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Author SHA1 Message Date
Tobias Geerinckx-Rice
1bd85824c7
gnu: ispell: Update to 3.4.03. 
* gnu/packages/aspell.scm (ispell): Update to 3.4.03.
 2021-06-02 15:40:03 +02:00
Ricardo Wurmus
011d586c2c
gnu: Add biobambam2. 
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
 2021-06-02 13:54:15 +02:00
Ricardo Wurmus
18e0081045
gnu: Add libmaus2. 
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
 2021-06-02 13:54:15 +02:00
Ricardo Wurmus
f01215635a
gnu: r-with-tests: Update to 4.1.0. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.1.0.
 2021-06-02 13:54:15 +02:00
Tobias Geerinckx-Rice
6fee3239b3
gnu: memtester: Update to 4.5.1. 
* gnu/packages/hardware.scm (memtester): Update to 4.5.1.
 2021-06-02 12:53:10 +02:00
Tobias Geerinckx-Rice
fa26ca54f9
gnu: osip: Update to 5.2.1. 
* gnu/packages/telephony.scm (osip): Update to 5.2.1.
 2021-06-02 12:53:10 +02:00
Tobias Geerinckx-Rice
6c0a09b341
gnu: retroarch: Update to 1.9.4. 
* gnu/packages/emulators.scm (retroarch): Update to 1.9.4.
 2021-06-02 12:53:09 +02:00
Tobias Geerinckx-Rice
57278dc214
gnu: libavif: Update to 0.9.1. 
* gnu/packages/image.scm (libavif): Update to 0.9.1.
 2021-06-02 12:53:09 +02:00
Paul Garlick
da340369ac
gnu: python-vedo: Make pkg-config a native input. 
* gnu/packages/python-science.scm (python-vedo)[inputs]: Move pkg-config to...
[native-inputs]: ...here.
 2021-06-02 10:27:59 +01:00
Mark H Weaver
873c6b4f21
gnu: icecat: Update to 78.11.0-guix0-preview1 [fixes CVE-2021-29967]. 
* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update upstream source hash.
 2021-06-02 04:28:52 -04:00
Xinglu Chen
49e40006f6
gnu: python-hg-evolve: Update to 10.3.1. 
* gnu/packages/version-control.scm (python-hg-evolve): Update to 10.3.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-02 10:36:12 +03:00
Vinicius Monego
51e8539566
gnu: python-sphinx-gallery: Update to 0.9.0. 
* gnu/packages/sphinx.scm (python-sphinx-gallery): Update to 0.9.0.
[source]: Build from PyPI.
[arguments]: Enable tests. Add custom 'check phase and phase to make
test files writable.
[native-inputs]: Add python-joblib, python-matplotlib, python-numpy,
python-pillow, python-pytest, python-pytest-cov, python-sphinx. Remove
python-pytest-runner.
[home-page]: Follow redirect.
(python2-sphinx-gallery): Remove package.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-02 10:22:01 +03:00
Simon Streit
841edfa491
gnu: redis: Update to 6.2.4 [security fixes]. 
Fixes CVE-2021-29477.

* gnu/packages/databases.scm (redis): Update to 6.2.4.
[arguments]: Disable the 'integration/failover' test.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-06-02 00:54:39 -04:00
Julien Lepiller
b94bc3ea30
gnu: Add frama-c. 
* gnu/packages/maths.scm (frama-c): New variable.
 2021-06-02 03:10:12 +02:00
Julien Lepiller
c9b3627d56
gnu: Add why3. 
* gnu/packages/maths.scm (why3): New variable.
 2021-06-02 03:10:04 +02:00
Zhu Zihao
2df1c4f134
gnu: rtl8821ce-linux-module: Update to 0.0.0-3.897e7c4. 
Fix the broken build with linux-libre 5.12.

* gnu/packages/linux.scm (rtl8821ce-linux-module): Update to 0.0.0-3.897e7c4.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-01 23:26:08 +02:00
Ludovic Courtès
2885c3568e
machine: ssh: Gracefully handle failure of the effectful bits. 
Previously, '&inferior-exception' raised by 'upgrade-shepherd-services'
and co. would go through as-is, leaving users with an ugly backtrace.

