --- gnu/packages/python-web.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e1c5412a93..1b7225c991 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -653,6 +653,30 @@ allows mocking or testing ASGI applications without having to spin up an ASGI server.") (license license:expat))) +(define-public python-a2wsgi + (package + (name "python-a2wsgi") + (version "1.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "a2wsgi" version)) + (sha256 + (base32 + "1cmsbgfg0vp8pwqz8nmkbmdi0axis1yl34qb280h5ssh08ngc1m9")))) + (build-system pyproject-build-system) + (arguments + (list #:build-backend "pdm.backend" + ;; Tests have a circular dependency on uvicorn. + #:tests? #f)) + (native-inputs + (list python-pdm-backend)) + (home-page "https://github.com/abersheeran/a2wsgi") + (synopsis "Convert WSGI to ASGI or vice versa") + (description + "This program converts a WSGI program to an ASGI program or the other +way around. It depends only on the Python standard library.") + (license license:asl2.0))) + (define-public python-css-html-js-minify (package (name "python-css-html-js-minify") From b2467d2354b8d0b43e53f15d8c349489110a1a97 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 22:02:40 +0800 Subject: [PATCH 379/440] gnu: Add python-html5tagger. * gnu/packages/python-web.scm (python-html5tagger): New variable. --- gnu/packages/python-web.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 1b7225c991..f8e040294a 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1725,6 +1725,26 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.") ;; indicate ASL2.0, including the LICENSE file for the whole project. (license (list license:asl2.0 license:gpl3)))) +(define-public python-html5tagger + (package + (name "python-html5tagger") + (version "1.3.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "html5tagger" version)) + (sha256 + (base32 + "1acd1a4f66gi4plqnsml7cf33qp83mxsnmnqpdwkpj7597xkvyl4")))) + (build-system pyproject-build-system) + (native-inputs + (list python-setuptools-scm)) + (home-page "https://github.com/sanic-org/html5tagger") + (synopsis "Create HTML documents from Python") + (description + "@code{html5tagger} provides a simplified HTML5 syntax that can +be written directly in Python without templates.") + (license license:unlicense))) + (define-public python-minio (package (name "python-minio") From c097775401b35b963a47e7353584906d9dda2782 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 22:07:45 +0800 Subject: [PATCH 380/440] gnu: Add python-tracerite. * gnu/packages/python-xyz.scm (python-tracerite): New variable. --- gnu/packages/python-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 51196e71c7..42ab90c608 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23337,6 +23337,26 @@ stack traces of Python programs. It exactly mimics the behavior of the Python interpreter when it prints a stack trace.") (license license:psfl))) +(define-public python-tracerite + (package + (name "python-tracerite") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "tracerite" version)) + (sha256 + (base32 + "0jwy5wwl0rcsgnx7hhq4z7ji3lx271sar4v2a1rmyh5vsj7sn784")))) + (build-system pyproject-build-system) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-html5tagger)) + (home-page "https://github.com/sanic-org/tracerite") + (synopsis "Human-readable HTML tracebacks") + (description + "@code{tracerite} converts Python tracebacks into useful error messages +in human-readable HTML format.") + (license license:unlicense))) + (define-public python-ratelimiter (package (name "python-ratelimiter") From 27954c3cb2b771fdd9a8892fed45c1d675f434cc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 22:28:07 +0800 Subject: [PATCH 381/440] gnu: Add python-pyproject-hooks. * gnu/packages/python-xyz.scm (python-pyproject-hooks): New variable. --- gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 42ab90c608..927c031869 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19315,6 +19315,30 @@ in Python. It allows you to declare the libraries your project depends on and it will manage (install/update) them for you.") (license license:expat))) +(define-public python-pyproject-hooks + (package + (name "python-pyproject-hooks") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyproject_hooks" version)) + (sha256 + (base32 + "1xaf4sharvacqlav6w3b38nc4j0rzg0p4axi7zamanbzp6cb4wgj")))) + (build-system pyproject-build-system) + (native-inputs + (list python-flit-core + python-testpath + python-pytest)) + (propagated-inputs (list python-tomli)) + (home-page "https://github.com/pypa/pyproject-hooks") + (synopsis "Low-level library for calling @file{pyproject.toml} backends") + (description + "@code{pyproject-hooks} is a low-level library for calling build backends +in @file{pyproject.toml}-based projects. It provides basic functionality to +write tooling that generates distribution files from Python projects.") + (license license:expat))) + (define-public python-lark-parser (package (name "python-lark-parser") From 08250bffab2ff09eb0dc12eaa39f4ecec3a9c3b5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 22:40:01 +0800 Subject: [PATCH 382/440] gnu: Add python-slotscheck. * gnu/packages/python-check.scm (python-slotscheck): New variable. --- gnu/packages/python-check.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 3a718954c5..0ccae07093 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -2023,6 +2023,31 @@ valid Python syntax that are likely to be commented out code.") behavior-driven development (TDD and BDD).") (license license:expat))) +(define-public python-slotscheck + (package + (name "python-slotscheck") + (version "0.17.0") + (home-page "https://github.com/ariebovenberg/slotscheck") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0k5jjabd219ndlssfqcdb5sn891ffrxzw84l5r8pirzy74i7znr4")))) + (build-system pyproject-build-system) + (native-inputs + (list python-poetry-core + python-pydantic + python-pytest + python-pytest-mock)) + (propagated-inputs (list python-click python-tomli)) + (synopsis "Ensure @code{__slots__} are working properly") + (description + "@code{slotscheck} is a tool to validate Python class @code{__slots__}.") + (license license:expat))) + (define-public python-stestr (package (name "python-stestr") From d546023c865b819c3d56d66b2e43ae6642300390 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 22:49:35 +0800 Subject: [PATCH 383/440] gnu: Add python-sphinx-basic-ng. * gnu/packages/sphinx.scm (python-sphinx-basic-ng): New variable. --- gnu/packages/sphinx.scm | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 173accd768..219063807e 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2017, 2019, 2020, 2021, 2023 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017 Leo Famulari ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016-2019, 2022 Marius Bakke +;;; Copyright © 2016-2019, 2022, 2023 Marius Bakke ;;; Copyright © 2017 Danny Milosavljevic ;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2017 Frederick M. Muriithi @@ -204,6 +204,24 @@ sources.") Apple help books.") (license license:bsd-2))) +(define-public python-sphinx-basic-ng + (package + (name "python-sphinx-basic-ng") + (version "1.0.0b2") + (source (origin + (method url-fetch) + (uri (pypi-uri "sphinx_basic_ng" version)) + (sha256 + (base32 + "1jaihs22d8jfvk1fnv5j7hcza89hxj979ib0b4mh130cr53mmicy")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-sphinx)) + (home-page "https://github.com/pradyunsg/sphinx-basic-ng") + (synopsis "Modernised skeleton for Sphinx themes") + (description + "This package provides a modern skeleton for Sphinx themes.") + (license license:expat))) + (define-public python-sphinx-click (package (name "python-sphinx-click") From 370c8bd78b06314dc860695a6aad820c209e1386 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 23:01:03 +0800 Subject: [PATCH 384/440] gnu: Add python-towncrier. * gnu/packages/python-xyz.scm (python-towncrier): New variable. --- gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 927c031869..0dd94edf8a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24096,6 +24096,40 @@ standard library. It provides two additional tokens @code{ESCAPED_NL} and and @code{tokens_to_src} to roundtrip.") (license license:expat))) +(define-public python-towncrier + (package + (name "python-towncrier") + (version "23.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "towncrier" version)) + (sha256 + (base32 + "1hbhzxcn30qlnab1rnk2bf09jfy5bpxzfdp6zfn8sz3jnidbsagw")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags + ;; TODO: Why is this failing? + #~'("-k" "not test_version"))) + (propagated-inputs + (list python-click + python-click-default-group + python-incremental + python-jinja2 + python-tomli)) + (native-inputs + (list git-minimal/pinned ;tests create git repositories + python-hatchling + python-packaging + python-pytest + python-twisted)) + (home-page "https://towncrier.readthedocs.io/en/stable/") + (synopsis "Manage release notes") + (description + "@code{towncrier} is a utility to produce useful, summarized news +files (also known as changelogs) for a project.") + (license license:expat))) + (define-public python-future-fstrings (package (name "python-future-fstrings") From f2e2c51ec945e78faea7d2325ea7f1ff8282a0de Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 23:18:54 +0800 Subject: [PATCH 385/440] gnu: Add python-pylsqpack. * gnu/packages/python-compression.scm (python-pylsqpack): New variable. --- gnu/packages/python-compression.scm | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 000d42524d..bc96bc05d3 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2018-2020, 2022 Efraim Flashner ;;; Copyright © 2020 Nicolas Goaziou -;;; Copyright © 2020, 2022 Marius Bakke +;;; Copyright © 2020, 2022, 2023 Marius Bakke ;;; Copyright © 2021 Brendan Tildesley ;;; ;;; This file is part of GNU Guix. @@ -207,6 +207,26 @@ compression algorithm.") and decompression by implementing Python bindings for the ISA-L library.") (license license:expat))) +(define-public python-pylsqpack + (package + (name "python-pylsqpack") + (version "0.3.17") + (source (origin + (method url-fetch) + (uri (pypi-uri "pylsqpack" version)) + (sha256 + (base32 + "1qiwmavmxy6ba89mrdkzk52hqrd4awnp4yca395pxp2np66pf81g")))) + ;; FIXME: Unbundle ls-qpack and xxhash! + (build-system pyproject-build-system) + (home-page "https://github.com/aiortc/pylsqpack") + (synopsis "Python bindings for @code{ls-qpack}") + (description + "@code{pylsqpack} is a wrapper around the @code{ls-qpack} library. +It provides Python Decoder and Encoder objects to read or write HTTP/3 +headers compressed with QPACK.") + (license license:expat))) + (define-public python-pyppmd (package (name "python-pyppmd") From 397a6860f64ee6b7f768e614c53eaca610437f8a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 23:21:01 +0800 Subject: [PATCH 386/440] gnu: Add python-aioquic. * gnu/packages/python-web.scm (python-aioquic): New variable. --- gnu/packages/python-web.