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Author SHA1 Message Date
Mădălin Ionel Patrașcu
6e0361d035
gnu: Add r-decontam. 
* gnu/packages/bioconductor.scm (r-decontam): New variable.
 2022-10-31 20:00:17 +01:00
Mădălin Ionel Patrașcu
fc27bf5d74
gnu: Add r-deconrnaseq. 
* gnu/packages/bioconductor.scm (r-deconrnaseq): New variable.
 2022-10-31 19:59:30 +01:00
Mădălin Ionel Patrașcu
ae94d879a1
gnu: Add r-decomptumor2sig. 
* gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable.
 2022-10-31 19:59:01 +01:00
Mădălin Ionel Patrașcu
a8631c816d
gnu: Add r-decomplexdisease. 
* gnu/packages/bioconductor.scm (r-decomplexdisease): New variable.
 2022-10-31 19:58:32 +01:00
Mădălin Ionel Patrașcu
41461b6e22
gnu: Add r-deco. 
* gnu/packages/bioconductor.scm (r-deco): New variable.
 2022-10-31 19:57:53 +01:00
Ricardo Wurmus
22c8783dff
gnu: Add ghc-6.10. 
* gnu/packages/haskell.scm (ghc-6.10): New variable.
 2022-10-31 19:51:40 +01:00
Ricardo Wurmus
26e1f3ec9a
gnu: ghc-6.6: Patch more references to /bin/sh. 
* gnu/packages/haskell.scm (ghc-6.6)[arguments]: Patch references to /bin/sh
in Cabal and process internals.
 2022-10-31 19:51:36 +01:00
Denis 'GNUtoo' Carikli
eaaba9d62c
gnu: Add wipe. 
* gnu/packages/disk.scm (wipe): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-10-31 11:42:25 -04:00
jgart
5da8e1e6e5
gnu: Add cl-airship-scheme. 
* gnu/packages/scheme.scm (cl-airship-scheme, sbcl-airship-scheme): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-10-31 16:01:12 +01:00
jgart
2bff470920
gnu: Add cl-zr-utils. 
* gnu/packages/lisp-xyz.scm (cl-zr-utils, ecl-zr-utils, sbcl-zr-utils): New
  variables.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-10-31 16:01:12 +01:00
Guillaume Le Vaillant
39816716c3
gnu: stumpwm: Update to 22.05-1.ff6cb73. 
* gnu/packages/wm.scm (stumpwm): Update to 22.05-1.ff6cb73.
 2022-10-31 16:01:12 +01:00
Guillaume Le Vaillant
1eee671d7d
gnu: sbcl: Update to 2.2.10. 
* gnu/packages/lisp.scm (sbcl): Update to 2.2.10.
  [arguments]: Remove obsolete fix from 'build-doc' phase.
 2022-10-31 16:01:12 +01:00
Mehmet Tekman
e90e47c00a
gnu: Add x11vnc. 
* gnu/packages/vnc.scm (x11vnc): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2022-10-31 09:48:50 -04:00
Nicolas Goaziou
61c002930e
gnu: silkaj: Update to 0.10.0. 
* gnu/packages/finance.scm (silkaj): Update to 0.10.0.
[build-system]: Use PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove it.
[native-inputs]: Add PYTHON-POETRY-CORE.
[inputs]: Remove input labels. Remove PYTHON-PYNACL. Add PYTHON-PENDULUM.
[description]: Do not overemphasize project name.
 2022-10-31 14:21:48 +01:00
Peter Polidoro
0f902e6a9e
gnu: kicad: Update to 6.0.8. 
* gnu/packages/engineering.scm (kicad): Update to 6.0.8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-10-31 12:57:23 +01:00
jgart
c9fb08a2b1
gnu: Add emacs-hare-mode. 
* gnu/packages/emacs-xyz.scm (emacs-hare-mode): New variable.

Co-authored-by: ( <paren@disroot.org>
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-31 12:18:06 +01:00
Nicolas Goaziou
a618505eeb
gnu: emacs-pyim: Update to 5.2.7. 
* gnu/packages/emacs-xyz.scm (emacs-pyim): Update to 5.2.7.
 2022-10-31 12:18:06 +01:00
Nicolas Goaziou
2b2564c0d8
gnu: emacs-mint-mode: Remove unnecessary #:INCLUDE. 
* gnu/packages/emacs-xyz.scm (emacs-mint-mode)[arguments]: Remove it.
Upstream provides no ".txt" and ".el" files are matched in %DEFAULT-INCLUDE.