* gnu/machine/ssh.scm (deploy-managed-host): Define
'eval/error-handling' and use it in lieu of EVAL as arguments to
'switch-to-system', 'upgrade-shepherd-services', and
'install-bootloader'.
 2021-06-01 23:26:07 +02:00
Ludovic Courtès
0db906c52c
services: cuirass: Do not export record type descriptors. 
* gnu/services/cuirass.scm (<cuirass-remote-server-configuration>)
(<cuirass-configuration>, <cuirass-remote-worker-configuration>): Do not
export.
 2021-06-01 23:26:07 +02:00
Ludovic Courtès
ec9307ea07
services: cuirass: Create the profile and GC root directory. 
* gnu/services/cuirass.scm (cuirass-activation): Create
/var/guix/profiles/per-user/cuirass/cuirass or similar.
 2021-06-01 23:26:07 +02:00
Ludovic Courtès
82d8ab01f5
maint: Require Guile 3.0. 
* configure.ac: Require Guile 3.0.
* doc/guix.texi (Requirements): Adjust accordingly.
* gnu/packages/package-management.scm (guile2.2-guix): Remove.
* guix/lint.scm (exception-with-kind-and-args?): Remove 'cond-expand'.
* guix/scripts/deploy.scm (deploy-machine*): Likewise.
* guix/store.scm (call-with-store): Likewise.
* guix/swh.scm (http-get*, http-post*): Likewise.
* guix/ui.scm (without-compiler-optimizations, guard*)
(call-with-error-handling): Likewise.
 2021-06-01 23:26:07 +02:00
Efraim Flashner
49b15701ad
gnu: llvm-7: Update to 7.1.0. 
* gnu/packages/llvm.scm (llvm-7): Update to 7.1.0.
 2021-06-01 22:50:47 +03:00
Marius Bakke
8d14d602ea
gnu: unbound: Enable DoH support. 
* gnu/packages/dns.scm (unbound)[inputs]: Add NGHTTP2:LIB.
[arguments]: Add "--with-libnghttp2" to #:configure-flags.
 2021-06-01 20:21:54 +02:00
Marius Bakke
304895d5e0
gnu: ungoogled-chromium: Update to 91.0.4472.77-0.6802c88. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 91.
(%chromium-version): Set to 91.0.4472.77.
(%ungoogled-revision): Set to 91.0.4472.77-1-0-g6802c88.
(%debian-patches): Remove obsolete patch.
(%ungoogled-origin): Update hash.
(ungoogled-chromium-snippet): Add substitution for an unbundling file.
(ungoogled-chromium): Update hash.
[arguments]: Add a substitution previously provided by a Debian patch.
[inputs]: Change from ICU-68 to ICU-69.
 2021-06-01 20:21:54 +02:00
Marius Bakke
e54c03c1f5
gnu: icu4c: Add 69.1. 
* gnu/packages/icu4c.scm (icu4c-69): New public variable.
 2021-06-01 20:21:54 +02:00
Efraim Flashner
9ea6e3f4d8
gnu: gcc-9: Update to 9.4.0. 
* gnu/packages/gcc.scm (gcc-9): Update to 9.4.0.
 2021-06-01 20:54:06 +03:00
Leo Prikler
cb821238ed
gnu: musescore: Add missing QML imports. 
This fixes an issue wherein the palettes sidebar would turn up empty.

* gnu/packages/music.scm (musescore)[build-system]: Use qt-build-systems.
[inputs]: Add qtgraphicaleffects.
 2021-06-01 18:52:48 +02:00
Jonathan Brielmaier
776a21a096
gnu: rust-cbindgen@0.17: Update to 0.19.0. 
* gnu/packages/rust-apps.scm (rust-cbindgen-0.17): Update to 0.19.0 and
rename to rust-cbindgen-0.19.
 2021-06-01 17:59:34 +02:00
Mathieu Othacehe
0b76b25a0e
tests: hpcguix-web: Fix it. 
* gnu/tests/web.scm (run-hpcguix-web-server-test): Increase the VM memory size
and add retries for the http-get test.
 2021-06-01 14:33:27 +02:00
Roel Janssen
7ae2b1f2dc
gnu: Add bamutils. 
* gnu/packages/bioinformatics.scm (bamutils): New variable.
 2021-06-01 13:14:38 +02:00
Pierre Neidhardt
b4e3b77270
gnu: sbcl: Update to 2.1.5. 
