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Author SHA1 Message Date
Ricardo Wurmus
52546a4512
gnu: r-biocparallel: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort
them.
 2023-06-02 12:50:47 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
341b4b2a97
gnu: Add java-maxent. 
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
 2023-06-02 11:34:17 +02:00
Andrew Tropin
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
Andrew Tropin
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
Andrew Tropin
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
Andrew Tropin
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
Andrew Tropin
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
Katherine Cox-Buday
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
jgart
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
jgart
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
Ricardo Wurmus
b4382b294e
gnu: Add python-colored. 
* gnu/packages/python-xyz.scm (python-colored): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus
eb2918aa96
gnu: Add python-plotext. 
* gnu/packages/python-xyz.scm (python-plotext): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus
d411b7d5e7
gnu: Add python-pyani. 
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus
525ef60ff4
gnu: Add python-illumina-utils. 
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
 2023-06-01 20:48:17 +02:00
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
ced6e0fe94
gnu: Add python-ete3. 
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
 2023-06-01 14:10:04 +02:00
Andy Tai
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Greg Hogan
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
Ricardo Wurmus
d019053aca
gnu: Add squashfuse. 
* gnu/packages/file-systems.scm (squashfuse): New variable.
 2023-06-01 09:15:26 +02:00
Mădălin Ionel Patrașcu
10d3f8aa7b
gnu: Add r-mbecs. 
* gnu/packages/bioconductor.scm (r-mbecs): New variable.
 2023-06-01 09:15:26 +02:00
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Leo Famulari
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
Ludovic Courtès
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
Ludovic Courtès
9f7cd1fcaf
gnu: Add updater input properties for R and Python packages. 
* gnu/packages/cran.scm (r-glue, r-xfun, r-vctrs)
(r-lifecycle): Turn comment about r-knitr into 'properties' field.
* gnu/packages/mpi.scm (python-mpi4py)[properties]: New field.
 2023-05-31 23:26:12 +02:00
Ludovic Courtès
57ceb64e34
upstream: Honor package properties for ignored and extra inputs. 
* guix/upstream.scm (update-package-inputs)[filtered-inputs]
[regular-inputs, native-inputs, propagated-inputs]: New procedures.
Use them in 'update-field' calls.
* tests/guix-refresh.sh (GUIX_TEST_UPDATER_TARGETS): Add "libreoffice"
to the dependencies of "the-test-package".  Add 'updater-ignored-inputs'
property to "the-test-package".
* doc/guix.texi (Invoking guix refresh): Document it.
 2023-05-31 23:25:26 +02:00
Ludovic Courtès
9e237fe0bd
import: gem: Updater provides input list. 
* guix/import/gem.scm (import-release): Add 'inputs' field.
* tests/gem.scm ("package-latest-release"): New test.
 2023-05-31 23:25:26 +02:00
Ludovic Courtès
e6f82fcd5f
import: gem: Factorize "bundler" special case for name mapping. 
* guix/import/gem.scm (ruby-package-name): Add "bundler" special case.
(gem->guix-package): Adjust accordingly.
* tests/gem.scm ("gem-recursive-import")
("gem-recursive-import with a specific version"): Remove "ruby-bundler"
from the expected packages.
 2023-05-31 23:25:26 +02:00