 2022-10-31 12:18:06 +01:00
jgart
7c25c94a27
gnu: emacs-mint-mode: Update to 2.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-mint-mode): Update to 2.0.0.
[description]: Update description for accuracy with current version.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-31 12:18:05 +01:00
Mathieu Othacehe
ab974ed709
installer: parted: Retry failing read-partition-uuid call. 
Fixes: <https://issues.guix.gnu.org/53541>.

* gnu/installer/parted.scm (read-partition-uuid/retry): New procedure.
(check-user-partitions): Use it.
 2022-10-31 09:34:13 +01:00
Efraim Flashner
5197b07e0e
gnu: mpv-mpris: Update to 0.9. 
* gnu/packages/video.scm (mpv-mpris): Update to 0.9.
 2022-10-31 08:12:44 +02:00
(unmatched-parenthesis
c3f391376b
* gnu/packages/golang.scm (notmuch-fixtures): New variable here... 
(go-github-com-zenhack-go-notmuch): ...and here.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
 2022-10-31 02:09:30 -04:00
Tobias Geerinckx-Rice
044985f5f9
gnu: jo: Update to 1.7. 
* gnu/packages/web.scm (jo): Update to 1.7.
 2022-10-23 02:00:00 +02:00
Tobias Geerinckx-Rice
128f3cf8a4
gnu: hamlib: Fix inputs. 
* gnu/packages/radio.scm (hamlib)[native-inputs]: Move lua and tcl…
[inputs]: …here.  Add python.
 2022-10-23 02:00:00 +02:00
Tobias Geerinckx-Rice
fad1165fdb
gnu: hamlib: Rebuild broken configure script. 
* gnu/packages/radio.scm (hamlib)[native-inputs]: Add autoconf, automake, and libtool.
[arguments]: Add a new 'force-bootstrap phase.
 2022-10-23 02:00:00 +02:00
Tobias Geerinckx-Rice
157db85f6d
gnu: sdrangel: Don't detect CPU extensions at build time. 
* gnu/packages/radio.scm (sdrangel)[arguments]:
Add a new 'fix-CPU-extension-detection phase.
 2022-10-23 02:00:00 +02:00
Christopher Baines
1f29136e25
gnu: tar: Add chained renames and Directory to hurd skipped tests. 
* gnu/packages/base.scm (tar)[arguments]: Include chained renames and
Directory in the tests skipped for when building for the hurd.
 2022-10-30 20:53:06 +00:00
Christopher Baines
8b8430c0ad
gnu: diffutils: Add large-subopt to XFAIL_TESTS for the hurd. 
* gnu/packages/base.scm (diffutils)[arguments]: Add large-subopt to
XFAIL_TESTS for the hurd.
 2022-10-30 20:52:24 +00:00
Christopher Baines
2b21d60a94
gnu: coreutils: Remove test-tls from XFAIL_TESTS for the hurd. 
As this test passes.

* gnu/packages/base.scm (coreutils)[arguments]: Remove test-tls from
XFAIL_TESTS for the hurd.
 2022-10-30 20:51:26 +00:00
Leo Famulari
5b87c7c1d2
gnu: linux-libre 4.9: Update to 4.9.331. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.331.
(linux-libre-4.9-pristine-source): Update hash.
 2022-10-30 14:57:19 -04:00
Leo Famulari
325326f516
gnu: linux-libre 4.14: Update to 4.14.296. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.296.
(linux-libre-4.14-pristine-source): Update hash.
 2022-10-30 14:57:19 -04:00
Leo Famulari
1be537bf3d
gnu: linux-libre 4.19: Update to 4.19.262. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.262.
(linux-libre-4.19-pristine-source): Update hash.
 2022-10-30 14:57:19 -04:00
Leo Famulari
33bf1e1fed
gnu: linux-libre 5.4: Update to 5.4.221. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.221.
(linux-libre-5.4-pristine-source): Update hash.
 2022-10-30 14:57:19 -04:00
Leo Famulari
41d24c88ec
gnu: linux-libre 5.10: Update to 5.10.152. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.152.
(linux-libre-5.10-pristine-source): Update hash.
 2022-10-30 14:57:19 -04:00
Leo Famulari
78602aae4e
gnu: linux-libre 5.15: Update to 5.15.76. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.76.
(linux-libre-5.15-pristine-source): Update hash.
 2022-10-30 14:57:08 -04:00
jgart
9eabe0e1fd
gnu: Add emacs-flymake-collection. 
