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Author SHA1 Message Date
Ricardo Wurmus 01911fa0a4
gnu: r-rbowtie2: Update to 2.4.2. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.4.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus ab6909adf0
gnu: r-motifbreakr: Update to 2.12.3. 
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.12.3.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus e952be7fb2
gnu: r-clusterexperiment: Update to 2.18.2. 
* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 7f7e39b89b
gnu: r-clusterprofiler: Update to 4.6.2. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.6.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 0e1edb67ae
gnu: r-sigpathway: Update to 1.66.2. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus f8c823274d
gnu: r-linnorm: Update to 2.22.2. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 969e7f1c4f
gnu: r-glmgampoi: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.10.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 590897d28f
gnu: r-diffbind: Update to 3.8.4. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.4.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus af9bcbe90f
gnu: r-scmap: Update to 1.20.2. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 8c8930691c
gnu: r-mutationalpatterns: Update to 3.8.1. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.8.1.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 364d9b7c17
gnu: r-muscat: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-muscat): Update to 1.12.1.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 586d2bb696
gnu: r-limma: Update to 3.54.2. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.54.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 810a8e5060
gnu: r-lfa: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 20b1ef8047
gnu: r-genomicalignments: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.34.1.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus 7f9346c031
gnu: r-annotationdbi: Update to 1.60.2. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.60.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus b9af764895
gnu: r-infercnv: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-infercnv): Update to 1.14.2.
 2023-03-15 17:40:42 +01:00
Ricardo Wurmus b28eff5aec
gnu: r-bandits: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.14.2.
 2023-03-15 17:40:41 +01:00
Ricardo Wurmus eeece329e8
gnu: r-bambu: Update to 3.0.8. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.0.8.
 2023-03-15 17:40:41 +01:00
Ricardo Wurmus fee92975a2
gnu: r-atena: Update to 1.4.1. 
* gnu/packages/bioconductor.scm (r-atena): Update to 1.4.1.
[propagated-inputs]: Add r-matrixstats.
 2023-03-15 17:40:41 +01:00
Ricardo Wurmus 9df1de70e1
gnu: r-alpsnmr: Update to 4.0.4. 
* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.0.4.
[propagated-inputs]: Add r-cli.
 2023-03-15 17:40:41 +01:00
Ricardo Wurmus accebcfce5
gnu: r-biocpkgtools: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.16.1.
[source]: Add snippet to remove bundled minified JavaScript files.
[native-inputs]: Add esbuild, js-bootstrap, js-d3, js-jquery, and
js-underscore.
[arguments]: Add build phase 'process-javascript.
 2023-03-15 17:40:41 +01:00
Ricardo Wurmus db17611dc9
gnu: r-mast: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-mast): Update to 1.24.1.
[source]: Delete minified JavaScript.
[arguments]: Add build phase 'process-javascript.
[native-inputs]: Add esbuild and js-jquery-sticky-kit.
 2023-03-15 17:40:38 +01:00
Pierre Neidhardt cacd7b6768
gnu: sbcl-nclasses: Update to 0.3.0. 
* gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.3.0.
 2023-03-15 17:33:16 +01:00
jgart 8a47949463
gnu: Add sbcl-stumpwm-hostname. 
* gnu/packages/wm.scm (sbcl-stumpwm-hostname): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-03-15 15:49:20 +01:00
jgart 2c58713241
gnu: sbcl-mcclim: Update project urls. 
* gnu/packages/lisp-xyz.scm (sbcl-mcclim)[source]: Update source url.
[home-page]: Update project home page.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2023-03-15 15:46:13 +01:00
Vagrant Cascadian a4f6a8a2cf
gnu: reprotest: Update to 0.7.23. 
* gnu/packages/diffoscope.scm (reprotest): Update to 0.7.23.
  [phases] Update adjust-locales.
 2023-03-15 15:39:14 +01:00
Vagrant Cascadian 84ce4459f1
gnu: diffoscope: Update to 238. 
* gnu/packages/diffoscope.scm (diffoscope): Update to 238.
  [native-inputs]: Switch from poppler to poppler-next.
 2023-03-15 15:39:10 +01:00
Andrew Tropin 201251b1ff
gnu: emacs-org-modern: Update to 0.9. 
* gnu/packages/emacs-xyz.scm (emacs-org-modern): Update to 0.9.
 2023-03-15 12:22:03 +04:00
Ricardo Wurmus d37b467631
gnu: r-rhandsontable: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-rhandsontable): Move this variable from
here...
* gnu/packages/cran.scm (r-rhandsontable): ...to here.
 2023-03-14 17:58:28 +01:00
Navid Afkhami 204c51cac4
gnu: Add r-premessa. 