* gnu/packages/lisp.scm (sbcl): Update to 2.1.5.
 2021-06-01 12:01:24 +02:00
Paul Garlick
641a88e8c8
gnu: Add python-vedo. 
* gnu/packages/python-science.scm (python-vedo): New variable.
 2021-06-01 10:24:46 +01:00
Paul Garlick
d769fcd683
gnu: vtk: Wrap python modules. 
* gnu/packages/image-processing.scm (vtk)[inputs]: Add python.
[arguments]: Add VTK_WRAP_PYTHON and VTK_PYTHON_VERSION flags.
 2021-06-01 10:19:48 +01:00
Mathieu Othacehe
fd0650eebe
gnu: guix: Update to 1.3.0-3.50dfbbf. 
* gnu/packages/package-management.scm (guix): Update to 1.3.0-3.50dfbbf.
 2021-06-01 11:03:45 +02:00
Roel Janssen
50dfbbf8ef
gnu: Add python-sinfo. 
* gnu/packages/python-xyz.scm (python-sinfo): New variable.
 2021-06-01 10:18:00 +02:00
Roel Janssen
b346a7c7db
gnu: Add python-stdlib-list. 
* gnu/packages/python-xyz.scm (python-stdlib-list): New variable.
 2021-06-01 10:13:38 +02:00
Christopher Baines
a6a1939251
gnu: guix-build-coordinator: Update to 0-30.f9af463. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-30.f9af463.
 2021-06-01 09:01:58 +01:00
Brice Waegeneire
ea55e1355b
services: dnsmasq: Extend 'activation-service'. 
* gnu/services/dns.scm (dnsmasq-activation): New procedure …
(dnsmasq-service-type): … use it.
 2021-05-31 22:06:54 +02:00
Brice Waegeneire
62a8d487d6
services: hostapd: Use package from configuration. 
* gnu/services/networking.scm (hostapd-shepherd-services): Replace
'hostapd' by the package specified in the configuration.
 2021-05-31 22:04:57 +02:00
Brice Waegeneire
8a0dc5f1bf
tests: Fix loadable-kernel-modules-service tests. 
* gnu/tests/linux-modules.scm
(run-loadable-kernel-modules-service-test): Actually load the modules
with kernel-module-loader-service-type.  Use a singleton service instead
of defining a custom one.
* doc/guix.texi (Service Reference): To give an example of
linux-loadable-module-service-type use a singleton instead of defining a
new service.
 2021-05-31 21:57:26 +02:00
Nicolas Goaziou
eb8928eeba
gnu: emacs-tramp: Update to 2.5.0.5. 
* gnu/packages/emacs-xyz.scm (emacs-tramp): Update to 2.5.0.5.
 2021-05-31 21:37:53 +02:00
Nicolas Goaziou
93744e470b
gnu: emacs-solaire-mode: Update to 2.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-solaire-mode): Update to 2.0.0.
 2021-05-31 21:37:15 +02:00
Nicolas Goaziou
4e74d25d85
gnu: texmacs: Update to 1.99.21. 
* gnu/packages/text-editors.scm (texmacs): Update to 1.99.21.
 2021-05-31 21:35:53 +02:00
Nicolas Goaziou
5af640b6d7
gnu: emacs-moody: Update to 0.5.5. 
* gnu/packages/emacs-xyz.scm (emacs-moody): Update to 0.5.5.
 2021-05-31 21:25:28 +02:00
Nicolas Goaziou
6cdc1c72f1
gnu: emacs-posframe: Update to 1.0.3. 
* gnu/packages/emacs-xyz.scm (emacs-posframe): Update to 1.0.3.
 2021-05-31 21:24:15 +02:00
Solene Rapenne via Guix-patches via
4092813037
gnu: lagrange: Update to 1.5.0. 
* gnu/packages/web-browsers.scm (lagrange): Update to 1.5.0.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-05-31 21:06:36 +02:00
Stefan Reichör
d16ddafcc7
gnu: Add emacs-eyebrowse. 
* gnu/packages/emacs-xyz.scm (emacs-eyebrowse): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-05-31 21:05:57 +02:00
Stefan Reichör
71854b7dfe
gnu: Add python-easy-ansi. 