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index f8e040294a..532f86e687 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -109,6 +109,7 @@ #: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-xyz) @@ -479,6 +480,28 @@ asynchronous DNS resolutions with a synchronous looking interface by using @url{https://github.com/saghul/pycares,pycares}.") (license license:expat))) +(define-public python-aioquic + (package + (name "python-aioquic") + (version "0.9.21") + (source (origin + (method url-fetch) + (uri (pypi-uri "aioquic" version)) + (sha256 + (base32 + "1xbfa4gmlmyj6bihdl5p4mr7nd6z79rfi92wcqkmcy4f643frivr")))) + (build-system pyproject-build-system) + (native-inputs (list python-pytest)) + (inputs (list openssl)) + (propagated-inputs + (list python-certifi python-pylsqpack python-pyopenssl)) + (home-page "https://github.com/aiortc/aioquic") + (synopsis "QUIC and HTTP3 implementation in Python") + (description + "@code{aioquic} is a library for the QUIC network protocol in Python. +It features a minimal TLS 1.3 implementation, a QUIC stack and an HTTP/3 stack.") + (license license:bsd-3))) + (define-public python-aiorpcx (package (name "python-aiorpcx") From 2b1eb3c1cf45cf916e30c3b32b3526d90a636cd9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 15 Sep 2023 11:18:25 +0800 Subject: [PATCH 387/440] gnu: uwufetch: Avoid top-level package references. * gnu/packages/admin.scm (uwufetch)[arguments]: Use the grep and gawk provided by INPUTS, instead of the top-level variables. --- gnu/packages/admin.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index f9fffcec2b..4ddd03fecf 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4074,15 +4074,15 @@ you are running, what theme or icon set you are using, etc.") #~(modify-phases %standard-phases (delete 'configure) (add-before 'build 'patch-source-paths - (lambda _ - (substitute* "fetch.c" - (("grep") - #$(file-append grep "/bin/grep")) - (("awk") - #$(file-append gawk "/bin/awk"))) - (substitute* "uwufetch.c" - (("(/usr(/local)?)(.*;)" all _ _ rest) - (string-append #$output rest))))) + (lambda* (#:key inputs #:allow-other-keys) + (let ((grep (search-input-file inputs "/bin/grep")) + (awk (search-input-file inputs "/bin/awk"))) + (substitute* "fetch.c" + (("grep") grep) + (("awk") awk)) + (substitute* "uwufetch.c" + (("(/usr(/local)?)(.*;)" all _ _ rest) + (string-append #$output rest)))))) ;; TODO this will be fixed in the next release of uwufetch (add-before 'install 'make-include-dir (lambda _ From 4163c617b84802fbe780b9668bb092eab479fc28 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 12:36:17 +0800 Subject: [PATCH 388/440] services: nftables: Add 'configuration' action. * gnu/services/networking.scm (nftables-shepherd-service)[actions]: New field. --- gnu/services/networking.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index befaca0aca..f4aff2d979 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1844,6 +1844,7 @@ table inet filter { (let ((nft (file-append package "/sbin/nft"))) (shepherd-service (documentation "Packet filtering and classification") + (actions (list (shepherd-configuration-action ruleset))) (provision '(nftables)) (start #~(lambda _ (invoke #$nft "--file" #$ruleset))) From 40f1f2d33befca62b54e6d8ec45b76c965905ab0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 14:10:26 +0800 Subject: [PATCH 389/440] gnu: Add python-dj-email-url. * gnu/packages/django.scm (python-dj-email-url): New variable. --- gnu/packages/django.scm | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 577789e988..08c44f1414 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2017 Ricardo Wurmus ;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; Copyright © 2019 Sam -;;; Copyright © 2020, 2021, 2022 Marius Bakke +;;; Copyright © 2020, 2021, 2022, 2023 Marius Bakke ;;; Copyright © 2021 Maxim Cournoyer ;;; Copyright © 2021 Luis Felipe López Acevedo ;;; Copyright © 2022 Pradana Aumars @@ -32,6 +32,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix gexp) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix deprecation) #:use-module (guix search-paths) @@ -691,6 +692,26 @@ dictionary, populated with all the data specified in your URL. There is also a conn_max_age argument to easily enable Django’s connection pool.") (license license:bsd-2))) +(define-public python-dj-email-url + (package + (name "python-dj-email-url") + (version "1.0.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "dj-email-url" version)) + (sha256 + (base32 + "16k91rvd9889xxrrf84a3zb0jpinizhfqdmafn54zxa8kqrf7zsm")))) + (build-system pyproject-build-system) + (home-page "https://github.com/migonzalvar/dj-email-url") + (synopsis "Configure email settings from URLs") + (description + "This package provides a facility for configuring Django email backend +settings from URLs.") + (license (list license:bsd-2 ;source code + license:cc-by4.0 ;documentation + license:cc0)))) ;configuration and data + (define-public python-django-picklefield (package (name "python-django-picklefield") From c463f184e316ce7c1302dc1995ef6c35f307b77a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 14:23:46 +0800 Subject: [PATCH 390/440] gnu: python-dj-database-url: Update to 2.1.0. * gnu/packages/django.scm (python-dj-database-url): Update to 2.1.0. --- gnu/packages/django.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 08c44f1414..2f7aa6a4d1 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -673,14 +673,16 @@ example, explicit calls to callables from templates and better performance.") (define-public python-dj-database-url (package (name "python-dj-database-url") - (version "0.5.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (pypi-uri "dj-database-url" version)) (sha256 (base32 - "0qs16g5y3lflxibsl8gwkwap21crhmmv98l60rdq6x1wawgypsja")))) + "0pqkifl5zradgsznjpk6g6zp64gnsxdav7x3knf56vh8w7pjq17j")))) (build-system python-build-system) + (propagated-inputs + (list python-django python-typing-extensions)) (home-page "https://github.com/kennethreitz/dj-database-url") (synopsis "Use Database URLs in your Django Application") (description @@ -690,7 +692,7 @@ DATABASE_URL environment variable to configure your Django application. The dj_database_url.config method returns a Django database connection dictionary, populated with all the data specified in your URL. There is also a conn_max_age argument to easily enable Django’s connection pool.") - (license license:bsd-2))) + (license license:bsd-3))) (define-public python-dj-email-url (package From ee401c1cb5172fb2942be63e82fbd527a4e0ef71 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 14:28:52 +0800 Subject: [PATCH 391/440] gnu: Add python-dj-search-url. * gnu/packages/django.scm (python-dj-search-url): New variable. --- gnu/packages/django.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 2f7aa6a4d1..3121ef30d5 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -714,6 +714,24 @@ settings from URLs.") license:cc-by4.0 ;documentation license:cc0)))) ;configuration and data +(define-public python-dj-search-url + (package + (name "python-dj-search-url") + (version "0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "dj-search-url" version)) + (sha256 + (base32 + "0h7vshhglym6af2pplkyivk6y0g0ncq0xpdzi88kq2sha9c1lka2")))) + (build-system pyproject-build-system) + (home-page "https://github.com/dstufft/dj-search-url") + (synopsis "Configure Haystack search from URLs") + (description + "This package provides a facility for configuring Django Haystack +applications with a @var{SEARCH_URL} variable.") + (license license:bsd-2))) + (define-public python-django-picklefield (package (name "python-django-picklefield") From c196c4c3536389094c3a2fc5b9bd62e63fd02689 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 14:34:09 +0800 Subject: [PATCH 392/440] gnu: Add python-django-cache-url. * gnu/packages/django.scm (python-django-cache-url): New variable. --- gnu/packages/django.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 3121ef30d5..b6f695b080 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -189,6 +189,26 @@ to the @dfn{don't repeat yourself} (DRY) principle.") ;; Use 3.2 LTS as the default until packages gain support for 4.x. (define-public python-django python-django-3.2) +(define-public python-django-cache-url + (package + (name "python-django-cache-url") + (version "3.4.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "django-cache-url" version)) + (sha256 + (base32 + "0dpx2wmcclmd3jkprdljz3makq12vd0sjv3xnvlj5vk1lg7glb7g")))) + (build-system pyproject-build-system) + (native-inputs + (list python-django)) + (home-page "https://github.com/epicserve/django-cache-url") + (synopsis "Configure Django cache settings from URLs") + (description + "This package provides a facility for configuring Django cache settings +with a @var{CACHE_URL} environment variable.") + (license license:expat))) + (define-public python-django-extensions (package (name "python-django-extensions") From 10c11d2b6d8a2ed97acc7149cc4d71537c579253 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 16:34:41 +0800 Subject: [PATCH 393/440] gnu: Add python-django-configurations. * gnu/packages/django.scm (python-django-configurations): New variable. --- gnu/packages/django.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index b6f695b080..ca696abf19 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -209,6 +209,46 @@ to the @dfn{don't repeat yourself} (DRY) principle.") with a @var{CACHE_URL} environment variable.") (license license:expat))) +(define-public python-django-configurations + (package + (name "python-django-configurations") + (version "2.4.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "django-configurations" version)) + (sha256 + (base32 + "11chll26iqqy5chyx62hya20cadk10nm2la7sch7pril70a5rhm6")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Taken from tox.ini. + (setenv "DJANGO_SETTINGS_MODULE" "tests.settings.main") + (setenv "DJANGO_CONFIGURATION" "Test") + (setenv "PYTHONPATH" + (string-append ".:" (getenv "GUIX_PYTHONPATH"))) + (invoke "django-cadmin" "test" "-v2"))))))) + (propagated-inputs + (list python-django)) + (native-inputs + (list python-dj-database-url + python-dj-email-url + python-dj-search-url + python-django-cache-url + python-setuptools-scm)) + (home-page "https://django-configurations.readthedocs.io/") + (synopsis "Helper module for organizing Django settings") + (description + "@code{django-configurations} helps you organize the configuration of +your Django project by providing glue code to bridge between Django'smodule +based settings system and programming patterns like mixins, facades, factories +and adapters that are useful for non-trivial configuration scenarios.") + (license license:bsd-3))) + (define-public python-django-extensions (package (name "python-django-extensions") From 75fe559afc75fe33e35d44129f67663f6361e530 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 16:47:56 +0800 Subject: [PATCH 394/440] gnu: Add python-django-ninja. * gnu/packages/django.scm (python-django-ninja): New variable. --- gnu/packages/django.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index ca696abf19..145860ec40 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -897,6 +897,36 @@ used to attach comments to any model, so you can use it for comments on blog entries, photos, book chapters, or anything else.") (license license:bsd-3))) +(define-public python-django-ninja + (package + (name "python-django-ninja") + (version "0.22.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "django_ninja" version)) + (sha256 + (base32 + "0b19w7nvw7c3z19dbza49m24c3384j59w2xcr5l6jshxazkvsgli")))) + (build-system pyproject-build-system) + (arguments + ;; FIXME: How to configure this test properly? + (list #:test-flags #~'("-k" "not test_improperly_configured"))) + (propagated-inputs + (list python-django python-pydantic)) + (native-inputs + (list python-flit-core + python-psycopg2 + python-pytest + python-pytest-asyncio + python-pytest-django)) + (home-page "https://django-ninja.rest-framework.com") + (synopsis "REST framework for Django") + (description + "Django Ninja is a web framework for building APIs with Django +and Python type hints. It is designed to be fast and easy to use thanks +to asyncio and Pydantic.") + (license license:expat))) + (define-public python-django-pipeline (package (name "python-django-pipeline") From 687ae1f8d1d39e1e2fbe2ca7aecfaf3f6e14267a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 20:39:41 +0800 Subject: [PATCH 395/440] gnu: python-django-picklefield: Update to 3.1.0. * gnu/packages/django.scm (python-django-picklefield): Update to 3.1.0. [propagated-inputs]: Change from PYTHON-DJANGO-2.2 to PYTHON-DJANGO. --- gnu/packages/django.