* gnu/packages/bioinformatics.scm (r-premessa): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-03-14 17:58:28 +01:00
Mark H Weaver 4ebc36206b
gnu: icecat: Update to 102.9.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2023-25751, CVE-2023-25752, CVE-2023-28162,
CVE-2023-28163, CVE-2023-28164, and CVE-2023-28176.

* gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2023-03-14 12:51:20 -04:00
Ricardo Wurmus 27c8ab4bf3
gnu: Add r-rhandsontable. 
* gnu/packages/bioinformatics.scm (r-rhandsontable): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2023-03-14 17:48:14 +01:00
Navid Afkhami 633c935e0a
gnu: r-tidyverse: Update to 2.0.0. 
* gnu/packages/cran.scm (r-tidyverse): Update to 2.0.0.
[propagated-inputs]: Remove r-crayon; add r-conflicted and r-ragg.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus 8fb1edcceb
gnu: pcb-rnd: Update to 3.1.0. 
* gnu/packages/engineering.scm (pcb-rnd): Update to 3.1.0.
[inputs]: Add librnd.
[arguments]: Use gexp; set LIBRND_PREFIX.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus eacd68aa44
gnu: Add librnd. 
* gnu/packages/engineering.scm (librnd): New variable.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus 42bb34e21a
gnu: pcb: Remove eudev. 
* gnu/packages/engineering.scm (pcb)[inputs]: Remove eudev as it is no longer
necessary to add it for mesa.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus e7dc5681a6
gnu: pcb: Drop input labels. 
* gnu/packages/engineering.scm (pcb)[inputs, native-inputs]: Remove package
labels.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus c2ff0e2d13
gnu: pcb: Update to 4.3.0. 
* gnu/packages/engineering.scm (pcb): Update to 4.3.0.
[arguments]: Remove obsolete build phases.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus 6822730c8d
gnu: pcb: Use gexp. 
* gnu/packages/engineering.scm (pcb)[arguments]: Use gexp and drop trailing #T
from build phases.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus c20e80b102
gnu: lepton-eda: Adjust format. 
* gnu/packages/engineering.scm (lepton-eda): Move arguments above inputs, and
reformat source field.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus 753fb6a54d
gnu: lepton-eda: Use gexp for arguments. 
* gnu/packages/engineering.scm (lepton-eda)[arguments]: Use gexp.
 2023-03-14 14:15:33 +01:00
Ricardo Wurmus 1c5ef6bd3c
gnu: lepton-eda: Drop input labels. 
* gnu/packages/engineering.scm (lepton-eda)[native-inputs, inputs]: Do not use
redundant package labels.
 2023-03-14 14:15:33 +01:00
Christopher Baines a6009e0bf8
gnu: guix-build-coordinator: Update to 0-73.7c1eedf. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-73.7c1eedf.
 2023-03-14 10:36:32 +00:00
Yovan Naumovski 476e1b270e
gnu: mruby: Update to 3.2.0. 
* gnu/packages/ruby.scm (mruby): Update to 3.2.0.
[arguments]: Remove unnecessary substitutions in the 'disable-broken-tests
phase.
[description]: Update.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:32 +00:00
Bruno Victal 056f743718
gnu: autokey: Update to 0.96.0. 
* gnu/packages/python-xyz.scm (autokey): Update to 0.96.0.
[source]: Patch tests.
[arguments]: Enable tests. Prefer PATH over substitute* in phase 'fix-paths.
Add phase 'setup-env-vars. Rename 'wrap-autokey-gi to 'wrap-autokey and set PATH.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest, python-pytest-cov and python-pyhamcrest.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:32 +00:00
kiasoc5 3a3231322a
gnu: tesseract-ocr: Update to 5.3.0. 
* gnu/packages/ocr.scm (tesseract-ocr): Update to 5.3.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:32 +00:00
kiasoc5 17a5d2019a
gnu: gimagereader: Update to 3.4.1. 
* gnu/packages/ocr.scm (gimagereader): Update to 3.4.1.
[inputs]: Remove quazip-0; add quazip.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:31 +00:00
Hilton Chain 8065e7fff3
gnu: phantomsocks: Update to 0.0.0-20230223180716-34d21f24a9eb. 
* gnu/packages/networking.scm (phantomsocks): Update to
0.0.0-20230223180716-34d21f24a9eb.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:31 +00:00
Bruno Victal cf59f6bb3b
gnu: rng-tools: Update to 6.16. 
* gnu/packages/linux.scm (rng-tools): Update to 6.16.
[arguments]: Disable qrypt.
[inputs]: Add libcap.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:31 +00:00
Bruno Victal cf111a37f3
gnu: rng-tools: Do not build randstat binary. 
This trivial binary is rarely useful.

* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/patches/rng-tools-revert-build-randstat.patch: New file.
* gnu/packages/linux.scm (rng-tools)[origin]: Add patch.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-03-14 10:36:31 +00:00