* gnu/packages/python-xyz.scm (python-easy-ansi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-05-31 21:05:03 +02:00
Xinglu Chen
dafd3265ad
gnu: Add emacs-evil-paredit. 
* gnu/packages/emacs-xyz.scm (emacs-evil-paredit): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-05-31 21:03:09 +02:00
Solene Rapenne via Guix-patches via
f7825ee85a
gnu: tome4: Update to 1.7.3. 
* gnu/packages/games.scm (tome4): Update to 1.7.3.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-05-31 20:59:29 +02:00
Ricardo Wurmus
f463f376e9
gnu: bits: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:10:20 +02:00
Ricardo Wurmus
d1e1c02e28
gnu: piranha: Use git-version. 
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
 2021-05-31 16:10:00 +02:00
Ricardo Wurmus
8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:35 +02:00
Ricardo Wurmus
3acfbd4811
gnu: f-seq: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:07 +02:00
Ricardo Wurmus
09b50a6ec2
gnu: bismark: Use git-file-name. 
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
 2021-05-31 16:08:47 +02:00
Ricardo Wurmus
f383f9e311
gnu: filevercmp: Use git-version. 
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
 2021-05-31 16:08:12 +02:00
Ricardo Wurmus
ec543ba672
gnu: r-chipseeker: Move out of experiment section. 
* gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the
"experiment" section to the section for regular Bioconductor packages.
 2021-05-31 15:54:41 +02:00
Ricardo Wurmus
a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
 2021-05-31 15:53:20 +02:00
Ricardo Wurmus
1a6108ce2b
gnu: r-geneoverlap: Move out of experiment section. 
* gnu/packages/bioconductor.scm (r-geneoverlap): Move the package definition
out of the "experiment" section into the section for regular Bioconductor
packages.
 2021-05-31 15:53:09 +02:00
Ricardo Wurmus
b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 15:46:30 +02:00
zimoun
c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun
7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun
36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:39:47 +02:00
zimoun
31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun
45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun
043c309d15
gnu: r-rhtslib: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun
e0c81584ea
gnu: r-zlibbioc: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
 2021-05-31 15:38:58 +02:00
zimoun
0006a66415
gnu: r-seqlogo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
 2021-05-31 15:38:21 +02:00
zimoun
c2a18aee16
gnu: r-motifrg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun
621aa3b442
gnu: r-sva: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun
900ef8fb1e
gnu: r-protgenerics: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun
720d2694a5
gnu: r-mzr: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun
88cf24febb
gnu: r-ensembldb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
fea33b9d1e
gnu: r-biovizbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
8d4311bb8e
gnu: r-vsn: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
96ae9822c4
gnu: r-affyio: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
8182e6a6fd
gnu: r-organismdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
d1ea2b7c8b
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
0b5b41c561
gnu: r-genomicfiles: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
ff65fa90d2
gnu: r-complexheatmap: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
84019edf38
gnu: r-gage: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun
d0a5503752
gnu: r-keggrest: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
22cda2e432
gnu: r-affy: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
32ae36e96f
gnu: r-fastseg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
9644745692
gnu: r-annotationhub: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
dfe6224f5f
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
f6f43a2d40
gnu: r-edaseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
ef954bb488
gnu: r-deseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
bb118f20fe
gnu: r-aroma-light: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
7756e08b44
gnu: r-mzid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun
ad46c8aa7f
gnu: r-pcamethods: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
 2021-05-31 15:37:57 +02:00
zimoun
d7fa9c1ffd
gnu: r-genomationdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:37:55 +02:00
zimoun
f8fe5497c7
gnu: r-genomation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
 2021-05-31 15:36:32 +02:00
zimoun
f3b50aa4fd
gnu: r-go-db: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
 2021-05-31 15:35:53 +02:00
zimoun
14fb30e5f6
gnu: r-seqpattern: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
 2021-05-31 15:35:30 +02:00
zimoun
b832fddbfc
gnu: r-impute: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun
a2a1d86a77
gnu: r-samr: Move to (gnu packages bioconductor). 
* gnu/packages/cran.scm (r-samr): Move from here...
* gnu/packages/bioconductor.scm (r-samr): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun
4f030cc0db
gnu: r-msnbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
8c7c78bfce
gnu: r-msnid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
537d48d869
gnu: r-bsgenome: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
 2021-05-31 15:34:39 +02:00
Efraim Flashner
d2d1f8bfae
gnu: Add julia-prettytables. 