* gnu/packages/emacs-xyz.scm (emacs-flymake-collection): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-30 10:54:01 +01:00
Nicolas Goaziou
631105947f
gnu: emacs-plz: Remove unnecessary call to MAKE-FILE-WRITABLE. 
* gnu/packages/emacs-xyz.scm (emacs-plz)[arguments]: Remove unnecessary
MAKE-FILE-WRITABLE call.
 2022-10-30 10:37:01 +01:00
Michael Rohleder
5b8b38d33a
gnu: emacs-plz: Patch path to curl. 
* gnu/packages/emacs-xyz.scm (emacs-plz)[arguments]: Add phase substitute-curl-path.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-30 10:34:57 +01:00
Nicolas Goaziou
2727cebef3
gnu: emacs-mentor: Update to 0.5. 
* gnu/packages/emacs-xyz.scm (emacs-mentor): Update to 0.5.
 2022-10-30 10:27:54 +01:00
Nicolas Goaziou
3684d9c119
gnu: wireshark: Update to 4.0.1. 
* gnu/packages/networking.scm (wireshark): Update to 4.0.1.
 2022-10-30 10:23:46 +01:00
Nicolas Goaziou
dc06ddee2e
gnu: keepassxc: Update to 2.7.4. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.7.4.
 2022-10-30 10:20:50 +01:00
Efraim Flashner
87727b6dcb
gnu: vim: Update to 9.0.0820. 
* gnu/packages/vim.scm (vim): Update to 9.0.0820.
 2022-10-30 09:57:49 +02:00
Efraim Flashner
2facc0eb37
gnu: vim: Patch another '/bin/sh' shebang. 
* gnu/packages/vim.scm (vim)[arguments]: Adjust custom phase
'patch-absolute-paths to use absolute value when checking for custom
cscope command.
 2022-10-30 09:57:46 +02:00
Tobias Geerinckx-Rice
63bf060138
gnu: nginx-documentation: Update to 1.23.1-2898-0b7e004b5061. 
* gnu/packages/web.scm (nginx-documentation): Update to 1.23.1-2898-0b7e004b5061.
 2022-10-23 02:00:27 +02:00
Tobias Geerinckx-Rice
a63f8b89cf
gnu: nginx: Update to 1.23.2. 
* gnu/packages/web.scm (nginx): Update to 1.23.2.
 2022-10-23 02:00:26 +02:00
Tobias Geerinckx-Rice
d03bd43f46
gnu: pgloader: Update to 3.6.9. 
* gnu/packages/databases.scm (pgloader): Update to 3.6.9.
 2022-10-23 02:00:26 +02:00
Tobias Geerinckx-Rice
086b63b0a9
gnu: libgphoto2: Update to 2.5.30. 
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.30.
 2022-10-23 02:00:00 +02:00
Tobias Geerinckx-Rice
754a6ea6f2
gnu: rsync: Update to 3.2.7. 
* gnu/packages/rsync.scm (rsync): Update to 3.2.7.
 2022-10-23 02:00:00 +02:00
Nicolas Goaziou
adeecacde9
gnu: helm: Improve package style. 
* gnu/packages/music.scm (helm)[arguments]: Use G-expressions.  Remove trailing  #T from phases.
[inputs]: Remove labels.  Sort alphabetically.
[native-inputs]: Sort alphabetically.
 2022-10-29 23:52:15 +02:00
Sughosha via Guix-patches via
6db22e5262
gnu: helm: fix not finding Factory Presets 
* gnu/packages/music.scm (helm): Fix not finding Factory Presets.
  This change fixes hardcoded paths so that Factory Presets can be found.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-29 23:52:15 +02:00
Aleksandr Vityazev
d231651696
gnu: emacs-tmr: Update arguments and license. 
* gnu/packages/emacs-xyz.scm (emacs-trm): [arguments]:
Rename PATCH-FFPLAY phase to PATCH-PATHS and substitute
TMR-SOUND-FILE variable. Add MAKEINFO phase;
[inputs]: Add SOUND-THEME-FREEDESKTOP;
[license]: Add fdl1.3+;
[use-modules]: Add (gnu packages libcanberra).

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-29 23:52:15 +02:00
(
9ffeec668e
gnu: wesnoth: Update to 1.16.6. 
* gnu/packages/games.scm (wesnoth): Update to 1.16.6.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-10-29 23:52:14 +02:00
Tobias Geerinckx-Rice
34e6c5d428
gnu: rapidjson: Fix powerpc64le-linux build. 
…by avoiding ‘-march=native’, which is an unnecessary risk even if the
result is not installed.