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 145860ec40..b1a5a1e86a 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -795,7 +795,7 @@ applications with a @var{SEARCH_URL} variable.") (define-public python-django-picklefield (package (name "python-django-picklefield") - (version "3.0.1") + (version "3.1.0") (home-page "https://github.com/gintas/django-picklefield") ;; Use a git checkout because the PyPI release lacks tests. (source @@ -807,7 +807,7 @@ applications with a @var{SEARCH_URL} variable.") (file-name (git-file-name name version)) (sha256 (base32 - "0ni7bc86k0ra4pc8zv451pzlpkhs1nyil1sq9jdb4m2mib87b5fk")))) + "00d8sm6cnkv5bxbs2a3qrm4g69nlaa1wari7mc697df8q91v6r0n")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -815,10 +815,7 @@ applications with a @var{SEARCH_URL} variable.") (lambda _ (invoke "python" "-m" "django" "test" "-v2" "--settings=tests.settings")))))) - (propagated-inputs - ;; XXX: Picklefield has not been updated in 10+ years and fails tests - ;; with Django 3.2. - `(("python-django@2.2" ,python-django-2.2))) + (propagated-inputs (list python-django)) (synopsis "Pickled object field for Django") (description "Pickled object field for Django") (license license:expat))) From c7cb52e3fa65f7f163e244c11036f0898fd01058 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 8 Sep 2023 23:12:28 +0800 Subject: [PATCH 396/440] gnu: websockify: Update to 0.11.0. * gnu/packages/web.scm (websockify): Update to 0.11.0. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Remove. [native-inputs]: Remove PYTHON-MOX3. [propagated-inputs]: Add PYTHON-JWCRYPTO, PYTHON-REDIS, PYTHON-REQUESTS, and PYTHON-SIMPLEJSON. --- gnu/packages/web.scm | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 631106028d..e850531a8e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1985,7 +1985,7 @@ of people.") (define-public websockify (package (name "websockify") - (version "0.8.0") + (version "0.11.0") (source (origin (method git-fetch) (uri (git-reference @@ -1994,15 +1994,16 @@ of people.") (file-name (git-file-name name version)) (sha256 (base32 - "0pcic8qs0gdwrfjgfaf893jyddaw97wcjm2mmvwn0xyhmy8mbmw1")))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; FIXME: 2 out of 6 tests fail with "ImportError: No module - ; named 'stubout'". The tests can be run by replacing the check phase with - ; the command "python setup.py nosetests --verbosity=3". - (native-inputs (list ; Required for tests: - python-mox3 python-nose)) - (propagated-inputs (list python-numpy)) + "0ysqylpyv17s52634wn3vrwf7y9b5ig7fdfv8vwj1272lvv68qgk")))) + (build-system pyproject-build-system) + (native-inputs (list python-nose2)) + (propagated-inputs + (list python-jwcrypto + python-numpy + python-redis + python-requests + ;; TODO: Remove simplejson for versions > 0.11.0. + python-simplejson)) (home-page "https://github.com/novnc/websockify") (synopsis "WebSockets support for any application/server") (description "Websockify translates WebSockets traffic to normal socket From 928d462ab1c8473d0b76fa07e3beafe6283f7392 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 8 Sep 2023 23:46:30 +0800 Subject: [PATCH 397/440] gnu: websockify: Don't propagate inputs. * gnu/packages/web.scm (websockify)[propagated-inputs]: Move everything ... [inputs]: ... here. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e850531a8e..38982d9c39 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1997,7 +1997,7 @@ of people.") "0ysqylpyv17s52634wn3vrwf7y9b5ig7fdfv8vwj1272lvv68qgk")))) (build-system pyproject-build-system) (native-inputs (list python-nose2)) - (propagated-inputs + (inputs (list python-jwcrypto python-numpy python-redis From b9142073c429f5ea37b7ff07830ff9275597710e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 18:28:12 +0800 Subject: [PATCH 398/440] gnu: python-httpx: Update to 0.24.1. * gnu/packages/python-web.scm (python-httpx): Update to 0.24.1. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 532f86e687..2ec53c36ea 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -6109,7 +6109,7 @@ Some things HTTP Core does do: (define-public python-httpx (package (name "python-httpx") - (version "0.24.0") + (version "0.24.1") (source (origin ;; PyPI tarball does not contain tests. @@ -6119,7 +6119,7 @@ Some things HTTP Core does do: (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1b35ywrbdk8kcsfvr39gvfp7bvx00scqfigi8b19a1czhacsmc3q")))) + (base32 "121cnzp5jq638wrvfmxa9q0rwank7q6v5fi1lnih50fd5219yvm8")))) (build-system pyproject-build-system) (arguments (list From 12af75086852d0aa0e9b2f925cd095e26ac96f5c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 20:48:46 +0800 Subject: [PATCH 399/440] gnu: graphite-web: Update to 1.1.10. * gnu/packages/monitoring.scm (graphite-web): Update to 1.1.10. [arguments]: Relax Django requirement. [propagated-inputs]: Remove PYTHON-WHISPER , PYTHON-SCANDIR, and PYTHON-TXAMPQ. Replace PYTHON-DJANGO-2.2 with PYTHON-DJANGO-3.2. --- gnu/packages/monitoring.scm | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 3238f11fb4..e77ae19194 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -454,14 +454,14 @@ and persisting them to disk using the Whisper time-series library.") (define-public graphite-web (package (name "graphite-web") - (version "1.1.7") + (version "1.1.10") (source (origin (method url-fetch) (uri (pypi-uri "graphite-web" version)) (sha256 (base32 - "1l5a5rry9cakqxamvlx4xq63jifmncb6815bg9vy7fg1zyd3pjxk")))) + "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z")))) (build-system python-build-system) (arguments `(#:tests? #f ;XXX: not in PyPI release & requires database @@ -471,22 +471,20 @@ and persisting them to disk using the Whisper time-series library.") (lambda _ (substitute* "setup.py" ;; Allow newer versions of django-tagging. - (("django-tagging==") - "django-tagging>=")) - #t)) + (("django-tagging==") "django-tagging>=") + ;; And Django. + (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4")))) ;; Don't install to /opt (add-after 'unpack 'do-not-install-to-/opt (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t))))) (propagated-inputs (list python-cairocffi - python-pytz - python-whisper - python-django-2.2 + python-django-3.2 python-django-tagging - python-scandir - python-urllib3 python-pyparsing - python-txamqp)) + python-pytz + python-six + python-urllib3)) (home-page "https://graphiteapp.org/") (synopsis "Scalable realtime graphing system") (description "Graphite is a scalable real-time graphing system that does From d9620855de56c090a9a4992f356e7f74ee19af60 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 20:55:04 +0800 Subject: [PATCH 400/440] gnu: Remove python-django@2.2. This version is no longer maintained and contains known security flaws. * gnu/packages/django.scm (python-django-2.2): Remove variable. --- gnu/packages/django.scm | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index b1a5a1e86a..ad778304d6 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -171,21 +171,6 @@ to the @dfn{don't repeat yourself} (DRY) principle.") ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo. (append python-pytz))))) -(define-public python-django-2.2 - (package - (inherit python-django-3.2) - (version "2.2.28") - (source (origin - (method url-fetch) - (uri (pypi-uri "Django" version)) - (sha256 - (base32 - "04vl7aivsshzsnn547lm4jdinr67afhdspc40f0c06xzmxbvc002")))) - (native-inputs - (modify-inputs (package-native-inputs python-django-3.2) - (prepend ;; 2.2 requires Selenium for the test suite. - python-selenium))))) - ;; Use 3.2 LTS as the default until packages gain support for 4.x. (define-public python-django python-django-3.2) From 7bdf4aa3bb89da7929b85eb39ddaa007f2a56ea0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 21:19:48 +0800 Subject: [PATCH 401/440] gnu: python-flex: Update to 6.14.1. * gnu/packages/python-xyz.scm (python-flex): Update to 6.14.1. [propagated-inputs]: Remove PYTHON-ISO8601. Add PYTHON-STRICT-RFC3339. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0dd94edf8a..a01507a36a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22702,23 +22702,23 @@ manipulation, or @code{stdout}.") (define-public python-flex (package (name "python-flex") - (version "6.10.0") + (version "6.14.1") (source (origin (method url-fetch) (uri (pypi-uri "flex" version)) (sha256 (base32 - "00pamnwla3khk8nyla7y28dq9jnh69swd7f4jfsl7sn1izs8n8zk")))) + "1sr91f5sqywj4040jm3cq4333fp8hbmmr7v6v05a3h0sgyixcbi9")))) (build-system python-build-system) (propagated-inputs (list python-click - python-iso8601 python-jsonpointer python-pyyaml python-requests python-rfc3987 python-six + python-strict-rfc3339 python-validate-email)) (home-page "https://github.com/pipermerriam/flex") (synopsis "Validates Swagger schemata") From 9d87b400a699f5d1ca4a303817549733b73dba1e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 16:32:21 +0800 Subject: [PATCH 402/440] gnu: python-deprecated: Update to 1.2.14. * gnu/packages/python-xyz.scm (python-deprecated): Update to 1.2.14. --- gnu/packages/python-xyz.scm | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a01507a36a..f42b605421 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6155,7 +6155,7 @@ software version simply.") (define-public python-deprecated (package (name "python-deprecated") - (version "1.2.13") + (version "1.2.14") (source (origin (method git-fetch) @@ -6165,14 +6165,8 @@ software version simply.") (file-name (git-file-name name version)) (sha256 (base32 - "0v4ys9xr8lski2r98da99spsj6hjlnnqgnhhmyhrm66myiix885c")))) - (build-system python-build-system) - (arguments - `(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest"))))))) + "0knjsacv0r4gyz6ngjn3ih6352yz05r63ll73y2cg162bzcak48z")))) + (build-system pyproject-build-system) (propagated-inputs (list python-wrapt)) (native-inputs From 977dbf25889d995595d2a9d82a497117fc9afb91 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 17:35:31 +0800 Subject: [PATCH 403/440] gnu: python-daemon: Update to 3.0.1. * gnu/packages/python-xyz.scm (python-daemon): Update to 3.0.1. [arguments]: Skip two more tests. [propagated-inputs]: Add PYTHON-PACKAGING and PYTHON-SETUPTOOLS. [native-inputs]: Remove PYTHON-COVERAGE, PYTHON-TWINE, and PYTHON-MOCK. --- gnu/packages/python-xyz.scm | 25 +++++++++++-------------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f42b605421..ffe4ecf5c1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5625,38 +5625,35 @@ logging and tracing of the execution.") (define-public python-daemon (package (name "python-daemon") - (version "2.3.