* gnu/packages/julia-xyz.scm (julia-prettytables): New variable.
 2021-05-31 12:54:49 +03:00
Efraim Flashner
9bb2e649a6
gnu: Add julia-formatting. 
* gnu/packages/julia-xyz.scm (julia-formatting): New variable.
 2021-05-31 12:54:49 +03:00
Efraim Flashner
adedfd0773
gnu: Add julia-typedtables. 
* gnu/packages/julia-xyz.scm (julia-typedtables): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
f34f8a3d22
gnu: Add julia-weakrefstrings. 
* gnu/packages/julia-xyz.scm (julia-weakrefstrings): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
9f92c8b51f
gnu: Add julia-pooledarrays. 
* gnu/packages/julia-xyz.scm (julia-pooledarrays): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
4541cda7d7
gnu: Add julia-indirectarrays. 
* gnu/packages/julia-xyz.scm (julia-indirectarrays): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
a33695945c
gnu: Add julia-rangearrays. 
* gnu/packages/julia-xyz.scm (julia-rangearrays): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
2262f79917
gnu: Add julia-graphics. 
* gnu/packages/julia-xyz.scm (julia-graphics): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
ea03851b01
gnu: Add julia-mappedarrays. 
* gnu/packages/julia-xyz.scm (julia-mappedarrays): New variable.
 2021-05-31 12:54:48 +03:00
Efraim Flashner
6a2d36c734
gnu: Add julia-tensorcore. 
* gnu/packages/julia-xyz.scm (julia-tensorcore): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
277fef2026
gnu: Add julia-quadmath. 
* gnu/packages/julia-xyz.scm (julia-quadmath): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
f273a4b799
gnu: Add julia-mocking. 
* gnu/packages/julia-xyz.scm (julia-mocking): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
73b6f78c98
gnu: Add julia-exprtools. 
* gnu/packages/julia-xyz.scm (julia-exprtools): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
2615a8bad5
gnu: Add julia-optimtestproblems. 
* gnu/packages/julia-xyz.scm (julia-optimtestproblems): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
fa945a540c
gnu: Add julia-matrixfactorizations. 
* gnu/packages/julia-xyz.scm (julia-matrixfactorizations): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
6dd2634da4
gnu: Add julia-arraylayouts. 
* gnu/packages/julia-xyz.scm (julia-arraylayouts): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
f7f1efeaa7
gnu: Add julia-statsapi. 
* gnu/packages/julia-xyz.scm (julia-statsapi): New variable.
 2021-05-31 12:54:47 +03:00
Efraim Flashner
2bd2406cd9
gnu: Add julia-tables. 
* gnu/packages/julia-xyz.scm (julia-tables): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
db2bfcb90d
gnu: Add julia-missings. 
* gnu/packages/julia-xyz.scm (julia-missings): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
209a80c109
gnu: Add julia-queryoperators. 
* gnu/packages/julia-xyz.scm (julia-queryoperators): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
a61e13f777
gnu: Add julia-tableshowutils. 
* gnu/packages/julia-xyz.scm (julia-tableshowutils): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
e886181bb6
gnu: Add julia-datavalues. 
* gnu/packages/julia-xyz.scm (julia-datavalues): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
3f40ba72c6
gnu: Add julia-tabletraits. 
* gnu/packages/julia-xyz.scm (julia-tabletraits): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
43f26eaeaa
gnu: Add julia-iteratorinterfaceextensions. 
* gnu/packages/julia-xyz.scm (julia-iteratorinterfaceextensions): New variable.
 2021-05-31 12:54:46 +03:00
Efraim Flashner
21df298ec9
gnu: Add julia-datavalueinterfaces. 
* gnu/packages/julia-xyz.scm (julia-datavalueinterfaces): New variable.
 2021-05-31 12:54:45 +03:00
Efraim Flashner
ccbf9c450e
gnu: Add julia-dataapi. 
* gnu/packages/julia-xyz.scm (julia-dataapi): New variable.
 2021-05-31 12:54:45 +03:00
Hartmut Goebel
c85edf2ca4
gnu: java-pep-adapter 2.1.23. 
* gnu/packages/pep.scm (java-pep-adapter): Update to 2.1.23.
  [source]: Switch to new git repo.
