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Author SHA1 Message Date
Ricardo Wurmus bf9cd9521a
gnu: r-htscluster: Update to 2.0.11. 
* gnu/packages/bioconductor.scm (r-htscluster): Update to 2.0.11.
 2023-09-14 00:04:05 +02:00
Ricardo Wurmus 8f59ac151f
gnu: r-abn: Update to 3.0.0. 
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.0.
[propagated-inputs]: Add r-mclogit and r-stringi.
 2023-09-13 23:14:38 +02:00
Ricardo Wurmus 4676f07f6d
gnu: r-glmnetutils: Update to 1.1.9. 
* gnu/packages/cran.scm (r-glmnetutils): Update to 1.1.9.
 2023-09-13 23:02:37 +02:00
Ricardo Wurmus b3b369f990
gnu: r-hmisc: Update to 5.1-1. 
* gnu/packages/statistics.scm (r-hmisc): Update to 5.1-1.
 2023-09-13 22:58:18 +02:00
Ricardo Wurmus ab1f8495f9
gnu: r-rstan: Update to 2.26.23. 
* gnu/packages/cran.scm (r-rstan): Update to 2.26.23.
[native-inputs]: Remove pandoc.
[propagated-inputs]: Add r-quickjsr.
 2023-09-13 22:57:03 +02:00
Ricardo Wurmus 455dadc41a
gnu: r-iheatmapr: Update to 0.7.0. 
* gnu/packages/cran.scm (r-iheatmapr): Update to 0.7.0.
[source]: Delete minified plotly JavaScript.
[native-inputs]: Add esbuild and js-plotly.
[arguments]: Add phase to minify plotly.js.
 2023-09-13 22:51:14 +02:00
Ricardo Wurmus f2d690c6c5
gnu: r-leaflet: Update to 2.2.0. 
* gnu/packages/cran.scm (r-leaflet): Update to 2.2.0.
[source]: Do not delete jquery.min.js, because it is no longer included.
[arguments]: Adjust minification accordingly.
[native-inputs]: Remove js-jquery.
[propagated-inputs]: Remove r-base64enc and r-markdown; add r-jquerylib and
r-xfun.
 2023-09-13 22:41:25 +02:00
Ricardo Wurmus 9049506d8b
gnu: python-hicmatrix: Remove custom 'check phase. 
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom
'check phase.
 2023-09-13 22:19:23 +02:00
Ricardo Wurmus bf98283741
gnu: r-radiant-data: Update to 1.6.1. 
* gnu/packages/cran.scm (r-radiant-data): Update to 1.6.1.
[propagated-inputs]: Add r-arrow.
 2023-09-13 22:18:27 +02:00
Ricardo Wurmus 080d088016
gnu: r-arrow: Update to 13.0.0. 
* gnu/packages/cran.scm (r-arrow): Update to 13.0.0.
 2023-09-13 22:18:27 +02:00
Ricardo Wurmus 6739c534f8
gnu: apache-arrow: Update to 13.0.0. 
* gnu/packages/databases.scm (apache-arrow): Update to 13.0.0.
 2023-09-13 22:18:27 +02:00
Ricardo Wurmus aaaaa2ea07
gnu: r-minqa: Update to 1.2.6. 
* gnu/packages/statistics.scm (r-minqa): Update to 1.2.6.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
 2023-09-13 22:18:27 +02:00
Ricardo Wurmus 4e8ec5a16b
gnu: r-dt: Update to 0.29. 
* gnu/packages/statistics.scm (r-dt): Update to 0.29.
[propagated-inputs]: Add r-httpuv.
 2023-09-13 22:18:27 +02:00
Mădălin Ionel Patrașcu 2c1d86e2e0
gnu: python-hicmatrix: Remove syntax error in setup.py. 
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase
remove-invalid-syntax.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-09-13 22:17:21 +02:00
Ricardo Wurmus dc172966ba
gnu: Add r-quickjsr. 
* gnu/packages/cran.scm (r-quickjsr): New variable.
 2023-09-13 22:17:21 +02:00
Ricardo Wurmus b6441f7bd0
upstream: Compare symbols to symbols. 
The UNCHANGED? comparison would always yield #FALSE, because we have been
comparing lists of strings with lists of symbols.

