83bd8d51c3
gnu: r-alpine: Update to 1.26.0.
...
* gnu/packages/bioconductor.scm (r-alpine): Update to 1.26.0.
2023-06-02 12:53:13 +02:00
f4639380ae
gnu: r-anvil: Update to 1.12.3.
...
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.3.
2023-06-02 12:53:13 +02:00
c2f0ce73a7
import/cran: string->license: Add another case for GPLv3+.
...
* guix/import/cran.scm (string->license): Translate "GPL (>=3)" to gpl3+.
2023-06-02 12:52:22 +02:00
4f7efc8db9
gnu: r-biocviews: Sort inputs.
...
* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them.
2023-06-02 12:51:15 +02:00
52546a4512
gnu: r-biocparallel: Sort inputs.
...
* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort
them.
2023-06-02 12:50:47 +02:00
cbbb619ddb
import/cran: Libraries should not use CRAN-GUIX-NAME.
...
* guix/import/cran.scm (source-dir->dependencies): Do not use CRAN-GUIX-NAME
when processing result of NEEDED-LIBRARIES-IN-DIRECTORY.
2023-06-02 12:49:25 +02:00
67183e25ad
import/cran: Also search Makevars file for libraries.
...
* guix/import/cran.scm (needed-libraries-in-directory): Look at Makevars in
addition to Makevars.in for libraries.
2023-06-02 12:48:42 +02:00
bb27e3b8b1
gnu: r-dismo: Replace bundled jars.
...
Fixes <https://issues.guix.gnu.org/63783 >.
* gnu/packages/cran.scm (r-dismo)[source]: Delete bundled jars.
[inputs]: Add java-maxent.
[native-inputs]: Add JDK and zip.
[arguments]: Add phases 'build-jars and 'strip-jar-timestamps.
2023-06-02 11:34:17 +02:00
341b4b2a97
gnu: Add java-maxent.
...
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
2023-06-02 11:34:17 +02:00
75bdd4b052
gnu: swaylock-effects: Update to 1.6.11.
...
* gnu/packages/wm.scm (swaylock-effects): Update to 1.6.11.
2023-06-02 10:47:06 +04:00
f9af75b2c3
gnu: xdg-desktop-portal-wlr: Update to 0.7.0.
...
* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Update to 0.7.0.
[inputs]: Add mesa.
2023-06-02 08:59:08 +04:00
69c3aa561d
gnu: xdg-desktop-portal-gtk: Update to 1.14.1.
...
* gnu/packages/freedesktop.scm (xdg-desktop-portal-gtk): Update to 1.14.1.
2023-06-02 08:59:08 +04:00
51c8e86350
gnu: xdg-desktop-portal: Update to 1.16.0.
...
* gnu/packages/freedesktop.scm (xdg-desktop-portal): Update to 1.16.0.
2023-06-02 08:59:08 +04:00
a9c8e8fd38
gnu: libportal: Update to 0.6.
...
* gnu/packages/freedesktop.scm (libportal): Update to 0.6.
[arguments]: Remove deprecated backends option from #:configure-flags. Add
set-qt-environment-variables phase.
2023-06-02 08:59:07 +04:00
195c91b793
gnu: gopls: Update to 0.12.0.
...
* gnu/packages/golang.scm (gopls): Update to 0.12.0.
2023-06-01 23:00:44 -05:00
9dacecb111
gnu: Update waybar to 0.9.18.
...
* gnu/packages/wm.scm (waybar): Update to 0.9.18.
2023-06-01 22:59:38 -05:00
ab4347a1ad
gnu: python-fire: Update to 0.5.0.
...
* gnu/packages/python-xyz.scm (python-fire): Update to 0.5.0.
[inputs]: Remove python-six and python-termcolor.
[propagated-inputs]: Add python-six and python-termcolor.
2023-06-01 22:59:38 -05:00
b4382b294e
gnu: Add python-colored.
...
