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Author SHA1 Message Date
Ricardo Wurmus
78ff15ae42
gnu: r-biocpkgtools: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.14.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
9af834ad37
gnu: r-biocviews: Update to 1.64.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.64.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
8441c1f9ea
gnu: r-bioccheck: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.32.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
e30b2aeaa2
gnu: r-cytoml: Update to 2.8.1. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.8.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
10c006c21d
gnu: r-opencyto: Update to 2.8.4. 
* gnu/packages/bioconductor.scm (r-opencyto): Update to 2.8.4.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
bceed10243
gnu: r-flowstats: Update to 4.8.2. 
* gnu/packages/bioconductor.scm (r-flowstats): Update to 4.8.2.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
eed76ad91a
gnu: r-flowviz: Update to 1.60.2. 
* gnu/packages/bioconductor.scm (r-flowviz): Update to 1.60.2.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
f82d20caae
gnu: r-ggcyto: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
1c3750c9ea
gnu: r-ncdfflow: Update to 2.42.1. 
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.1.
 2022-10-03 19:08:08 +02:00
Ricardo Wurmus
23e42e77d4
gnu: r-rsubread: Update to 2.10.5. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.5.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
597106f234
gnu: r-rgadem: Update to 2.44.1. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
83f0c1a39d
gnu: r-enrichplot: Update to 1.16.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.2.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
842431a036
gnu: r-dose: Update to 3.22.1. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.22.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
2b4a7fa22e
gnu: r-residualmatrix: Update to 1.6.1. 
* gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
1cb30ba714
gnu: r-ggtree: Update to 3.4.4. 
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
a047448aad
gnu: r-treeio: Update to 1.20.2. 
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.2.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
41f029c12a
gnu: r-scaledmatrix: Update to 1.4.1. 
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.1.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
e581479be8
gnu: r-diffbind: Update to 3.6.4. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
309cfcedca
gnu: r-zellkonverter: Update to 1.6.5. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.5.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
039d894b9d
gnu: r-limma: Update to 3.52.4. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.4.
 2022-10-03 19:08:07 +02:00
Ricardo Wurmus
a16c87fae1
gnu: r-genomicfeatures: Update to 1.48.4. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.4.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
a15ad5ebe3
gnu: r-genomeinfodb: Update to 1.32.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.4.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
ba6a3e7d39
gnu: r-gage: Update to 2.46.1. 
* gnu/packages/bioconductor.scm (r-gage): Update to 2.46.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
c82320aa21
gnu: r-complexheatmap: Update to 2.12.1. 
* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
038eeeaf2a
gnu: r-chipseeker: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.1.
[propagated-inputs]: Add r-ggvenndiagram.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
15243c2f84
gnu: r-biostrings: Update to 2.64.1. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
29a947216c
gnu: r-annotationforge: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.1.
 2022-10-03 19:08:06 +02:00
Ricardo Wurmus
96b560ac8b
gnu: r-dearseq: Update to 1.8.4. 
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.4.
 2022-10-03 19:08:03 +02:00
Maxim Cournoyer
d573494387
doc: Mention sourcing system profile when chrooting. 
* doc/guix.texi (Chrooting into an existing system): Add sourcing of system
profile along user profile.
 2022-10-03 11:22:19 -04:00
Maxim Cournoyer
06201b76e5
gnu: Remove ocaml-craml. 
The package doesn't build from source and is unmaintained according to its
maintainer:
https://github.com/realworldocaml/craml/pull/8#issuecomment-529235628.

* gnu/packages/ocaml.scm (ocaml-craml): Delete variable.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
67e9513e40
gnu: r-spams: Update to 2.6.1. 
* gnu/packages/statistics.scm (r-spams): Update to 2.6.1.
[source]: Migrate from gforge.inria.fr to gitlab.inria.fr, fetching from git.
[phases]: Use gexps.
{patch-paths, mkdist}: New phases.
{no-mtune}: Delete trailing #t.
[native-inputs]: New field.
[home-page]: Update URL.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
1390e38264
gnu: ocaml-dose3: Migrate from gforce.inria.fr. 
* gnu/packages/ocaml.scm (ocaml-dose3) [source]: Fetch from git from inill's gitlab
instance.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
a93781b83c
gnu: Remove unused scotch patches. 
* gnu/packages/patches/scotch-build-parallelism.patch: Delete file.
* gnu/packages/patches/scotch-integer-declarations.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): De-register them.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
8ad1978695
gnu: mpfi: Update to 1.5.4-1.b982534. 
* gnu/packages/multiprecision.scm (mpfi): Update to 1.5.4-1.b982534.
[source]: Fetch from git and use latest commit available.
[tests?]: Delete argument, enabling test suite.