* guix/upstream.scm (update-package-inputs): Convert string labels to symbols
before comparison.
 2023-09-13 22:17:21 +02:00
Andy Tai 67268d9a81
gnu: octave-cli: Update to 8.3.0 
* gnu/packages/maths.scm (octave-cli): Update to 8.3.0

Signed-off-by: Eric Bavier <bavier@posteo.net>
 2023-09-13 09:22:28 -05:00
Andre A. Gomes 4f933f977d
gnu: nyxt: Update to 3.7.0. 
* gnu/packages/web-browsers.scm (nyxt): Update to 3.7.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-09-13 13:38:18 +02:00
Andre A. Gomes 828b08d585
gnu: cl-nasdf: Update to 0.1.8. 
* gnu/packages/lisp-xyz.scm (sbcl-nasdf): Update to 0.1.8.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-09-13 13:37:15 +02:00
Artyom Bologov 3007f77596
gnu: cl-njson: Update to 1.2.0. 
* gnu/packages/lisp-xyz.scm (sbcl-njson): Update to 1.2.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-09-13 13:32:42 +02:00
Navid Afkhami cda20190bc
gnu: Add r-interactivedisplay. 
* gnu/packages/bioconductor.scm (r-interactivedisplay): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-09-13 12:10:06 +02:00
Andreas Enge 6a01c1142b
gnu: hdf4, hdf4-alt: Update to 4.2.16-2. 
* gnu/packages/maths.scm (hdf4)[source]: Update to 4.2.16-2. Drop patches
that do not apply any more.
[arguments]: Drop configure flag related to libtirpc. Add configure flag
to build xdr library and drop unneeded substitutions.
* gnu/packages/patches/hdf4-architectures.patch,
gnu/packages/patches/hdf4-tirpc.patch: Remove files.
* gnu/local.mk (dist_patch_DATA): Unregister patches.
 2023-09-13 11:18:42 +02:00
Munyoki Kilyungi c30c9df5e9
gnu: yoyo-migrations: Update to 8.2.0. 
* gnu/packages/databases.scm (yoyo-migrations): Update to 8.2.0.
[propagated-inputs]: Add python-importlib-metadata.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:21 +01:00
Zheng Junjie 79988ab742
gnu: libvterm: Update arguments style. 
* gnu/packages/terminals.scm (libvterm)[arguments]: Update arguments style.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:20 +01:00
Zheng Junjie 8d5304b143
gnu: libvterm: Update to 0.3.3. 
* gnu/packages/terminals.scm (libvterm): Update to 0.3.3.
[source]: Use launchpad.net url.
[arguments]: Use CC-FOR-TARGET.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:20 +01:00
Hendursaga 901eaca92b
gnu: tennix: Update to 1.3.4. 
* gnu/packages/games.scm (tennix): Update to 1.3.4.
[arguments]<#:phases>: Update style and remove fix-include phase.
[inputs]: Remove labels, update to SDL2, add SDL2_gfx dependency.
[license]: Remove LGPL license, as SDL_rotozoom is no longer included.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:20 +01:00
Sharlatan Hellseher 7f150a1895
gnu: python-qtsass: Update to 0.4.0. 
This also fixes test failures preventing the package from building.