* gnu/packages/python-xyz.scm (python-colored): New variable.
2023-06-01 20:48:17 +02:00
eb2918aa96
gnu: Add python-plotext.
...
* gnu/packages/python-xyz.scm (python-plotext): New variable.
2023-06-01 20:48:17 +02:00
d411b7d5e7
gnu: Add python-pyani.
...
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
2023-06-01 20:48:17 +02:00
525ef60ff4
gnu: Add python-illumina-utils.
...
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
2023-06-01 20:48:17 +02:00
cf388642ce
gnu: libtommath: Honor the #:tests? flag.
...
* gnu/packages/multiprecision.scm (libtommath)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
2023-06-01 15:52:37 +03:00
b428b49d8f
gnu: libtommath: Prevent possible integer overflow.
...
* gnu/packages/multiprecision.scm (libtommath)[source]: Add patch.
* gnu/packages/patches/libtommath-integer-overflow.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2023-06-01 15:52:37 +03:00
7c52ae295b
gnu: bear: Update to 3.1.2.
...
* gnu/packages/build-tools.scm (bear): Update to 3.1.2.
2023-06-01 15:24:23 +03:00
ced6e0fe94
gnu: Add python-ete3.
...
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
2023-06-01 14:10:04 +02:00
e6705f994f
gnu: parallel: Update to 20230522.
...
* gnu/packages/parallel.scm (parallel): Update to 20230522.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:55:09 +03:00
9511488941
gnu: zenity: Update to 3.44.1.
...
* gnu/packages/gnome.scm (zenity): Update to 3.44.1.
[native-inputs]: Add gtk+:bin.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:44:58 +03:00
21388dce63
gnu: iperf: Update to 3.13.
...
* gnu/packages/networking.scm (iperf): Update to 3.13.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:42:43 +03:00
3ab95b2753
gnu: iotop: Update to 1.23.
...
* gnu/packages/linux.scm (iotop): Update to 1.23.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:41:37 +03:00
fd76ffb974
gnu: html-xml-utils: Update to 8.6.
...
* gnu/packages/xml.scm (html-xml-utils): Update to 8.6.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:39:58 +03:00
e6fb7f6467
gnu: hstr: Update to 3.1.
...
* gnu/packages/shellutils.scm (hstr): Update to 3.1.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:38:13 +03:00
dc61b7fcf7
gnu: glances: Update to 3.4.0.3.
...
* gnu/packages/python-xyz.scm (glances): Update to 3.4.0.3.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:36:35 +03:00
f7d5722d36
gnu: fish: Update to 3.6.1.
...
* gnu/packages/shells.scm (fish): Update to 3.6.1.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:18:31 +03:00
247ac4b73f
gnu: fio: Update to 3.35.
...
* gnu/packages/benchmark.scm (fio): Update to 3.35.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:15:01 +03:00
dc6afa69eb
gnu: atop: Update to 2.9.0.
...
* gnu/packages/admin.scm (atop): Update to 2.9.0.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01 12:13:08 +03:00
4abf0af4b1
gnu: openblas: Update make-flags comments and coding style.
...
* gnu/packages/maths.scm (openblas)[arguments]: In the make-flags use
the target-* macros. Adjust the wording describing why the different
architectures have the flags they do.
2023-06-01 11:14:03 +03:00
076688fa1e
gnu: openblas: Update architectures we provide substitutes for.
...
* gnu/packages/maths.scm (openblas)[arguments]: Adjust the substitutable?
flag to only not provide substitutes when building for powerpc-linux.
Adjust the comment accordingly.
2023-06-01 11:14:03 +03:00
872e1434f1
gnu: openblas-ilp64: Add powerpc64le-linux as a supported system.
...
* gnu/packages/maths.scm (openblas-ilp64)[supported-systems]: Add
powerpc64le-linux.
2023-06-01 11:14:03 +03:00
93804e978f
gnu: r-mbecs: Fix indentation.
...