  [arguments]<make-flags>: Enable release-build, use new target names.
  [arguments]<phases>{fix-includes}: Remove phase.
  {pin-shared-lib-path}: Update file paths.
  {build-codegen}: New phase.
  {install}: Use "(install)".
  [native-inputs]: Add graphviz.
  [inputs]: Fix input util-linux.
 2021-05-31 10:45:54 +02:00
Hartmut Goebel
140087faa5
gnu: python-pep-adapter: Update to 2.1.3. 
* gnu/packages/pep.scm (python-pep-adapter): Update to 2.1.3.
  [source]: Switch to new git repo.
  [arguments]<phases>{remove-wheel-requirement}: New phase.
  [native-inputs]: Add python-pytest and python-pytest-forked.
  [inputs]: Remove asn1c, add python-setuptools-scm. util-linux.
 2021-05-31 10:45:53 +02:00
Hartmut Goebel
c178f859b5
gnu: libpEpAdapter: Update to 2.1.21. 
* gnu/packages/pep.scm (libpEpAdapter): Update to 2.1.21.
  [source]: Swicht to new git repo.
  [arguments]<make-flags>: Enable release-build.
 2021-05-31 10:45:53 +02:00
Hartmut Goebel
85d80283b6
gnu: pep-engine: Update to 2.1.34. 
* gnu/packages/pep.scm (fdik-libetpan): Update to current development
  version. [source]: Switch to pep.foundation.
  (pep-engine): Update to 2.1.34. [source]: Switch to new git repo.
  [arguments]<make-flags>: Enable release-build.
  [inputs]: Use normal sequoia.
* gnu/packages/sequoia.scm (sequoia4pEp): Remove variable.
 2021-05-31 10:45:53 +02:00
Hartmut Goebel
c7f023723c
gnu: yml2: Update to 2.7.0. 
* gnu/packages/pep.scm (yml2): Update to 2.7.0.
  [source]: Switch to new git repo.
 2021-05-31 10:45:53 +02:00
Roel Janssen
47f31c0afe
gnu: Add python-pyflow. 
* gnu/packages/python-science.scm (python-pyflow): New variable.
 2021-05-31 09:30:51 +02:00
Roel Janssen
ad7c7b5bf6
gnu: Add python-google. 
* gnu/packages/python-web.scm (python-google): New variable.
 2021-05-31 09:21:45 +02:00
Efraim Flashner
221141ca70
gnu: gnuastro: Update to 0.15. 
* gnu/packages/astronomy.scm (gnuastro): Update to 0.15.
 2021-05-31 09:44:47 +03:00
Tobias Geerinckx-Rice
6086e6ed1a
gnu: r-benchmarkmedata: Fix typo in description. 
* gnu/packages/cran.scm (r-benchmarkmedata)[description]: Fix typo.
 2021-05-30 15:13:41 +02:00
Tobias Geerinckx-Rice
836f5fc4c5
gnu: zoxide: Fix typo in synopsis. 
* gnu/packages/rust-apps.scm (zoxide)[synopsis]: Fix typo.
 2021-05-30 15:13:40 +02:00
Tobias Geerinckx-Rice
d342d06630
gnu: julia-plotutils: Fix typo in description. 
* gnu/packages/julia-xyz.scm (julia-plotutils)[description]: Fix typo.
 2021-05-30 15:13:40 +02:00
Tobias Geerinckx-Rice
bf2a361643
gnu: cryptsetup: Rewrite synopsis & description. 
* gnu/packages/cryptsetup.scm (cryptsetup)[synopsis, description]:
Be more explicit about stuff.
 2021-05-30 15:13:40 +02:00
Tobias Geerinckx-Rice
e9cbb97ac8
gnu: cryptsetup: Update to 2.3.6. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 2.3.6.
 2021-05-30 15:13:40 +02:00
Tobias Geerinckx-Rice
32a44fb581
gnu: vapoursynth: Update to 53. 
* gnu/packages/video.scm (vapoursynth): Update to 53.
 2021-05-30 15:13:40 +02:00
Ricardo Wurmus
17ace33aa6
gnu: axoloti-runtime: Patch firmware Makefile. 
* gnu/packages/axoloti.scm (axoloti-runtime)[arguments]: Patch out whitespace
substitution.
 2021-05-30 14:51:04 +02:00