* gnu/packages/python-xyz.scm (python-qtsass): Update to 0.4.0, fix build.
[native-inputs]: Add python-flaky.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:20 +01:00
Sharlatan Hellseher de2ee9cae6
gnu: python-libsass: Update to 0.22.0. 
* gnu/packages/python-xyz.scm (python-libsass): Update to 0.22.0.
[phases]: Add new phase 'silent-failing-tests and disable 2 failing
tests to complete build.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:20 +01:00
Valter Nazianzeno 10bc07671e
gnu: emilua: Update to 0.4.3. 
* gnu/packages/lua.scm (emilua): Update to 0.4.3.
[source]: Remove recursive? and replace with inputs.
[arguments]: Update style, add patch phase, enable tests and enable some more
features.
[native-inputs]: Add gperf, gawk and xdd.
[inputs]: Add emilua-http and trial-protocol as origin is no longer recursive,
also add serd, sord, libcap and liburing.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-13 09:22:14 +01:00
Ricardo Wurmus 07d43c66d5
gnu: Add swineherd. 
* gnu/packages/admin.scm (swineherd): New variable.
 2023-09-12 23:30:58 +02:00
Maxim Cournoyer 4cb2e08b8e
gnu: python-django-4.0: Use $TZDIR. 
* gnu/packages/django.scm (python-django-4.0) [native-search-paths]: Use
$TZDIR.
 2023-09-12 10:05:00 -04:00
Maxim Cournoyer f0e05411bd
search-paths: Add $TZDIR. 
* guix/search-paths.scm ($TZDIR): New search path.
 2023-09-12 10:03:44 -04:00
Maxim Cournoyer 076b3384df
gnu: qemu: Reinstate the iothreads-commit-active test. 
* gnu/packages/virtualization.scm (qemu) [arguments]: Add set-SOCK_DIR phase.
(qemu-minimal) [arguments]: Delete the disable-extra-tests phase.
 2023-09-12 09:59:47 -04:00
Ricardo Wurmus 9996896dc2
gnu: Add python-peaks2utr. 
* gnu/packages/bioinformatics.scm (python-peaks2utr): New variable.
 2023-09-12 12:28:32 +02:00
Ricardo Wurmus 30ec6f2fb5
gnu: macs: Update to 2.2.9.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Move python-cython from here...
[inputs]: ...and python-numpy from here...
[propagated-inputs]: ...to here.
 2023-09-12 12:28:32 +02:00
宋文武 e2a7c227de
gnu: xfce4-terminal: Update to 1.1.0. 
* gnu/packages/xfce.scm (xfce4-terminal): Update to 1.1.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:39:21 +01:00
Artyom V. Poptsov cdddc6bc28
gnu: guile-png: Update to 0.7.1 
* gnu/packages/guile-xyz.scm (guile-png): Update to 0.7.1.
[arguments]: Update style and delete "strip" phase.
[description]: Update.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:36:29 +01:00
Hilton Chain 8294f45dfc
gnu: python-cgatcore: Update to 0.6.15. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:31:23 +01:00
Hilton Chain d6ad06cd6c
gnu: python-apsw: Update to 3.42.0.1. 
* gnu/packages/databases.scm (python-apsw): Update to 3.42.0.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:30:10 +01:00
Hilton Chain 8d51e31f86
gnu: sqlite-next: Update to 3.42.0. 
* gnu/packages/sqlite.scm (sqlite-next): Update to 3.42.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:30:08 +01:00
Andy Tai 3acd355455
gnu: svt-av1: Update to 1.7.0. 
* gnu/packages/video.scm (svt-av1): Update to 1.7.0.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:25:09 +01:00
Christopher Baines 93cb2880d6
gnu: nar-herder: Use guile-next. 
As this provides suspendable soft/custom ports, which I'd like to use.

* gnu/packages/package-management.scm (nar-herder)[native-inputs,inputs]: Use
guile-next.
 2023-09-12 08:15:07 +01:00
Christopher Baines 53f510dad6
gnu: skalibs: Remove i586-gnu from %supported-systems. 
* gnu/packages/skarnet.scm (skalibs)[supported-systems]: Remove i586-gnu.
 2023-09-12 08:03:49 +01:00
Christopher Baines 0e08ad7f19
gnu: linux-libre-headers: Remove i586-gnu from supported-systems. 
As I don't think attempting to build for the Hurd is useful.

* gnu/packages/heads.scm (make-linux-libre-headers*): Remove i586-gnu from
supported-systems.
 2023-09-12 08:03:49 +01:00
Christopher Baines 288799d3e8
gnu: musl-cross: Remove i586-gnu from supported-systems. 
As I don't think musl supports the Hurd.

* gnu/packages/heads.scm (musl-cross)[supported-systems]: Remove i586-gnu.
 2023-09-12 08:03:49 +01:00
Maxim Cournoyer daeeaa2216
gnu: emacs-magit: Update to 3.3.0-6.7a1d503. 
* gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.3.0-6.7a1d503.
 2023-09-11 23:48:19 -04:00
Maxim Cournoyer 2a7f031ca9
gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. 
This reinstate commit a5b5df7f7f with a fix to
the inner expand-uri procedure.
 2023-09-11 23:39:13 -04:00
Maxim Cournoyer a9d5d1d9dd
Revert "gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs." 
This reverts commit a5b5df7f7f.  Pushed too
early.
 2023-09-11 23:30:43 -04:00
Maxim Cournoyer a5b5df7f7f
gnu-maintenance: Support URI list of mixed mirrors, HTTP URLs. 
Fixes <https://issues.guix.gnu.org/58697>.

* guix/gnu-maintenance.scm (import-html-updatable-release): Update doc.
<expand-uri>: New nested procedure.  Apply it to the origin URI.

Reported-by: kiasoc5 <kiasoc5@disroot.org>
 2023-09-11 22:53:38 -04:00
Cayetano Santos 5ff9afb5fd
gnu: emacs-mastodon: Update to 1.0.0-1.20dec88. 
* gnu/packages/emacs-xyz.scm (emacs-mastodon): Update to 1.0.0-1.20dec88.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-09-11 23:54:50 +02:00