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116161 Commits (53bf9fba0c9542a46702bb30251f5796da371e64)

Author SHA1 Message Date
Ricardo Wurmus 302b916b2b
gnu: r-basilisk-utils: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 6d54b5cc23
gnu: r-megadepth: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.10.0.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 0beada7cb0
gnu: r-s4arrays: Update to 1.0.4. 
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.4.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus f06bd3e740
gnu: r-biocviews: Update to 1.68.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.68.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 438d2b80f7
gnu: r-rsubread: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.14.2.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 08e1e36942
gnu: r-treeio: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.24.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 93350d89a2
gnu: r-apeglm: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.22.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus e6faedd0c9
gnu: r-zellkonverter: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.10.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 071c31583b
gnu: r-scmap: Update to 1.22.3. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 2a35673351
gnu: r-limma: Update to 3.56.1. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 21342c3bcf
gnu: r-edger: Update to 3.42.4. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.4.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 15ffd4014e
gnu: r-biostrings: Update to 2.68.1. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.68.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 9e9e21dc46
gnu: r-biocparallel: Update to 1.34.2. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 6693480b46
gnu: r-densvis: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 3b20a9e600
gnu: r-delayedarray: Update to 0.26.3. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus f947aa3ac9
gnu: r-dearseq: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus ca0c012d4a
gnu: r-bambu: Update to 3.2.3. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 4f7efc8db9
gnu: r-biocviews: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them.
 2023-06-02 12:51:15 +02:00
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