* gnu/packages/web.scm (rapidjson)[arguments]: Replace the outdated
'patch-aarch-march-detection phase with an unconditional
'fix-march=native one.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
04ec2a15b9
gnu: dehydrated: ‘Build’ reproducibly. 
* gnu/packages/tls.scm (dehydrated)[arguments]: Invoke gzip with ‘-n’.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
4f5e87f751
gnu: dehydrated: Use G-expressions. 
* gnu/packages/tls.scm (dehydrated)[arguments]:
Rewrite as G-expressions.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
019be3f652
gnu: dehydrated: Update to 0.7.0-0.6fb8eba. 
* gnu/packages/tls.scm (dehydrated): Update to 0.7.0-0.6fb8eba.
[source]: Use GIT-FETCH & GIT-FILE-NAME.
[arguments]: Adjust accordingly.  Don't explicitly return #t from phases.
[native-inputs]: Remove tar.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
6e7102c5f7
gnu: pinentry-tty: Update to 1.2.1. 
* gnu/packages/gnupg.scm (pinentry-tty): Update to 1.2.1.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
69521e7adc
gnu: goffice: Update to 0.10.53. 
* gnu/packages/gnome.scm (goffice): Update to 0.10.53.
 2022-10-23 02:00:15 +02:00
Tobias Geerinckx-Rice
4674eb5718
gnu: memtest86+: Build reproducibly. 
* gnu/packages/hardware.scm (memtest86+)[source]: Add patch.
* gnu/packages/patches/memtest86+-build-reproducibly.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2022-10-23 02:00:15 +02:00
Guillaume Le Vaillant
1ea1fa96fe
gnu: Add ndppd. 
* gnu/packages/admin.scm (ndppd): New variable.
 2022-10-29 13:58:45 +02:00
Nicolas Goaziou
db3c80e8ab
gnu: emacs-nano-modeline: Update to 0.7.2. 
* gnu/packages/emacs-xyz.scm (emacs-nano-modeline): Update to 0.7.2.
 2022-10-29 10:46:21 +02:00
Christopher Baines
e4fcb6d1b3
gnu: guix-build-coordinator: Update to 0-68.3768aec. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-68.3768aec.
 2022-10-29 09:37:43 +01:00
Christopher Baines
067deee14f
gnu: bzip2: Fix script interpreters when cross-compiling. 
Add bash-minimal as an input fixes the interpreters for various scripts (like
bzdiff and bzgrep) when cross-compiling.

* gnu/packages/compression.scm (bzip2)[inputs]: Add bash-minimal when cross
compiling.
 2022-10-29 09:29:32 +01:00
Christopher Baines
a0c5f19dc6
gnu: xz: Fix script interpreters when cross-compiling. 
Add bash-minimal as an input fixes the interpreters for various scripts (like
xzgrep and xzless) when cross-compiling.

* gnu/packages/compression.scm (xz)[inputs]: Add bash-minimal when cross
compiling.
 2022-10-29 09:29:32 +01:00
Christopher Baines
01cfc22700
gnu: gzip: Fix script interpreters when cross-compiling. 
Add bash-minimal as an input fixes the interpreters for various scripts (like
zcat and zless) when cross-compiling.

* gnu/packages/compression.scm (gzip)[inputs]: Add bash-minimal when cross
compiling.
 2022-10-29 09:29:31 +01:00
Christopher Baines
42c8315316
gnu: gnome-control-center: Update to 42.4. 
* gnu/packages/gnome.scm (gnome-control-center): Update to 42.4.
 2022-10-29 09:28:11 +01:00
Danny Milosavljevic
0a604c16b3
gnu: Add seer-gdb. 
* gnu/packages/debug.scm (seer-gdb): New variable.
 2022-10-28 21:55:39 +02:00
Vagrant Cascadian
ed70f80ccd
gnu: texlive-latex-atveryend: Fix typo. 
* gnu/packages/tex.scm (texlive-latex-atveryend)[description]: Fix incorrectly
  pluralized use of "package".
 2022-10-28 11:51:00 -07:00
Ricardo Wurmus
b669735356
gnu: python-rpy2: Update to 3.5.5. 
* gnu/packages/statistics.scm (python-rpy2): Update to 3.5.5.
[arguments]: Run all tests; run them conditionally.
 2022-10-28 20:40:47 +02:00
Christopher Baines
7797570479
gnu: sed: Skip failing test on GNU/Hurd. 
* gnu/packages/base.scm (sed)[arguments]: Add #:make-flags.
 2022-10-28 15:16:54 +01:00
Christopher Baines
2a152e1a42
gnu: diffutils: Skip failing test on GNU/Hurd. 