[phases]: New argument.
[native-inputs]: New field.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
a001be9664
gnu: mpfi: Use gexps and remove input labels. 
* gnu/packages/multiprecision.scm (mpfi) [source]: Re-indentation.
[configure-flags]: Use gexps.
[native-inputs]: Remove labels.
 2022-10-03 11:16:15 -04:00
Maxim Cournoyer
efb974a6fa
gnu: isl: Remove outdated comment. 
* gnu/packages/gcc.scm (isl) [source]: Remove outdated comment.
 2022-10-03 11:16:14 -04:00
Maxim Cournoyer
384b98028c
gnu: gappa: Honor TESTS?. 
* gnu/packages/algebra.scm (gappa) [phases] {check}: Honor TESTS?.
 2022-10-03 11:16:14 -04:00
Maxim Cournoyer
0f46559331
gnu: gappa: Update to 1.4.1. 
* gnu/packages/algebra.scm (gappa): Update to 1.4.1.
[source]: Fetch from git.
[arguments]: Use gexps.
[phases]: Delete trailing #t.
[native-inputs]: New field.
 2022-10-03 11:16:14 -04:00
Maxim Cournoyer
bcc61c08be
gnu: gmp-ecm: Update to 7.0.5. 
* gnu/packages/algebra.scm (gmp-ecm): Update to 7.0.5.
[source]: Fetch from git from gitlab.inria.fr.
[arguments]: Use gexps.
[phases] {patch-paths}: New phase
[native-inputs]: New field.
[home-page]: Update URL.
 2022-10-03 11:16:14 -04:00
Maxim Cournoyer
795f90ea4e
gnu: gf2x: Update to 1.3.0. 
* gnu/packages/algebra.scm (gf2x): Update to 1.3.0.
 2022-10-03 11:16:13 -04:00
Maxim Cournoyer
2b08945cbb
gnu: gf2x: Migrate from gforge.inria.fr to gitlab.inria.fr. 
* gnu/packages/algebra.scm (gf2x) [source]: Fetch from git, adjust URL.
[native-inputs]: Add autoconf, automake and libtool.
[home-site]: Update URL.
 2022-10-03 11:16:13 -04:00
Maxim Cournoyer
9945f9419d
gnu-maintenance: Remove retired 'gforge.inria.fr' site. 
* guix/gnu-maintenance.scm (html-updatable-package?): Remove "gforge.inria.fr".
 2022-10-03 11:16:13 -04:00
Thiago Jung Bauermann
aeaabc4253
news: Add 'pt' translation. 
* etc/news.scm: Add Portuguese translation of entry about the --with-source
option being recursive.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-10-03 16:23:16 +02:00
Thiago Jung Bauermann
ee8211a62c
etc: teams: Add news.scm to translations team scope. 
* etc/teams.scm.in (translations)[#:scope]: Add etc/news.scm.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2022-10-03 15:33:29 +02:00
Michael Rohleder
f64c80a538
gnu: emacs-ag: Do not propagate the-silver-searcher. 
* gnu/packages/emacs-xyz.scm (emacs-ag)[phases]: Add phase substitute-ag-path
to avoid propagating ag.
[inputs]: Add the-silver-searcher.
[propagated-inputs]: Remove the-silver-searcher.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-10-03 10:26:42 +03:00
Michael Rohleder
3fbe68d9fc
gnu: emacs-ag: Use gexps. 
* gnu/packages/emacs-xyz.scm (emacs-ag)[phases]: Use gexps.
{install-info}: Adjust for gexps.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-10-03 10:26:41 +03:00
Greg Hogan
582b1f626f
gnu: python-louvain: Fix test. 
* gnu/packages/graph.scm (python-louvain)[source]: Add patch.
* gnu/packages/patches/python-louvain-fix-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-10-02 23:22:07 +02:00
Greg Hogan
d1c3de6583
gnu: python-setools: Update to 4.4.0. 
* gnu/packages/selinux.scm (python-setools): Update to 4.4.0.
[source, home-page]: Update url.
[inputs]: Add python-pyqt.
[native-inputs]: Add python-cython.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-10-02 23:21:58 +02:00
Greg Hogan
35c92a6324
gnu: python-cfn-lint: Update to 0.65.0. 
* gnu/packages/python-web.scm (python-cfn-lint): Update to 0.65.0.
[arguments]<#:phases>: Add 'skip-network-test.
[propagated-inputs]: Add python-importlib-resources,
python-jschema-to-python, python-sarif-om.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-10-02 23:21:51 +02:00
Greg Hogan
56d8907c5f
gnu: Add python-sarif-om. 
* gnu/packages/python-web.scm (python-sarif-om): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-10-02 23:21:47 +02:00