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (pypi-uri "python-daemon" version)) (sha256 (base32 - "1bxfn2bq56sd4w0nm9mqy8y0905m7fc8vmhnjxlrf49vcbqr7adx")))) + "1rfsnij687hk97ppzs2q6mwmxgr632nh672ajd0gzsppf8ilamvc")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'check 'adjust-tests (lambda _ - ;; Drop use of testtools.helpers.safe_hasattr which has - ;; been removed in favor of hasattr. - (substitute* "test/test_metadata.py" - (("testtools\\.helpers\\.safe_hasattr") - "hasattr")) ;; FIXME: Determine why test fails (substitute* "test/test_daemon.py" (("test_detaches_process_context") - "skip_test_detaches_process_context"))))))) + "skip_test_detaches_process_context")) + (substitute* "test/scaffold.py" + (("test_exception_instance") + "skip_test_exception_instance") + (("test_exception_types") + "skip_test_exception_types"))))))) (propagated-inputs - (list python-lockfile)) + (list python-lockfile python-packaging python-setuptools)) (native-inputs - (list python-coverage - python-testtools + (list python-docutils python-testscenarios - python-twine - python-mock - python-docutils)) + python-testtools)) (home-page "https://pagure.io/python-daemon/") (synopsis "Python library for making a Unix daemon process") (description "Python-daemon is a library that assists a Python program to From b8113fce0281054597f0c928317dbccf20be3baf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 23:04:15 +0800 Subject: [PATCH 404/440] gnu: python-pkginfo: Update to 1.9.6. * gnu/packages/python-xyz.scm (python-pkginfo): Update to 1.9.6. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [native-inputs]: Remove PYTHON-WHEEL. Add PYTHON-PYTEST. --- gnu/packages/python-xyz.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ffe4ecf5c1..03f40ab806 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23252,16 +23252,16 @@ design and layout.") (define-public python-pkginfo (package (name "python-pkginfo") - (version "1.8.3") + (version "1.9.6") (source (origin (method url-fetch) (uri (pypi-uri "pkginfo" version)) (sha256 - (base32 "0z46w559hrl79gf7navgzimj21ma821wka27jh58fvyqilqs8kd8")))) - (build-system python-build-system) + (base32 "0inh57664sx2vlbd3913dsc9nz21ysb9vk591qpkg90qhxp8kmcg")))) + (build-system pyproject-build-system) (native-inputs - (list python-wheel)) + (list python-pytest)) (home-page "https://code.launchpad.net/~tseaver/pkginfo/trunk") (synopsis "Query metadatdata from sdists, bdists, and installed packages") (description From 1af18a07d32470d1472fdb8b93bef4d23874af19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Sep 2023 16:39:36 +0800 Subject: [PATCH 405/440] gnu: python-pytest-django: Update to 4.5.2. * gnu/packages/django.scm (python-pytest-django): Update to 4.5.2. [native-inputs]: Remove PYTHON-DJANGO and PYTHON-PYTEST-XDIST. --- gnu/packages/django.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index ad778304d6..0c70616dee 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -424,13 +424,13 @@ size and quality.") (define-public python-pytest-django (package (name "python-pytest-django") - (version "4.4.0") + (version "4.5.2") (source (origin (method url-fetch) (uri (pypi-uri "pytest-django" version)) (sha256 (base32 - "0mglnz0w6k7dgw1jn6giv56pmdjd6a3zwwkhxb2kyzmzk0viw5xm")))) + "1hp61jbnnhnjxzdrz9ni08lzrv8q7iiycnnxvcwnkhxpkdsny1yr")))) (build-system python-build-system) (arguments ;; The test suite is disabled because there are many test failures (see: @@ -454,7 +454,7 @@ size and quality.") " and not test_urls_cache_is_cleared"))) (format #t "test suite not run~%"))))))) (native-inputs - (list python-django python-setuptools-scm python-pytest-xdist)) + (list python-setuptools-scm)) (propagated-inputs (list python-pytest)) (home-page "https://pytest-django.readthedocs.org/") From 0b0a33665c0e832b408162c81f1f977eafaf29d7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 21:14:09 +0800 Subject: [PATCH 406/440] gnu: python-django@3.2: Update to 3.2.21. * gnu/packages/django.scm (python-django-3.2): Update to 3.2.21. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 0c70616dee..70da159e8e 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -142,13 +142,13 @@ to the @dfn{don't repeat yourself} (DRY) principle.") (define-public python-django-3.2 (package (inherit python-django-4.0) - (version "3.2.18") + (version "3.2.21") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "1fikqpf75zjlx7dgdrrrz4212cajp6rl79rw0zzlzdifi7z8s808")))) + "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5")))) (native-search-paths '()) ;no need for TZDIR (propagated-inputs (modify-inputs (package-propagated-inputs python-django-4.0) From c909cf9f03950afc277b0166aa27e343ce922e2e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 21:16:46 +0800 Subject: [PATCH 407/440] gnu: python-asgiref: Update to 3.7.2. * gnu/packages/python-web.scm (python-asgiref): Update to 3.7.2. [native-inputs]: Add PYTHON-MYPY. [propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS. --- gnu/packages/python-web.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 2ec53c36ea..e7c20d67b5 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -571,12 +571,12 @@ stream is an enhanced asynchronous iterable.") (define-public python-asgiref (package (name "python-asgiref") - (version "3.4.1") + (version "3.7.2") (source (origin (method url-fetch) (uri (pypi-uri "asgiref" version)) (sha256 - (base32 "1saqgpgbdvb8awzm0f0640j0im55hkrfzvcw683cgqw4ni3apwaf")))) + (base32 "1vdgj8mikd2j6ijlhf7b4n2nxkvq72r1c0hj8mdvl6d8jfmf634y")))) (build-system python-build-system) (arguments '(#:phases @@ -586,7 +586,9 @@ stream is an enhanced asynchronous iterable.") (when tests? (invoke "pytest" "-vv"))))))) (native-inputs - (list python-pytest python-pytest-asyncio)) + (list python-mypy python-pytest python-pytest-asyncio)) + (propagated-inputs + (list python-typing-extensions)) (home-page "https://github.com/django/asgiref/") (synopsis "ASGI specs, helper code, and adapters") (description From 8e9a2932d6827243a8df87df462b87800b1a23e9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 9 Sep 2023 21:14:33 +0800 Subject: [PATCH 408/440] gnu: python-django@4: Update to 4.2.5. * gnu/packages/django.scm (python-django-4.0): Rename to ... (python-django-4.2): ... this. Update to 4.2.5. (python-django-3.2): Adjust inherits accordingly. --- gnu/packages/django.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 70da159e8e..4060819a35 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -54,16 +54,16 @@ #:use-module (gnu packages time) #:use-module (gnu packages xml)) -(define-public python-django-4.0 +(define-public python-django-4.2 (package (name "python-django") - (version "4.0.7") + (version "4.2.5") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "0qblhh7s7fcznqr79919yp2d7wiz3ixv39navmifb677dg9mlvcw")))) + "1ha6c5j3pizbsfzw37r52lvdz8z5lblq4iwa99mpkdzz92aiqp2y")))) (build-system python-build-system) (arguments '(#:phases @@ -141,7 +141,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.") (define-public python-django-3.2 (package - (inherit python-django-4.0) + (inherit python-django-4.2) (version "3.2.21") (source (origin (method url-fetch) @@ -151,7 +151,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.") "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5")))) (native-search-paths '()) ;no need for TZDIR (propagated-inputs - (modify-inputs (package-propagated-inputs python-django-4.0) + (modify-inputs (package-propagated-inputs python-django-4.2) ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo. (append python-pytz))))) From 73c8574314295f32faa5424bc4623442d73e8444 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 04:35:25 +0800 Subject: [PATCH 409/440] gnu: python-bleach: Update to 6.0.0. * gnu/packages/python-xyz.scm (python-bleach): Update to 6.0.0. [propagated-inputs]: Remove PYTHON-WEBENCODINGS. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 03f40ab806..e800baa482 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15117,13 +15117,13 @@ systems, as a command line tool, and as a Python library.") (define-public python-bleach (package (name "python-bleach") - (version "5.0.1") + (version "6.0.0") (source (origin (method url-fetch) (uri (pypi-uri "bleach" version)) (sha256 - (base32 "0p089853pkwzf1j2zjlmw67pwbkk0whpzfx9dbrd56zb8xf2a0qd")) + (base32 "054lp46iymchq3np0nar3k2h4da3wq4rzw652kdxh1syb70qa6hs")) (snippet #~(begin (use-modules (guix build utils)) @@ -15131,7 +15131,7 @@ systems, as a command line tool, and as a Python library.") (("bleach\\._vendor\\.html5lib") "html5lib")) (delete-file-recursively "bleach/_vendor/html5lib"))))) (build-system pyproject-build-system) - (propagated-inputs (list python-html5lib python-tinycss2 python-webencodings)) + (propagated-inputs (list python-html5lib python-tinycss2)) (native-inputs (list python-pytest)) (home-page "https://github.com/mozilla/bleach") (synopsis "Whitelist-based HTML-sanitizing tool") From 9d285c8bebc714bc757f889f1509932a8f485849 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 14:46:38 +0800 Subject: [PATCH 410/440] gnu: python-platformdirs: Update to 3.10.0. * gnu/packages/python-xyz.scm (python-platformdirs): Update to 3.10.0. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [native-inputs]: Add PYTHON-HATCHLING and PYTHON-HATCH-VCS. Remove PYTHON-SETUPTOOLS-SCM. --- gnu/packages/python-xyz.scm | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e800baa482..0426220ef2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -31475,23 +31475,20 @@ compatible with a wide range of versions of the Stripe API.") (define-public python-platformdirs (package (name "python-platformdirs") - (version "2.4.1") + (version "3.10.0") (source (origin (method url-fetch) (uri (pypi-uri "platformdirs" version)) (sha256 - (base32 "1njz0h4iky8iglrb85cd07hpa3lp1a2dfr934dj65hxwzvfk61j4")))) - (build-system python-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv"))))))) + (base32 "0vbzyw1k6wvg8gv9cg99ds5pri007c6rqx9668d6kk6pnbd9cmml")))) + (build-system pyproject-build-system) (native-inputs - (list python-appdirs python-pytest python-pytest-mock - python-setuptools-scm)) + (list python-appdirs + python-hatchling + python-hatch-vcs + python-pytest + python-pytest-mock)) (home-page "https://github.com/platformdirs/platformdirs") (synopsis "Determine the appropriate platform-specific directories") (description "When writing applications, finding the right location to From c08b919b67dc1a0b1e6e537bdc19a4b19b8dc84a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 15:02:23 +0800 Subject: [PATCH 411/440] gnu: python-distlib: Update to 0.3.7. * gnu/packages/python-xyz.scm (python-distlib): Update to 0.3.7. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Remove redundant phases. [native-inputs]: Remove PYTHON-PYPA-BUILD. --- gnu/packages/python-xyz.scm | 26 +++++++------------------- 1 file changed, 7 insertions(+), 19 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0426220ef2..b574ec2efe 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8537,42 +8537,30 @@ and therefore easier to read and write.") (define-public python-distlib (package (name "python-distlib") - (version "0.3.5") + (version "0.3.7") (source (origin (method url-fetch) (uri (pypi-uri "distlib" version)) (sha256 (base32 - "1zmjraasgqkz0gfv4mc4w4fj4k2fxj62h1pf5dgb5qqbqwvmgxx7")))) - (build-system python-build-system) + "1a27f5p93j9i1l3324qgahs3g8ai91fmx783jpyyla506i5ybbwx")))) + (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'build - (lambda _ - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) (add-before 'build 'no-/bin/sh (lambda _ (substitute* '("distlib/scripts.py" "tests/test_scripts.py") (("/bin/sh") (which "sh"))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) + (add-before 'check 'prepare-test-environment + (lambda _ (setenv "HOME" "/tmp") ;; NOTE: Any value works, the variable just has to be present. - (setenv "SKIP_ONLINE" "1") - (when tests? - (invoke "pytest" "-vv")))) - (replace 'install - (lambda _ - (let ((whl (car (find-files "dist" "\\.whl$")))) - (invoke "pip" "--no-cache-dir" "--no-input" - "install" "--no-deps" "--prefix" #$output whl))))))) + (setenv "SKIP_ONLINE" "1")))))) (native-inputs - (list python-pypa-build python-pytest)) + (list python-pytest)) (home-page "https://github.com/pypa/distlib") (synopsis "Distribution utilities") (description "Distlib is a library which implements low-level functions that From a0aff95db93f2730b57fe3411fdf2e1d8eb194ff Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 10 Sep 2023 15:34:49 +0800 Subject: [PATCH 412/440] gnu: python-distlib: Don't reference the implicit bash input. * gnu/packages/python-xyz.scm (python-distlib)[inputs]: Add BASH-MINIMAL. [arguments]: Use SEARCH-INPUT-FILE instead of WHICH. --- gnu/packages/python-xyz.