* gnu/packages/bioconductor.scm (r-mbecs)[arguments]: Adjust indentation and
spelling of comment.
2023-06-01 09:21:57 +02:00
d019053aca
gnu: Add squashfuse.
...
* gnu/packages/file-systems.scm (squashfuse): New variable.
2023-06-01 09:15:26 +02:00
10d3f8aa7b
gnu: Add r-mbecs.
...
* gnu/packages/bioconductor.scm (r-mbecs): New variable.
2023-06-01 09:15:26 +02:00
13e2138c23
gnu: Remove linux-libre 6.2.
...
This kernel series is no longer supported upstream.
* gnu/packages/linux.scm (linux-libre-6.2-version, linux-libre-6.2-gnu-revision,
deblob-scripts-6.2, linux-libre-6.2-pristine-source, linux-libre-6.2-source,
linux-libre-headers-6.2, linux-libre-6.2): Remove variables.
* gnu/packages/aux-files/linux-libre/6.2-arm.conf,
gnu/packages/aux-files/linux-libre/6.2-arm64.conf,
gnu/packages/aux-files/linux-libre/6.2-i686.conf,
gnu/packages/aux-files/linux-libre/6.2-x86_64.conf: Delete files.
* Makefile.am (AUX_FILES): Remove them.
2023-05-31 21:21:25 -04:00
35bdf804cb
gnu: linux-libre 4.14: Update to 4.14.316.
...
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.316.
(linux-libre-4.14-pristine-source): Update hash.
2023-05-31 21:21:25 -04:00
c428ed520d
gnu: linux-libre 4.19: Update to 4.19.284.
...
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.284.
(linux-libre-4.19-pristine-source): Update hash.
2023-05-31 21:21:24 -04:00
1bd5d06736
gnu: linux-libre 5.4: Update to 5.4.244.
...
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.244.
(linux-libre-5.4-pristine-source): Update hash.
2023-05-31 21:21:24 -04:00
a939d7cfee
gnu: linux-libre 5.10: Update to 5.10.181.
...
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.181.
(linux-libre-5.10-pristine-source): Update hash.
2023-05-31 21:21:24 -04:00
9ab028e70e
gnu: linux-libre 5.15: Update to 5.15.114.
...
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.114.
(linux-libre-5.15-pristine-source): Update hash.
2023-05-31 21:21:23 -04:00
876486476a
gnu: linux-libre 6.1: Update to 6.1.31.
...
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.31.
(linux-libre-6.1-pristine-source): Update hash.
2023-05-31 21:21:23 -04:00
7576eff1bf
gnu: linux-libre: Update to 6.3.5.
...
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.5.
(linux-libre-6.3-pristine-source): Update hash.
2023-05-31 21:21:12 -04:00
654fcf9971
tests: Use quasiquoted 'match' patterns for package sexps.
...
Turns out it's easier to read.
* tests/cpan.scm ("cpan->guix-package"): Use a quasiquoted pattern.
* tests/elpa.scm (eval-test-with-elpa): Likewise.
* tests/gem.scm ("gem->guix-package")
("gem->guix-package with a specific version")
("gem-recursive-import")
("gem-recursive-import with a specific version"): Likewise.
* tests/hexpm.scm ("hexpm-recursive-import"): Likewise.
* tests/opam.scm ("opam->guix-package"): Likewise.
* tests/pypi.scm ("pypi->guix-package, no wheel")
("pypi->guix-package, wheels")
("pypi->guix-package, no usable requirement file.")
("pypi->guix-package, package name contains \"-\" followed by digits"):
Likewise.
* tests/texlive.scm ("texlive->guix-package"): Likewise.
2023-05-31 23:50:06 +02:00
Ricardo Wurmus
Andrew Tropin
Katherine Cox-Buday
jgart
Efraim Flashner
Andy Tai
Greg Hogan
Mădălin Ionel Patrașcu
Leo Famulari
Ludovic Courtès