* gnu/packages/base.scm (diffutils)[arguments]: Add #:make-flags.
* gnu/packages/commencement.scm (diffutils-boot0)[arguments]: Adjust to always
use substitute-keyword-arguments.
 2022-10-28 15:16:54 +01:00
Mădălin Ionel Patrașcu
fe20121dc7
gnu: Add r-damefinder. 
* gnu/packages/bioconductor.scm (r-damefinder): New variable.
 2022-10-28 15:11:29 +02:00
Mădălin Ionel Patrașcu
812cbd9321
gnu: Add r-dama. 
* gnu/packages/bioconductor.scm (r-dama): New variable.
 2022-10-28 15:08:58 +02:00
Ricardo Wurmus
77a81280b2
gnu: Add ghc-6.6. 
* gnu/packages/haskell.scm (ghc-6.6): New variable.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
171b729005
gnu: ghc-6.0: Adjust configuration. 
* gnu/packages/haskell.scm (ghc-6.0)[arguments]: Pass --enable-src-tree-happy
option; remove --with-hc option because we use the same GHC for everything;
add --with-gcc option to embed absolute file name of GCC.
[native-inputs]: Remove unused python-2.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
65ad002ff1
gnu: ghc-4: Embed absolute file name of GCC in GHC. 
* gnu/packages/haskell.scm (ghc-4)[arguments]: Pass "--with-gcc" option to
configure script.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
75b24abf09
gnu: flair: Update to 1.6.4. 
* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4.
[propagated-inputs]: Add python-numpy and python-scipy.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
bb4f24b3ae
gnu: flair: Set R_HOME. 
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
 2022-10-28 15:00:21 +02:00
Ricardo Wurmus
28950ed561
gnu: flair: Add missing R package. 
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
 2022-10-28 15:00:20 +02:00
Mădălin Ionel Patrașcu
917b96cef7
gnu: Add r-debcam. 
* gnu/packages/bioconductor.scm (r-debcam): New variable.
 2022-10-28 15:00:20 +02:00
Mădălin Ionel Patrașcu
0d713c865b
gnu: Add r-dmwr2. 
* gnu/packages/cran.scm (r-dmwr2): New variable.
 2022-10-28 15:00:16 +02:00
Nicolas Goaziou
7d92434326
gnu: emacs-modus-themes: Update to 3.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-modus-themes): Update to 3.0.0.
 2022-10-28 11:16:08 +02:00
Nicolas Goaziou
575790f5f5
gnu: emacs-ediprolog: Update to 2.2. 
* gnu/packages/emacs-xyz.scm (emacs-ediprolog): Update to 2.2.
 2022-10-28 11:16:07 +02:00
Nicolas Goaziou
a31c653cb1
gnu: emacs-subed: Update to 1.0.16. 
* gnu/packages/emacs-xyz.scm (emacs-subed): Update to 1.0.16.
 2022-10-28 11:16:07 +02:00
Nicolas Goaziou
8b204f4e94
gnu: emacs-mmm-mode: Update to 0.5.9. 
* gnu/packages/emacs-xyz.scm (emacs-mmm-mode): Update to 0.5.9.
 2022-10-28 11:16:07 +02:00
Nicolas Goaziou
5b86417d91
gnu: emacs-ement: Update to 0.4.1. 
* gnu/packages/emacs-xyz.scm (emacs-ement): Update to 0.4.1.
 2022-10-28 11:16:06 +02:00
Lars-Dominik Braun
652c5d8a01
gnu: r-mixedpower: Fix faulty commit. 
Fix previous commit, which did not contain the following changes:

* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (r-mixedpower)[source]: Use it.
 2022-10-28 10:17:55 +02:00
Jonathan Brielmaier
328fa8b290
gnu: icedove: Update to 102.4.1. 
* gnu/packages/gnuzilla.scm (%icedove-build-id, %icedove-version) Update to 102.4.1.
 2022-10-28 10:02:35 +02:00
Lars-Dominik Braun
332568d3e8
gnu: r-mixedpower: Improve compatibility with R>=4.2. 
Upstream’s fix is incomplete and thus commit
7871447cf5 was insufficient.

* gnu/packages/patches/r-mixedpower-r2power.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (r-mixedpower)[source]: Use it.
 2022-10-28 09:59:11 +02:00
Maxim Cournoyer
3511ad2857
gnu: rottlog: Apply patch adding a Texinfo direntry. 
Relates to <https://issues.guix.gnu.org/58821>.

* gnu/packages/patches/rottlog-direntry.patch: Add patch.