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b574ec2efe..5445318157 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8551,9 +8551,10 @@ and therefore easier to read and write.") #:phases #~(modify-phases %standard-phases (add-before 'build 'no-/bin/sh - (lambda _ - (substitute* '("distlib/scripts.py" "tests/test_scripts.py") - (("/bin/sh") (which "sh"))))) + (lambda* (#:key inputs #:allow-other-keys) + (let ((/bin/sh (search-input-file inputs "bin/sh"))) + (substitute* '("distlib/scripts.py" "tests/test_scripts.py") + (("/bin/sh") /bin/sh))))) (add-before 'check 'prepare-test-environment (lambda _ (setenv "HOME" "/tmp") @@ -8561,6 +8562,8 @@ and therefore easier to read and write.") (setenv "SKIP_ONLINE" "1")))))) (native-inputs (list python-pytest)) + (inputs + (list bash-minimal)) (home-page "https://github.com/pypa/distlib") (synopsis "Distribution utilities") (description "Distlib is a library which implements low-level functions that From 36821b23b7f5320a6d3926afcff22d2bfe3ed0eb Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 16:24:42 +0800 Subject: [PATCH 413/440] gnu: python-cachetools: Update to 5.3.1. * gnu/packages/python-xyz.scm (python-cachetools): Update to 5.3.1. * gnu/packages/matrix.scm (python-matrix-nio)[arguments]: Add phase to loosen cachetools requirement. --- gnu/packages/matrix.scm | 7 +++++++ gnu/packages/python-xyz.scm | 4 ++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm index 6107dfc979..32ae62fcb4 100644 --- a/gnu/packages/matrix.scm +++ b/gnu/packages/matrix.scm @@ -171,6 +171,13 @@ homeserver and generally help bootstrap the ecosystem.") (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + ;; Remove upper bounds of cachetool pin. + (("cachetools (.*version = )\"\\^4" _ match) + (string-append "cachetools " match + "\">=4"))))) (add-before 'check 'install-tests (lambda* (#:key inputs outputs #:allow-other-keys) (copy-recursively (string-append diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 5445318157..d569e334d6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -742,13 +742,13 @@ from a docstring rather than the other way around.") (define-public python-cachetools (package (name "python-cachetools") - (version "4.2.2") + (version "5.3.1") (source (origin (method url-fetch) (uri (pypi-uri "cachetools" version)) (sha256 (base32 - "1zqc098gk6y614lxwqd9z2gm8lldgvrpid133pnlm4m048gfvdb1")))) + "0azn5c4nkwpq7s5wjzs605if9nxjzblghjnlihm767sfkcnkzs6w")))) (build-system python-build-system) (home-page "https://github.com/tkem/cachetools/") (synopsis "Extensible memoizing collections and decorators") From be44b0033716f32fec9242d0ebe7d048a998d417 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 17:16:09 +0800 Subject: [PATCH 414/440] gnu: python-cmarkgfm: Update to 2022.10.27. * gnu/packages/markup.scm (python-cmarkgfm): Update to 2022.10.27. [arguments]: Remove obsolete phase. --- gnu/packages/markup.scm | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index cdd9891352..6cb54d0d8f 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -253,13 +253,13 @@ implementation. (define-public python-cmarkgfm (package (name "python-cmarkgfm") - (version "0.8.0") + (version "2022.10.27") (source (origin (method url-fetch) (uri (pypi-uri "cmarkgfm" version)) (sha256 (base32 - "1jxk9cdir4q1bpjla7b7y1qfjmr7mkd0f802b2sb88njk079p1gy")) + "16875bazqd7p7qiky343w0fzasqziyvf72nipyh1r47a2rvsrnck")) (modules '((guix build utils))) (snippet '(begin @@ -270,13 +270,6 @@ implementation. (arguments (list #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - ;; Don't depend on bleeding-edge CFFI, as it is - ;; apparently only needed for Python >= 3.10. - (substitute* "setup.py" - (("cffi>=1\\.15\\.0") - "cffi>=1.0")))) (add-after 'unpack 'copy-cmark-gfm (lambda _ ;; This package needs the cmark-gfm source files From be3c0cf68e1a113b1ee5979b8354da2580db553e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 20:30:47 +0800 Subject: [PATCH 415/440] gnu: python-websockets: Update to 11.0.3. * gnu/packages/python-web.scm (python-websockets): Update to 11.0.3. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e7c20d67b5..ca65ea162f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -6299,7 +6299,7 @@ files.") (define-public python-websockets (package (name "python-websockets") - (version "10.3") + (version "11.0.3") (source (origin (method git-fetch) @@ -6309,7 +6309,7 @@ files.") (file-name (git-file-name name version)) (sha256 (base32 - "1vk7g5z977mi89hamwiqawpmibwvv9ghrf3pqva1waxmyc7gyjb5")))) + "1hn1qzpk1fvhi5j5nz4xlvzwkj9y16c9gryrb4n4dza84qi1pna5")))) (build-system python-build-system) (arguments (list #:phases From 0e25cba87d7fa915b4e357e475759e10b953cac6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 11 Sep 2023 21:50:59 +0800 Subject: [PATCH 416/440] gnu: python-uvicorn: Update to 0.23.2. * gnu/packages/python-web.scm (python-uvicorn): Update to 0.23.2. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Adjust accordingly. [native-inputs]: Add PYTHON-A2WSGI and PYTHON-HATCHLING. [propagated-inputs]: Remove PYTHON-ASGIREF. --- gnu/packages/python-web.scm | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index ca65ea162f..6aaa7504c4 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -5784,7 +5784,7 @@ and fairly speedy.") (define-public python-uvicorn (package (name "python-uvicorn") - (version "0.17.6") + (version "0.23.2") (source (origin ;; PyPI tarball has no tests. @@ -5794,23 +5794,21 @@ and fairly speedy.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0npwls02nhna2lyw2nksxij16l9agf12c9f42pvxb5yrpi9l16c8")))) - (build-system python-build-system) + (base32 "1qa4cwifss9cnasfr0ffn76rvh7wcfjkl6nw99yz43rjmdpj3h7p")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" "-o" "asyncio_mode=auto" - "-k" - (string-append - ;; These error or fail due to networking. - "not test_keepalive " - "and not test_bind_unix_socket_works_with_" - "reload_or_workers ")))))))) + (list #:test-flags + #~(list "-o" "asyncio_mode=auto" + "-k" + (string-join + ;; These error or fail due to networking. + '("not test_keepalive" + "not test_bind_unix_socket_works_with_reload_or_workers") + " and ")))) (native-inputs - (list python-httpx-bootstrap + (list python-a2wsgi + python-hatchling + python-httpx-bootstrap python-pytest python-pytest-asyncio python-pytest-mock @@ -5818,8 +5816,7 @@ and fairly speedy.") python-trustme python-wsproto)) (propagated-inputs - (list python-asgiref - python-click + (list python-click python-dotenv python-h11 python-httptools From e7fe89d716be3f13f17d5539eeb9c7aa35d9a9ee Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 15 Sep 2023 23:12:46 +0800 Subject: [PATCH 417/440] gnu: python-psycopg-pool: Update to 3.1.7. * gnu/packages/databases.scm (python-psycopg-pool): Update to 3.1.7. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 8a2063ee29..cd1a810a18 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3830,13 +3830,13 @@ libraries with SQLALchemy.") (name "python-psycopg-pool") ;; The connection pooling code is on a different release cadence ;; from the driver code, so fetch the latest PyPI release. - (version "3.0.3") + (version "3.1.7") (source (origin (method url-fetch) (uri (pypi-uri "psycopg-pool" version)) (sha256 (base32 - "1nx139pwzsgrz253zjxw2sf8h713s79h4cp1falmpc39j08djb46")))) + "1pkx7nj1mhacwpna7ldzqfqxd1xg8826600r0bs9ad1h93f429yh")))) (build-system python-build-system) (arguments (list #:tests? #f ;run for psycopg below From 90a3a0b5880c4dd1235e5488be7233fccd9f6878 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 15 Sep 2023 23:13:13 +0800 Subject: [PATCH 418/440] gnu: python-psycopg: Update to 3.1.10. * gnu/packages/databases.scm (python-psycopg): Update to 3.1.10. --- gnu/packages/databases.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index cd1a810a18..210b838b4a 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -3855,7 +3855,7 @@ with the @code{psycopg} PostgreSQL driver.") (define-public python-psycopg (package (name "python-psycopg") - (version "3.0.8") + (version "3.1.10") (source (origin ;; Fetch from git because PyPI contains only cythonized sources. (method git-fetch) @@ -3865,7 +3865,7 @@ with the @code{psycopg} PostgreSQL driver.") (file-name (git-file-name name version)) (sha256 (base32 - "16i19jqd9lg9r7bc63ssh527cccrpf49g1nlayikk5qlswpzp75y")))) + "0hqk45wlaflz69cy1r0hbv11bwb89p6hjb7zmgqas26gdhg37n0r")))) (build-system python-build-system) (arguments (list #:phases @@ -3907,13 +3907,19 @@ with the @code{psycopg} PostgreSQL driver.") "-o" "asyncio_mode=auto" ;; FIXME: Many of the typing tests are failing, ;; conveniently tagged as slow... - "-k" "not slow")))))))) + "-k" "not slow"))))) + ;; The sanity check phase attempts loading the C extension + ;; before the Python library, which results in the following: + ;; . + (delete 'sanity-check)))) (native-inputs (list python-cython-3 python-mypy python-psycopg-pool python-pytest python-pytest-asyncio + python-anyio python-tenacity pproxy tzdata-for-tests)) From 767b8586beea7d792e79daf434a76a5153fec881 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 21 Sep 2023 12:23:08 +0800 Subject: [PATCH 419/440] gnu: python-hyperlink: Update to 21.0.0. * gnu/packages/python-web.scm (python-hyperlink): Update to 21.0.0. [build-system]: Change to PYPROJECT-BUILD-SYSTEM. [arguments]: New field. [native-inputs]: Add PYTHON-PYTEST. --- gnu/packages/python-web.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 6aaa7504c4..9939a994b6 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -5311,15 +5311,24 @@ ecosystem.") (define-public python-hyperlink (package (name "python-hyperlink") - (version "19.0.0") + (version "21.0.0") (source (origin (method url-fetch) (uri (pypi-uri "hyperlink" version)) (sha256 (base32 - "0m2nhi0j8wmgfscf974wd5v1xfq8mah286hil6npy1ys0m3y7222")))) - (build-system python-build-system) + "0sx50lkivsfjxx9zr4yh7l9gll2l9kvl0v0w8w4wk2x5v9bzjyj2")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pretend-to-be-CI + (lambda _ + ;; Pretend to be a CI system to skip flaky tests. + (setenv "CI" "true")))))) + (native-inputs + (list python-pytest)) (propagated-inputs (list python-idna)) (home-page "https://github.com/python-hyper/hyperlink") From a392ec814f44578cf231fb9f1880a663820e0f5c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 21 Sep 2023 12:39:57 +0800 Subject: [PATCH 420/440] gnu: python-txaio: Update to 23.1.1. * gnu/packages/python-xyz.scm (python-txaio): Update to 23.1.1. [build-system]: Change to PYPROJECT-BUILD-SYSTEM. [propagated-inputs]: Remove. [native-inputs]: Add PYTHON-PYTEST and PYTHON-TWISTED. --- gnu/packages/python-xyz.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d569e334d6..48b61a7e0e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -26504,17 +26504,17 @@ and dates in \"human readable\" forms. For example, it would display (define-public python-txaio (package (name "python-txaio") - (version "18.8.1") + (version "23.1.1") (source (origin (method url-fetch) (uri (pypi-uri "txaio" version)) (sha256 (base32 - "1zmpdph6zddgrnkkcykh6qk5s46l7s5mzfqrh82m4b5iffn61qv7")))) - (build-system python-build-system) - (propagated-inputs - (list python-twisted python-six)) + "017p9x0bssf7g9slmf30ddh1baawsmxas4nivx334pkfjxp23agr")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest python-twisted)) (home-page "https://github.com/crossbario/txaio") (synopsis "Compatibility layer between Python asyncio and Twisted") (description "Txaio provides a compatibility layer between the Python From c95fb7778130d9559d9c5c3edb70ea142d407a0c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 21 Sep 2023 13:03:10 +0800 Subject: [PATCH 421/440] gnu: python-incremental: Update to 22.10.0. * gnu/packages/python-xyz.scm (python-incremental): Update to 22.10.0. --- 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 48b61a7e0e..82806222d7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21446,14 +21446,14 @@ system.") (define-public python-incremental (package (name "python-incremental") - (version "17.5.0") + (version "22.10.0") (source (origin (method url-fetch) (uri (pypi-uri "incremental" version)) (sha256 (base32 - "1cylxdz1cnkm5g3pklna3h2n0i0rks95ir1pnpxfnvpkmab1cxbv")))) + "1l0b9k158n04cmcccdq9phdy20h08lpis922dy71iq7pw2sywbwi")))) (build-system python-build-system) (home-page "https://github.com/hawkowl/incremental") (synopsis "Library for versioning Python projects") From d9b13b1e0f33df1541a8da1d679e7e0cc935211c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 21 Sep 2023 20:20:56 +0800 Subject: [PATCH 422/440] gnu: barectf: Update to 3.1.2. * gnu/packages/instrumentation.scm (barectf): Update to 3.1.2. [source]: Switch to GIT-FETCH. [build-system]: Change to PYPROJECT-BUILD-SYSTEM. [arguments]: Remove version pins. Set CC before building. [native-inputs]: Add PYTHON-POETRY-CORE and PYTHON-PYTEST. Remove GCC-TOOLCHAIN, GNU-MAKE, PYTHON-PYYAML-5, and PYTHON-TOX. Move PYTHON-JINJA2, PYTHON-JSONSCHEMA, and PYTHON-TERMCOLOR ... [propagated-inputs]: ... here. Add PYTHON-PYYAML. --- gnu/packages/instrumentation.scm | 46 +++++++++++++++++++++++--------- 1 file changed, 33 insertions(+), 13 deletions(-) diff --git a/gnu/packages/instrumentation.scm b/gnu/packages/instrumentation.scm index d8dc3b3e36..7fa7b2f7ba 100644 --- a/gnu/packages/instrumentation.scm +++ b/gnu/packages/instrumentation.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2021, 2022 Olivier Dion ;;; Copyright © 2023 Andy Tai +;;; Copyright © 2023 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,7 +25,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) - #:use-module (gnu packages commencement) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages datastructures) @@ -47,6 +48,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-xyz) #:use-module (gnu packages sphinx) @@ -58,6 +60,7 @@ #:use-module (guix build-system copy) #:use-module (guix build-system gnu) #:use-module (guix build-system linux-module) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix download) #:use-module (guix gexp) @@ -141,21 +144,38 @@ bindings, and the command-line tool @command{babeltrace2}.") (define-public barectf (package (name "barectf") - (version "3.1.1") + (version "3.1.2") (source (origin - (method url-fetch) - (uri (pypi-uri "barectf" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/efficios/barectf") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0zhc9d4qnnl4fjj6354qb4bng4ykywn8x3l3acpv6sx439q6ylwd")))) - (build-system python-build-system) - (native-inputs (list gcc-toolchain - gnu-make - python-jinja2 - python-jsonschema - python-pyyaml-5 - python-termcolor - python-tox)) + "0v7w830dqi46bq753x84d0z75dw4cf4r93gpfrv4sjynvmylbs95")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + ;; Remove version constraints as the program appears + ;; to work (tests pass!) with later versions. + ;; Try removing these when updating barectf. + (substitute* "pyproject.toml" + (("pyyaml = '\\^5") + "pyyaml = '>=5") + (("jsonschema = '\\^3") + "jsonschema = '>=3")))) + (add-before 'check 'set-CC + (lambda _ + ;; Some tests invoke a compiler. + (setenv "CC" "gcc")))))) + (native-inputs + (list python-poetry-core python-pytest)) + (propagated-inputs + (list python-jinja2 python-jsonschema python-pyyaml python-termcolor)) (home-page "https://barectf.org") (synopsis "CTF tracer generator") (description From 90322126825a0c358262e227b19af659e824abea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 00:14:29 +0800 Subject: [PATCH 423/440] gnu: python-sphinxcontrib-autoprogram: Update to 0.1.8. * gnu/packages/sphinx.scm (python-sphinxcontrib-autoprogram): Update to 0.1.8. [native-inputs]: Move PYTHON-SPHINX ... [propagated-inputs]: ... here. --- gnu/packages/sphinx.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 219063807e..a7c437d6b4 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -1086,19 +1086,17 @@ widgets, and supports thebelab for live code execution with minimal effort.") (define-public python-sphinxcontrib-autoprogram (package (name "python-sphinxcontrib-autoprogram") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (pypi-uri "sphinxcontrib-autoprogram" version)) (sha256 (base32 - "06hzim0d3fd72kf30fyjbbm5n8ibyybic0kf62gm79qp50zjwr5w")))) + "02pi450qml429disph075jyqwjrawrhbsjfkqvjf10yjp6fp4sas")))) (build-system python-build-system) (propagated-inputs - (list python-six)) - (native-inputs - (list python-sphinx)) + (list python-six python-sphinx)) (home-page "https://github.com/sphinx-contrib/autoprogram") (synopsis "Documenting CLI programs") (description From c2e078c602989134ab973183d558edd0202e946d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 00:39:43 +0800 Subject: [PATCH 424/440] gnu: python-libnacl: Update to 2.1.0. * gnu/packages/python-crypto.scm (python-libnacl): Update to 2.1.0. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Adjust hack for locating libsodium. Add custom check phase. [native-inputs]: Remove PYTHON-PYHAMCREST. Add PYTHON-POETRY-CORE. --- gnu/packages/python-crypto.scm | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 1ff742717c..e5ca69429d 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -1149,25 +1149,32 @@ none of them have everything that I'd like, so here's one more. It uses (define-public python-libnacl (package (name "python-libnacl") - (version "1.7.2") + (version "2.1.0") (source (origin (method url-fetch) (uri (pypi-uri "libnacl" version)) (sha256 (base32 - "0srx7i264v4dq9and8y6gpzzhrg8jpxs5iy9ggw4plimfj0rjfdm")))) - (build-system python-build-system) + "0q18j8kfibhi5qckakhf0b0psf8nkll91nfp3yqxkri9vykqshgk")))) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'locate-libsodium (lambda* (#:key inputs #:allow-other-keys) (substitute* "libnacl/__init__.py" - (("/usr/local/lib/libsodium.so") - (search-input-file inputs "/lib/libsodium.so")))))))) + (("ctypes\\.util\\.find_library\\('sodium'\\)") + (string-append "'" + (search-input-file inputs "/lib/libsodium.so") + "'"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "unittest" "discover" + "--start-directory" "tests" "-v"))))))) (native-inputs - (list python-pyhamcrest)) + (list python-poetry-core)) (inputs (list libsodium)) (home-page "https://libnacl.readthedocs.org/") From c23e2f61d35d850099e8c5179f38cb0496f14634 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 00:52:48 +0800 Subject: [PATCH 425/440] gnu: python-duniterpy: Update to 1.1.1. * gnu/packages/finance.scm (python-duniterpy): Update to 1.1.1. [build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Add more tweaks for hard coded version ranges. [native-inputs]: Add PYTHON-POETRY-CORE. --- gnu/packages/finance.scm | 37 ++++++++++++++++++++++++++----------- 1 file changed, 26 insertions(+), 11 deletions(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index a1e2216ae0..78bd55fc15 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -18,7 +18,7 @@ ;;; Copyright © 2020 Kei Kebreau ;;; Copyright © 2020 Christine Lemmer-Webber ;;; Copyright © 2020 Tom Zander -;;; Copyright © 2020 Marius Bakke +;;; Copyright © 2020, 2023 Marius Bakke ;;; Copyright © 2020, 2021, 2022 Vinicius Monego ;;; Copyright © 2020 Carlo Holl ;;; Copyright © 2020 Giacomo Leidi @@ -1378,14 +1378,14 @@ Luhn and family of ISO/IEC 7064 check digit algorithms.") (define-public python-duniterpy (package (name "python-duniterpy") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (pypi-uri "duniterpy" version)) (sha256 - (base32 "18i5bqz58vjp740pxb4wb4ixg1g2d73cwi0d8gp85fmj5p8f2gx7")))) - (build-system python-build-system) + (base32 "0h0fsawsrjd50lb1bkysb21ph39qlhmiymd3r5vs695qxvbwaqaa")))) + (build-system pyproject-build-system) (arguments ;; FIXME: Tests fail with: "TypeError: block_uid() missing 1 required ;; positional argument: 'value'". @@ -1393,19 +1393,34 @@ Luhn and family of ISO/IEC 7064 check digit algorithms.") #:phases (modify-phases %standard-phases (add-after 'unpack 'loosen-requirements (lambda _ - (substitute* "setup.py" - (("mnemonic>=0\\.19,<0.20") - "mnemonic>=0.19"))))))) + (substitute* "pyproject.toml" + (("mnemonic = \"\\^0\\.19") + "mnemonic = \">=0.19") + (("jsonschema = \"\\^3\\.2") + "jsonschema = \">=3.2")))) + (add-after 'unpack 'adjust-for-new-libnacl + (lambda _ + ;; Mimic upstream commit ad8f6a26e9e7067; remove + ;; for newer versions of duniterpy. + (substitute* "pyproject.toml" + (("libnacl = \"1\\.8") + "libnacl = \">=1.9")) + (substitute* "duniterpy/key/ascii_armor.py" + (("from libnacl\\.version import version as libnacl_version") + "import importlib.metadata +libnacl_version = importlib.metadata.version('libnacl')"))))))) + (native-inputs + (list python-poetry-core)) (propagated-inputs (list python-attrs python-base58 + python-graphql-core python-jsonschema python-libnacl - python-pyaes - python-graphql-core python-mnemonic - python-websocket-client - python-pypeg2)) + python-pyaes + python-pypeg2 + python-websocket-client)) (home-page "https://git.duniter.org/clients/python/duniterpy") (synopsis "Python implementation of Duniter API") (description "@code{duniterpy} is an implementation of From 86d1f1236337461b3208e985da1c4006a5260abd Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 01:11:18 +0800 Subject: [PATCH 426/440] gnu: python-arboreto: Add missing inputs. * gnu/packages/bioinformatics.scm (python-arboreto)[propagated-inputs]: Add PYTHON-LZ4 and PYTHON-PYARROW. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6acf37b312..4fdb5d57eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17816,8 +17816,10 @@ pycisTarget and SCENIC.") (list python-bokeh python-dask python-distributed + python-lz4 python-numpy python-pandas + python-pyarrow python-scikit-learn python-scipy python-tornado-6)) From fdfafaa48c43b86d45f86ef0c4ed9ea8ff1caaac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 01:17:55 +0800 Subject: [PATCH 427/440] gnu: python-bwapy: Fix typo. * gnu/packages/bioinformatics.scm (python-bwapy)[synopsis]: Fix typo. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4fdb5d57eb..dd14bada47 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19855,7 +19855,7 @@ sequences") (inputs (list zlib)) (home-page "https://github.com/ACEnglish/bwapy") - (synopsis "Python bindings to bwa alinger") + (synopsis "Python bindings to bwa aligner") (description "This package provides Python bindings to the bwa mem aligner.") ;; These Python bindings are licensed under Mozilla Public License 2.0, From 86507c96ed8a029db1892b0831000a62d03834f0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 22 Sep 2023 01:42:34 +0800 Subject: [PATCH 428/440] teams: Add self to 'python'. * etc/teams.scm.in (Marius Bakke): New person. --- etc/teams.scm.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/etc/teams.scm.in b/etc/teams.scm.in index e07c758117..876050da9c 100644 --- a/etc/teams.scm.in +++ b/etc/teams.scm.in @@ -639,6 +639,10 @@ GLib/GIO, GTK, GStreamer and Webkit." "cox.katherine.e+guix@gmail.com") emacs go lisp) +(define-member (person "Marius Bakke" + "marius@gnu.org") + python) + (define (find-team name) (or (hash-ref %teams (string->symbol name)) From fc1b85740adefcef2056702a82b1d95ebce8fb0e Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 21 Sep 2023 14:13:52 +0200 Subject: [PATCH 429/440] gnu: Add openjdk@20. * gnu/packages/java.scm (openjdk20): New variable. --- gnu/packages/java.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 436688526b..a87c688749 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1546,6 +1546,10 @@ blacklisted.certs.pem" ;; Fix for "valid range 1980-01-01T00:00:02Z to 2099-12-31T23:59:59Z". (setenv "SOURCE_DATE_EPOCH" "1234567890"))))))))) +(define-public openjdk20 + (make-openjdk openjdk19 "20" + "0pk5lpwijfv9qv7vwpsq2xfklbnqdfs6xbdhc5aamrpar4xi4ykx")) + ;;; Convenience alias to point to the latest version of OpenJDK. (define-public openjdk openjdk19) From ec8c5d027f87bb39ce3fd03c40a13d7b316d9dac Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 21 Sep 2023 14:14:45 +0200 Subject: [PATCH 430/440] gnu: Add openjdk@21. * gnu/packages/java.scm (openjdk21): New variable. * gnu/packages/patches/openjdk-21-fix-rpath.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/java.scm | 17 +++++++++++++++++ gnu/packages/patches/openjdk-21-fix-rpath.patch | 16 ++++++++++++++++ 3 files changed, 34 insertions(+) create mode 100644 gnu/packages/patches/openjdk-21-fix-rpath.patch diff --git a/gnu/local.mk b/gnu/local.mk index e05f687467..b059689954 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1696,6 +1696,7 @@ dist_patch_DATA = \ %D%/packages/patches/openjdk-10-pointer-comparison.patch \ %D%/packages/patches/openjdk-10-setsignalhandler.patch \ %D%/packages/patches/openjdk-15-xcursor-no-dynamic.patch \ + %D%/packages/patches/openjdk-21-fix-rpath.patch \ %D%/packages/patches/openmpi-mtl-priorities.patch \ %D%/packages/patches/openmw-assume-nonconst-SIGSTKSZ.patch \ %D%/packages/patches/openssh-trust-guix-store-directory.patch \ diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index a87c688749..0307b09acf 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1550,6 +1550,23 @@ blacklisted.certs.pem" (make-openjdk openjdk19 "20" "0pk5lpwijfv9qv7vwpsq2xfklbnqdfs6xbdhc5aamrpar4xi4ykx")) +(define-public openjdk21 + (make-openjdk openjdk20 "21" + "06wjfwrkqykjdkis2s1nh91cy8vwincnmc699cxvyk3fc12jf3vw" + (source (origin + (inherit (package-source base)) + (patches (search-patches "openjdk-21-fix-rpath.patch" + "openjdk-15-xcursor-no-dynamic.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + #~(modify-phases #$phases + (replace 'fix-java-shebangs + (lambda _ + ;; 'blacklisted' was renamed back to 'blocked'. + (substitute* "src/java.base/share/data/blockedcertsconverter/blocked.certs.pem" + (("^#!.*") "#! java BlockedCertsConverter SHA-256\n")))))))))) + ;;; Convenience alias to point to the latest version of OpenJDK. (define-public openjdk openjdk19) diff --git a/gnu/packages/patches/openjdk-21-fix-rpath.patch b/gnu/packages/patches/openjdk-21-fix-rpath.patch new file mode 100644 index 0000000000..62e2a50a52 --- /dev/null +++ b/gnu/packages/patches/openjdk-21-fix-rpath.patch @@ -0,0 +1,16 @@ +Author: Danny Milosavljevic +Date: 2023-09-20 + +diff -ru openjdk-21/make/modules/jdk.internal.le/Lib.gmk.orig openjdk-21.drv-4/source/make/modules/jdk.internal.le/Lib.gmk +--- openjdk-21/make/modules/jdk.internal.le/Lib.gmk.orig 1970-01-01 01:00:01.000000000 +0100 ++++ openjdk-21/make/modules/jdk.internal.le/Lib.gmk 2023-09-20 21:42:04.626821839 +0200 +@@ -34,7 +34,8 @@ + TOOLCHAIN := TOOLCHAIN_LINK_CXX, \ + OPTIMIZATION := LOW, \ + CFLAGS := $(CXXFLAGS_JDKLIB), \ +- LDFLAGS := $(LDFLAGS_JDKLIB), \ ++ LDFLAGS := $(LDFLAGS_JDKLIB) \ ++ $(call SET_SHARED_LIBRARY_ORIGIN), \ + LIBS_unix := $(JDKLIB_LIBS) $(LIBCXX), \ + LIBS_windows := $(JDKLIB_LIBS) user32.lib, \ + )) From 5ef168f91c37635835e30bf049e6516d673e97c7 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Thu, 21 Sep 2023 17:33:24 +0200 Subject: [PATCH 431/440] gnu: Add jbr@21-b240.22. * gnu/packages/java.scm (jbr21): New variable. --- gnu/packages/java.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0307b09acf..502bd30247 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -61,6 +61,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) + #:use-module (gnu packages freedesktop) ; wayland #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) @@ -1641,6 +1642,44 @@ OpenJDK.") (home-page "https://www.jetbrains.com/") (license license:gpl2+))) +(define-public jbr21 + (package + (inherit openjdk21) + (name "jbr") + (version "21-b240.22") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JetBrains/JetBrainsRuntime.git") + (commit (string-append "jb" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1sx48mm5vap4ab1qr6hy25wlgxljmhvpvrqiqiq692izr8dh7j4c")) + (patches (search-patches "openjdk-21-fix-rpath.patch" + "jbr-17-xcursor-no-dynamic.patch")))) + (inputs + `(("wayland" ,wayland) + ,@(package-inputs openjdk21))) + (arguments + (substitute-keyword-arguments (package-arguments openjdk21) + ((#:configure-flags configure-flags) + #~(append #$configure-flags + (list "--with-jvm-features=shenandoahgc" + "--enable-cds=yes" + "--with-vendor-name=JetBrains s.r.o" + "--with-vendor-url=https://www.jetbrains.com/" + "--with-vendor-bug-url=https://youtrack.jetbrains.com/issues/JBR"))))) + (synopsis "JetBrains Java Runtime") + (description "This package provides a Java runtime environment for +and Java development kit. It supports enhanced class redefinition (DCEVM), +includes a number of improvements in font rendering, keyboards support, +windowing/focus subsystems, HiDPI, accessibility, and performance, +provides better desktop integration and bugfixes not yet present in +OpenJDK.") + (home-page "https://www.jetbrains.com/") + (license license:gpl2+))) + (define-public ant/java8 (package From 7a898188fddc4788258894515c79ae62ad1ad766 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 432/440] gnu: w3m: Add graphics support. This increases the closure by a whopping 0.1 MiB. * gnu/packages/w3m.scm (w3m)[arguments]: Add "-enable-image=fb,x11" to the #:configure-flags. --- gnu/packages/w3m.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm index 498bf0f111..065731092e 100644 --- a/gnu/packages/w3m.scm +++ b/gnu/packages/w3m.scm @@ -61,7 +61,8 @@ '(#:tests? #f ; no check target ;; Use $EDITOR instead of a hard-coded value. #:configure-flags (list "--with-editor=" - "--with-imagelib=imlib2") + "--with-imagelib=imlib2" + "--enable-image=fb,x11") #:phases (modify-phases %standard-phases (add-before 'configure 'fix-perl From 5d2593be0a9a766dfb1d93490047940b7b81d381 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 17 Sep 2023 02:00:00 +0200 Subject: [PATCH 433/440] gnu: w3m: Remove input labels. * gnu/packages/w3m.scm (w3m)[native-inputs]: Remove input labels. --- gnu/packages/w3m.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm index 065731092e..f87cab998b 100644 --- a/gnu/packages/w3m.scm +++ b/gnu/packages/w3m.scm @@ -78,9 +78,7 @@ openssl zlib)) (native-inputs - `(("gettext" ,gettext-minimal) - ("perl" ,perl) - ("pkg-config" ,pkg-config))) + (list gettext-minimal perl pkg-config)) (home-page "https://w3m.sourceforge.net/") (synopsis "Text-mode web browser") (description From f4a0e472a949bfb91b85ec0612efdeabb9c60c56 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 11 Sep 2023 19:56:12 +0300 Subject: [PATCH 434/440] doc: contributing: Clarify generating the pre-inst-env script. Lack of clarity reported by lrustland on IRC. * doc/contributing.texi (Running Guix Before It Is Installed): Refer to the Building from Git section when giving instructions for generating the pre-inst-env script. --- doc/contributing.texi | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index 4de659c7ed..ce4b9db366 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -210,12 +210,11 @@ To that end, all the command-line tools can be used even if you have not run @code{make install}. To do that, you first need to have an environment with all the dependencies available (@pxref{Building from Git}), and then simply prefix each command with @command{./pre-inst-env} -(the @file{pre-inst-env} script lives in the top build tree of Guix; it -is generated by running @command{./bootstrap} followed by -@command{./configure}). As an example, here is how you would build the -@code{hello} package as defined in your working tree (this assumes -@command{guix-daemon} is already running on your system; it's OK if it's -a different version): +(the @file{pre-inst-env} script lives in the top build tree of Guix; +@pxref{Building from Git} to generate it). As an example, here is how you +would build the @code{hello} package as defined in your working tree (this +assumes @command{guix-daemon} is already running on your system; it's OK if +it's a different version): @example $ ./pre-inst-env guix build hello From f45c0c82289d409b4fac00464ea8b323839ba53f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 22 Sep 2023 09:32:11 +0300 Subject: [PATCH 435/440] gnu: wfa2-lib: Mark package as tunable. * gnu/packages/bioinformatics.scm (wfa2-lib)[properties]: New field. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd14bada47..ccee9d1f60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18422,6 +18422,7 @@ Cflags: -I${includedir}~%" (description "The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.") + (properties `((tunable? . #t))) (license license:expat))) (define-public vcflib From 6d33c1f8061e86d63ab5c9ec75df9c58130c7264 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Wed, 6 Sep 2023 15:01:00 +0200 Subject: [PATCH 436/440] git: Avoid touching the network unless needed in 'reference-available?'. Follow-up of 756e336fa008c2469b4a7317ad5c641ed48f25d6 fixing the issue. * guix/git/scm (reference-available?): Address case by case to determine whether the reference exists in the local Git checkout. --- guix/git.scm | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/guix/git.scm b/guix/git.scm index 1cb87a4560..1b3355109e 100644 --- a/guix/git.scm +++ b/guix/git.