* gnu/packages/admin.scm (rottlog): Apply it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2022-10-27 23:34:46 -04:00
Maxim Cournoyer
ff097b450b
gnu: rottlog: Use gexps and bootstrap Autotools build system. 
* gnu/packages/admin.scm (rottlog) [snippet]: Delete build system files.
Delete trailing #t.  Patch Makefile.am instead of Makefile.in.  Do not patch
INSTALL_RC and INSTALL_SCRIPT variables default values.
[arguments]: Use gexps.  Delete trailing #t.
[make-flags]: Override INSTALL_RC and INSTALL_SCRIPT.
[phases]{fix-configure}: Delete phase.
[native-inputs]: Add autoconf.  Sort inputs.
 2022-10-27 23:34:46 -04:00
Leo Famulari
e04baf43ab
gnu: linux-libre: Update to 5.19.17. 
* gnu/packages/linux.scm (linux-libre-5.19-version): Update to 5.19.17.
(linux-libre-5.19-pristine-source): Update hash.
 2022-10-27 21:02:02 -04:00
Ludovic Courtès
d520fdec3c
gnu: findutils: Skip failing test on GNU/Hurd. 
* gnu/packages/base.scm (findutils)[arguments]: Add #:make-flags.
* gnu/packages/commencement.scm (findutils-boot0)[arguments]: Likewise.
 2022-10-28 01:27:22 +02:00
Ludovic Courtès
6c16eb24d1
gnu: grep: Skip failing tests on GNU/Hurd. 
* gnu/packages/base.scm (grep)[arguments]: Add #:make-flags.
 2022-10-28 01:27:22 +02:00
Ludovic Courtès
842b73fd2b
gnu: coreutils: Skip failing tests on GNU/Hurd. 
* gnu/packages/base.scm (coreutils)[arguments]: Add
"tests/df/unreadable.sh" and "test-perror2" to the 'XFAIL_TESTS' list.
 2022-10-28 01:27:21 +02:00
Vagrant Cascadian
ac51b9c86d
gnu: swftools: Fix typos. 
* gnu/packages/animation.scm (swftools)[description]: Avoid uses of "allows
  to".
 2022-10-27 14:13:17 -07:00
Marius Bakke
f8ce707252
gnu: pypy: Remove unused module imports. 
This is a follow-up to commit 6e7ed04033.

* gnu/packages/pypy.scm: Remove unused modules.
 2022-10-27 21:38:56 +02:00
Marius Bakke
e944734ef9
build-system/pyproject: Always run tests verbosely for supported backends. 
* guix/build-system/pyproject.scm (pyproject-build): Default to '() instead of
 #false for TEST-FLAGS.
* guix/build/pyproject-build-system.scm (check): Unconditionally enable
verbose test flags.
* doc/guix.texi (Build Systems): Document this change.
* gnu/packages/fontutils.scm (python-glyphslib)[arguments]: Remove verbosity
from #:test-flags.
* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]: Likewise.
* gnu/packages/python-web.scm (python-openapi-spec-validator)[arguments]: Likewise.
* gnu/packages/python-xyz.scm (python-path, python-tempora)[arguments]: Likewise.
 2022-10-27 21:30:03 +02:00
Marius Bakke
f928abac36
gnu: python-deepmerge: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-deepmerge)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:08 +02:00
Marius Bakke
7b83b3a77c
gnu: python-scikit-build: Switch to pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-scikit-build)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:08 +02:00
Marius Bakke
9ffbcb8a06
gnu: python-cattrs: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-cattrs)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke
d2e88c383b
gnu: python-path: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-path-bootstrap)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
(python-path): Remove #:phases.  Add #:test-flags.
 2022-10-27 19:43:08 +02:00
Marius Bakke
5e17453f18
gnu: python-openapi-spec-validator: Use pyproject-build-system. 
* gnu/packages/python-web.scm (python-openapi-spec-validator)[build-system]:
Set to PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke
3c685772de
gnu: python-openapi-schema-validator: Use pyproject-build-system. 
* gnu/packages/python-web.scm (python-openapi-schema-validator)[build-system]:
Set to PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke
7b499ef116
gnu: zabbix-cli: Switch to pyproject-build-system. 
* gnu/packages/monitoring.scm (zabbix-cli)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove check phase.
 2022-10-27 19:43:08 +02:00
Marius Bakke
e05e2a7a75
gnu: python-pygmsh: Use pyproject-build-system. 
* gnu/packages/simulation.scm (python-pygmsh)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
b8efe89eb4
gnu: python-tempora: Switch to pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-tempora)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
8bdc4c1547
gnu: python-mypy-protobuf: Switch to pyproject-build-system. 
* gnu/packages/protobuf.scm (python-mypy-protobuf)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
eecc807ea4
gnu: python-ufolib2: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-ufolib2)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:07 +02:00
Marius Bakke
10f8534929
gnu: python-statmake: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-statmake)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
6f6257a6bc
gnu: python-glyphslib: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-glyphslib)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:07 +02:00
Marius Bakke
df095a1813
gnu: weasyprint: Use pyproject-build-system. 
* gnu/packages/pdf.scm (weasyprint)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.  Add #:test-flags.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
4c8e0b3274
gnu: python-pydyf: Use pyproject-build-system. 
* gnu/packages/pdf.scm (python-pydyf)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove #:phases.  Add #:test-flags.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke
ee1f51011c
gnu: python-autopage: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-autopage)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
 2022-10-27 19:43:07 +02:00
Lars-Dominik Braun
400a7a4c80
build-system: Add pyproject-build-system. 
This is an experimental build system based on python-build-system
that implements PEP 517-compliant builds.

* doc/guix.texi (Build Systems): Add pyproject-build-system section.
* doc/contributing.texi (Python Modules): Mention pyproject.toml and the
PYTHON-TOOLCHAIN package, as well as differences to python-build-system.
* guix/build-system/pyproject.scm,
guix/build/pyproject-build-system.scm,
gnu/packages/aux-files/python/sanity-check-next.py,
gnu/packages/python-commencement.scm: New files.
* Makefile.am (MODULES): Register the new build systems.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add python-commencement.scm.
* gnu/packages/python.scm (python-sans-pip, python-sans-pip-wrapper): New
variables.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Marius Bakke
b4e2effb30
gnu: python-pip: Move to (gnu packages python-build). 
* gnu/packages/python-xyz.scm (python-pip): Move from here ...
* gnu/packages/python-build.scm (python-pip): ... to here.
 2022-10-27 19:43:06 +02:00
Lars-Dominik Braun
6e7ed04033
gnu: pypy: Move to separate module. 
This removes the need to import (gnu packages python-xyz) in (gnu packages
python), avoiding issues with circular imports.

* gnu/packages/python.scm (pypy): Move…
* gnu/packages/pypy.scm (pypy): …here
* gnu/local.mk: Register new file.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Lars-Dominik Braun
c485a9d8af
gnu: python-setuptools: Move to python-build. 
* gnu/packages/python-xyz.scm (python-setuptools): Move…
* gnu/packages/python-build.scm: …here.
* gnu/packages/chemistry.scm,
gnu/packages/messaging.scm,
gnu/packages/sequoia.scm,
tests/lint.scm: Adjust module imports accordingly.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Marius Bakke
cae327a3b0
gnu: Zabbix: Update to 6.0.9. 
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 6.0.9.
 2022-10-27 19:43:06 +02:00
Marius Bakke
593548f063
gnu: zabbix-agentd: Enable TLS support. 
* gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Pass "--with-gnutls"
in #:configure-flags.
[inputs]: Add GNUTLS.
(zabbix-server): Inherit these changes.
 2022-10-27 19:43:06 +02:00
Ricardo Wurmus
176a501360
gnu: flair: Add missing R packages. 
* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
 2022-10-27 18:21:22 +02:00
Nicolas Goaziou
302eae2fc3
gnu: emacs-buttercup: Update to 1.28. 
* gnu/packages/emacs-xyz.scm (emacs-buttercup): Update to 1.28.
 2022-10-27 17:37:40 +02:00
Mădălin Ionel Patrașcu
aef2425666
gnu: Add r-aseb. 
* gnu/packages/bioconductor.scm (r-aseb): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
695d7720ef
gnu: Add r-asgsca. 
* gnu/packages/bioconductor.scm (r-asgsca): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
b8b91756ab
gnu: Add r-aspli. 
* gnu/packages/bioconductor.scm (r-aspli): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
a8e0069f87
gnu: Add r-assessorf. 
* gnu/packages/bioconductor.scm (r-assessorf): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
f1750236c1
gnu: Add r-asset. 
* gnu/packages/bioconductor.scm (r-asset): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
c0278aa51e
gnu: Add r-atena. 
* gnu/packages/bioconductor.scm (r-atena): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
70d30096b3
gnu: Add r-atsnp. 
* gnu/packages/bioconductor.scm (r-atsnp): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
599655dc49
gnu: Add r-attract. 
* gnu/packages/bioconductor.scm (r-attract): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
3f755098cb
gnu: Add r-awfisher. 
* gnu/packages/bioconductor.scm (r-awfisher): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu
930b1e0458
gnu: Add r-awst. 
* gnu/packages/bioconductor.scm (r-awst): New variable.
 2022-10-27 16:40:18 +02:00
Marius Bakke
d9686315bd
gnu: ungoogled-chromium: Update to 107.0.5304.68-1. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for M107.
(%chromium-version): Set to 107.0.5304.68.
(%ungoogled-origin): Update hash.
(%chromium-gcc-patchset, gcc-patch): Remove.
(%gcc-patches): Empty list.
(ungoogled-chromium)[source]: Update hash.
[arguments]: Add clang_base_path and use_system_libwayland_server to
 #:configure-flags.  Adjust substitutions.
[inputs]: Add QTBASE-5.
 2022-10-27 16:15:09 +02:00
Mădălin Ionel Patrașcu
38cc09493c
gnu: Add r-barcodetrackr. 
* gnu/packages/bioconductor.scm (r-barcodetrackr): New variable.
 2022-10-27 15:58:45 +02:00
Mădălin Ionel Patrașcu
01944e0eb8
gnu: Add r-banocc. 
* gnu/packages/bioconductor.scm (r-banocc): New variable.
 2022-10-27 15:57:30 +02:00
Mădălin Ionel Patrașcu
fe2be9c0cf
gnu: Add r-bandits. 
* gnu/packages/bioconductor.scm (r-bandits): New variable.
 2022-10-27 15:56:40 +02:00
Mădălin Ionel Patrașcu
9b337c2735
gnu: Add r-bambu. 
* gnu/packages/bioconductor.scm (r-bambu): New variable.
 2022-10-27 15:51:55 +02:00
Mădălin Ionel Patrașcu
f0d0b6a0c5
gnu: Add r-badregionfinder. 
* gnu/packages/bioconductor.scm (r-badregionfinder): New variable.
 2022-10-27 15:50:33 +02:00
Mădălin Ionel Patrașcu
c969517cec
gnu: Add r-bader. 
* gnu/packages/bioconductor.scm (r-bader): New variable.
 2022-10-27 15:35:22 +02:00
Mădălin Ionel Patrașcu
0ad89a84c3
gnu: Add r-bac. 
* gnu/packages/bioconductor.scm (r-bac): New variable.
 2022-10-27 15:34:01 +02:00
Mădălin Ionel Patrașcu
f31b494bb6
gnu: Add r-basespacer. 
* gnu/packages/bioconductor.scm (r-basespacer): New variable.
 2022-10-27 15:30:25 +02:00
Mădălin Ionel Patrașcu
3417a28080
gnu: Add r-eulerr. 
* gnu/packages/cran.scm (r-eulerr): New variable.
 2022-10-27 15:28:22 +02:00
Mădălin Ionel Patrașcu
9f8ab16fb5
gnu: Add r-tximportdata. 
* gnu/packages/bioconductor.scm (r-tximportdata): New variable.
 2022-10-27 15:24:06 +02:00
Mădălin Ionel Patrașcu
f180a5990b
gnu: Add r-fishpond. 
* gnu/packages/bioconductor.scm (r-fishpond): New variable.
 2022-10-27 15:19:36 +02:00
Mădălin Ionel Patrașcu
fe7b421d05
gnu: Add python-multivelo. 
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
 2022-10-27 15:15:19 +02:00
Hong.Li@mdc-berlin.de
358a1fdf7b
gnu: Add r-seuratwrappers. 
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
 2022-10-27 15:03:21 +02:00
Ricardo Wurmus
87763421a9
gnu: r-seurat: Update to 4.2.0. 
* gnu/packages/cran.scm (r-seurat): Update to 4.2.0.
 2022-10-27 15:03:21 +02:00
Ricardo Wurmus
1cc12eace3
gnu: r-seuratobject: Update to 4.1.2. 
* gnu/packages/cran.scm (r-seuratobject): Update to 4.1.2.
 2022-10-27 15:03:21 +02:00
Mădălin Ionel Patrașcu
4b9fa56cad
gnu: Add r-baalchip. 
* gnu/packages/bioconductor.scm (r-baalchip): New variable.
 2022-10-27 13:54:18 +02:00
Mădălin Ionel Patrașcu
8e6a9b23d0
gnu: Add python-jupytext. 
* gnu/packages/python-xyz.scm (python-jupytext): New variable.
 2022-10-27 13:25:15 +02:00