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2021 Marius Bakke ;;; Copyright © 2022 Maxime Devos ;;; Copyright © 2023 Tobias Geerinckx-Rice +;;; Copyright © 2023 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -360,21 +361,16 @@ dynamic extent of EXP." (define (reference-available? repository ref) "Return true if REF, a reference such as '(commit . \"cabba9e\"), is definitely available in REPOSITORY, false otherwise." - ;; Note: this must not rely on 'resolve-reference', as that procedure always - ;; resolves the references for branch names such as master. The semantic we - ;; want here is that unless the reference is exact (e.g. a commit), the - ;; reference should not be considered available, as it could have changed on - ;; the remote. (match ref - ((or ('commit . commit) - ('tag-or-commit . (? commit-id? commit))) - (let ((len (string-length commit)) - (oid (string->oid commit))) - (false-if-git-not-found - (->bool (if (< len 40) - (object-lookup-prefix repository oid len OBJ-COMMIT) - (commit-lookup repository oid)))))) + (('commit . (? commit-id? commit)) + (let ((oid (string->oid commit))) + (->bool (commit-lookup repository oid)))) + ((or ('tag . str) + ('tag-or-commit . str)) + (false-if-git-not-found + (->bool (resolve-reference repository ref)))) (_ + ;; For the others REF as branch or symref, the REF cannot be available #f))) (define (clone-from-swh url tag-or-commit output) From 47ba771548b50914895448552b7f85973694d579 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Fri, 15 Sep 2023 18:03:47 +0200 Subject: [PATCH 437/440] gnu: bap: Update to 2.5.0-alpha-0.a972f8a. * gnu/packages/ocaml.scm (bap): Explicitly refer to commit instead of mutable Git tag. --- gnu/packages/ocaml.scm | 147 +++++++++++++++++++++-------------------- 1 file changed, 75 insertions(+), 72 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index ea9d3e3594..8f4dd1b357 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5324,82 +5324,85 @@ necessary set of rewriters.") (license license:expat))) (define-public bap - (package - (name "bap") - (version "2.5.0-alpha") - (home-page "https://github.com/BinaryAnalysisPlatform/bap") - (source (origin - (method git-fetch) - (uri (git-reference - (url home-page) - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1fw9pp0xnssc08qqfkcafffap4f46hw7zmk80gif5yc4nazga8w5")))) - (build-system ocaml-build-system) - (arguments - (list - #:use-make? #t - #:phases - #~(modify-phases %standard-phases - (add-before 'configure 'fix-ncurses - (lambda _ - (substitute* "oasis/llvm" - (("-lcurses") "-lncurses")) - #t)) - (replace 'configure - (lambda* (#:key outputs inputs #:allow-other-keys) - (for-each make-file-writable (find-files "." ".")) - ;; Package name changed - (substitute* "oasis/elf-loader" - (("bitstring.ppx") "ppx_bitstring")) - ;; We don't have a monolithic llvm - (substitute* "oasis/llvm.setup.ml.in" - (("llvm_static = \"true\"") "true")) - (invoke "./configure" "--prefix" - (assoc-ref outputs "out") - "--libdir" - (string-append + (let (;; Let pin one commit because -alpha is subject to change. + (revision "0") + (commit "a972f8a419294dfb21847db5172ba58c5d7767eb")) + (package + (name "bap") + (version (git-version "2.5.0-alpha" revision commit)) + (home-page "https://github.com/BinaryAnalysisPlatform/bap") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fw9pp0xnssc08qqfkcafffap4f46hw7zmk80gif5yc4nazga8w5")))) + (build-system ocaml-build-system) + (arguments + (list + #:use-make? #t + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'fix-ncurses + (lambda _ + (substitute* "oasis/llvm" + (("-lcurses") "-lncurses")) + #t)) + (replace 'configure + (lambda* (#:key outputs inputs #:allow-other-keys) + (for-each make-file-writable (find-files "." ".")) + ;; Package name changed + (substitute* "oasis/elf-loader" + (("bitstring.ppx") "ppx_bitstring")) + ;; We don't have a monolithic llvm + (substitute* "oasis/llvm.setup.ml.in" + (("llvm_static = \"true\"") "true")) + (invoke "./configure" "--prefix" (assoc-ref outputs "out") - "/lib/ocaml/site-lib") - (string-append "--with-llvm-version=" #$(package-version llvm)) - "--with-llvm-config=llvm-config" - "--disable-ghidra" - "--disable-llvm-static" - "--enable-llvm" - "--enable-everything")))))) - (native-inputs (list clang ocaml-oasis ocaml-ounit)) - (propagated-inputs - (list - camlzip - ocaml-bitstring - ocaml-cmdliner - ocaml-core-kernel - ocaml-ezjsonm - ocaml-fileutils - ocaml-frontc - ocaml-graph - ocaml-linenoise - ocaml-ocurl - ocaml-piqi - ocaml-ppx-bap - ocaml-ppx-bitstring - ocaml-re - ocaml-uri - ocaml-utop - ocaml-uuidm - ocaml-yojson - ocaml-z3 - ocaml-zarith)) - (inputs - (list gmp llvm ncurses)) - (synopsis "Binary Analysis Platform") - (description "Binary Analysis Platform is a framework for writing program + "--libdir" + (string-append + (assoc-ref outputs "out") + "/lib/ocaml/site-lib") + (string-append "--with-llvm-version=" #$(package-version llvm)) + "--with-llvm-config=llvm-config" + "--disable-ghidra" + "--disable-llvm-static" + "--enable-llvm" + "--enable-everything")))))) + (native-inputs (list clang ocaml-oasis ocaml-ounit)) + (propagated-inputs + (list + camlzip + ocaml-bitstring + ocaml-cmdliner + ocaml-core-kernel + ocaml-ezjsonm + ocaml-fileutils + ocaml-frontc + ocaml-graph + ocaml-linenoise + ocaml-ocurl + ocaml-piqi + ocaml-ppx-bap + ocaml-ppx-bitstring + ocaml-re + ocaml-uri + ocaml-utop + ocaml-uuidm + ocaml-yojson + ocaml-z3 + ocaml-zarith)) + (inputs + (list gmp llvm ncurses)) + (synopsis "Binary Analysis Platform") + (description "Binary Analysis Platform is a framework for writing program analysis tools, that target binary files. The framework consists of a plethora of libraries, plugins, and frontends. The libraries provide code reusability, the plugins facilitate extensibility, and the frontends serve as entry points.") - (license license:expat))) + (license license:expat)))) (define-public ocaml-camomile (package From 3a7a81b4712a76dd40699bc0940ac366680f053a Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Fri, 15 Sep 2023 13:12:11 +0200 Subject: [PATCH 438/440] gnu: bap: Update to 2.6.0-alpha-0.f995d28. * gnu/packages/ocaml.scm (bap): Update to 2.6.0-alpha-0.f995d28. --- gnu/packages/ocaml.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 8f4dd1b357..8543505dbb 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5325,11 +5325,12 @@ necessary set of rewriters.") (define-public bap (let (;; Let pin one commit because -alpha is subject to change. + ;; The last stable release v2.5.0 is from July 2022. (revision "0") - (commit "a972f8a419294dfb21847db5172ba58c5d7767eb")) + (commit "f995d28a4a34abb4cef8e0b3bd3c41cd710ccf1a")) (package (name "bap") - (version (git-version "2.5.0-alpha" revision commit)) + (version (git-version "2.6.0-alpha" revision commit)) (home-page "https://github.com/BinaryAnalysisPlatform/bap") (source (origin (method git-fetch) @@ -5339,7 +5340,7 @@ necessary set of rewriters.") (file-name (git-file-name name version)) (sha256 (base32 - "1fw9pp0xnssc08qqfkcafffap4f46hw7zmk80gif5yc4nazga8w5")))) + "1zfkc8nagf8kvxbypalbhf6gs0c7i48zx53hlpak2ipjwhvm5im5")))) (build-system ocaml-build-system) (arguments (list From 5bae1fea205070a44bcf5f3caec8afa8d3b1a4c0 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Fri, 15 Sep 2023 17:48:42 +0200 Subject: [PATCH 439/440] gnu: python-glcontext: Update to 2.4.0-0.beebc1f. * gnu/packages/python-xyz.scm (python-glcontext): Explicitly refer to commit instead of mutable Git tag. --- gnu/packages/python-xyz.scm | 100 +++++++++++++++++++----------------- 1 file changed, 52 insertions(+), 48 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 82806222d7..319ccd2ae5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23051,55 +23051,59 @@ library.") "This is the Cython-coded accelerator module for PyOpenGL."))) (define-public python-glcontext - (package - (name "python-glcontext") - (version "2.4.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/moderngl/glcontext") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0zzpwyqg19y600n09xz07cxk4jimh9vjraszda7g7ipijq6iasac")))) - (build-system pyproject-build-system) - (arguments - (list #:phases #~(modify-phases %standard-phases - (add-before 'build 'fix-lib-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((mesa (assoc-ref inputs "mesa")) - (libx11 (assoc-ref inputs "libx11"))) - (substitute* '("glcontext/x11.cpp" - "glcontext/egl.cpp") - (("\"libGL.so\"") - (string-append "\"" mesa "/lib/libGL.so\"")) - (("\"libEGL.so\"") - (string-append "\"" mesa "/lib/libEGL.so\"")) - (("\"libX11.so\"") - (string-append "\"" libx11 "/lib/libX11.so\""))) - (substitute* '("glcontext/__init__.py") - (("find_library\\('GL'\\)") - (string-append "'" mesa "/lib/libGL.so'")) - (("find_library\\('EGL'\\)") - (string-append "'" mesa "/lib/libEGL.so'")) - (("find_library\\(\"X11\"\\)") - (string-append "'" libx11 "/lib/libX11.so'")))))) - (replace 'check - (lambda* (#:key inputs outputs tests? - #:allow-other-keys) - (when tests? - (system "Xvfb :1 &") - (setenv "DISPLAY" ":1") - (add-installed-pythonpath inputs outputs) - (invoke "pytest" "tests"))))))) - (inputs (list libx11 mesa)) - (native-inputs (list xorg-server-for-tests python-pytest python-psutil)) - (home-page "https://github.com/moderngl/glcontext") - (synopsis "Portable OpenGL Context for ModernGL") - (description "Python-glcontext is a library providing an OpenGL + (let (;; Upstream is known for abusing mutable tag, hence pinpoint the + ;; relevant commit. + (revision "0") + (commit "beebc1fd08ee850f06f4390be4b280824e383074")) + (package + (name "python-glcontext") + (version (git-version "2.4.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/moderngl/glcontext") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0zzpwyqg19y600n09xz07cxk4jimh9vjraszda7g7ipijq6iasac")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'build 'fix-lib-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((mesa (assoc-ref inputs "mesa")) + (libx11 (assoc-ref inputs "libx11"))) + (substitute* '("glcontext/x11.cpp" + "glcontext/egl.cpp") + (("\"libGL.so\"") + (string-append "\"" mesa "/lib/libGL.so\"")) + (("\"libEGL.so\"") + (string-append "\"" mesa "/lib/libEGL.so\"")) + (("\"libX11.so\"") + (string-append "\"" libx11 "/lib/libX11.so\""))) + (substitute* '("glcontext/__init__.py") + (("find_library\\('GL'\\)") + (string-append "'" mesa "/lib/libGL.so'")) + (("find_library\\('EGL'\\)") + (string-append "'" mesa "/lib/libEGL.so'")) + (("find_library\\(\"X11\"\\)") + (string-append "'" libx11 "/lib/libX11.so'")))))) + (replace 'check + (lambda* (#:key inputs outputs tests? + #:allow-other-keys) + (when tests? + (system "Xvfb :1 &") + (setenv "DISPLAY" ":1") + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "tests"))))))) + (inputs (list libx11 mesa)) + (native-inputs (list xorg-server-for-tests python-pytest python-psutil)) + (home-page "https://github.com/moderngl/glcontext") + (synopsis "Portable OpenGL Context for ModernGL") + (description "Python-glcontext is a library providing an OpenGL implementation for ModernGL on multiple platforms.") - (license license:expat))) + (license license:expat)))) (define-public python-rencode (package From ec130e1a1b7f3b87b1a6e626754f7e7a07f6b717 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Fri, 15 Sep 2023 19:09:54 +0200 Subject: [PATCH 440/440] gnu: python-glcontext: Update to 2.4.0-1.0af21b7. * gnu/packages/python-xyz.scm (python-glcontext): Update to 2.4.0-1.0af21b7. --- gnu/packages/python-xyz.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 319ccd2ae5..bebcfb50e9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23053,8 +23053,8 @@ library.") (define-public python-glcontext (let (;; Upstream is known for abusing mutable tag, hence pinpoint the ;; relevant commit. - (revision "0") - (commit "beebc1fd08ee850f06f4390be4b280824e383074")) + (revision "1") + (commit "0af21b7c8a8cc0e76f4d9aff6a4f156f43d37333")) (package (name "python-glcontext") (version (git-version "2.4.0" revision commit)) @@ -23066,7 +23066,7 @@ library.") (file-name (git-file-name name version)) (sha256 (base32 - "0zzpwyqg19y600n09xz07cxk4jimh9vjraszda7g7ipijq6iasac")))) + "03xpw776pvv8c5n58049yczlkgcqdh9vfcpjlghh3p6cal3yiq8a")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases