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Author SHA1 Message Date
Efraim Flashner
d6a5bdf000
gnu: igraph: Update to 0.9.8. 
* gnu/packages/graph.scm (igraph): Update to 0.9.8.
 2022-04-14 22:57:06 +03:00
Efraim Flashner
7034746e15
gnu: scregseg: Remove cythonized file. 
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
 2022-04-14 22:55:33 +03:00
Paul A. Patience
5059e7f01e
gnu: cl-py4cl: Update to 0.0.0-1.2f2a008. 
* gnu/packages/lisp-xyz.scm (sbcl-py4cl): Update to 0.0.0-1.2f2a008.
  [arguments]<#:phases>: Adjust substitutions to renamed files.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-14 20:31:59 +02:00
jgart
8f5b2f0693
gnu: Add emacs-org-modern. 
* gnu/packages/emacs-xyz.scm (emacs-org-modern): New variable.

Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
 2022-04-14 11:34:03 -04:00
Paul A. Patience
0ddca9d682
gnu: Add cl-numpy-file-format. 
* gnu/packages/lisp-xyz.scm (cl-numpy-file-format, ecl-numpy-file-format,
  sbcl-numpy-file-format): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-14 16:33:52 +02:00
Foo Chuan Wei
0f6aaf2f62
gnu: cl-who: Update to 1.1.4-3.07dafe9. 
* gnu/packages/lisp-xyz.scm (sbcl-cl-who): Update to 1.1.4-3.07dafe9.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-14 16:33:52 +02:00
Leo Famulari
6bf6529792
gnu: linux-libre 5.10: Update to 5.10.111. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.111.
(linux-libre-5.10-pristine-source): Update hash.
 2022-04-14 10:22:54 -04:00
Leo Famulari
0b20c8e071
gnu: linux-libre 5.15: Update to 5.15.34. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.34.
(linux-libre-5.15-pristine-source): Update hash.
 2022-04-14 10:22:54 -04:00
Leo Famulari
1b7f05f72c
gnu: linux-libre: Update to 5.16.20. 
* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.20.
(linux-libre-5.16-pristine-source): Update hash.
 2022-04-14 10:22:54 -04:00
Leo Famulari
0a3fee824b
gnu: linux-libre 5.17: Update to 5.17.3. 
* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.3.
(linux-libre-5.17-pristine-source): Update hash.
 2022-04-14 10:22:54 -04:00
Leo Famulari
aaf4b08c6b
gnu: Update linux-libre 5.17 configuration files. 
This option that adds new hardware support appeared after the 5.17 release.

* gnu/packages/aux-files/linux-libre/5.17-arm.conf,
gnu/packages/aux-files/linux-libre/5.17-arm64.conf,
gnu/packages/aux-files/linux-libre/5.17-i686.conf,
gnu/packages/aux-files/linux-libre/5.17-x86_64.conf: Enable support for Realtek
Ethernet switch chips.
 2022-04-14 10:22:54 -04:00
Mădălin Ionel Patrașcu
b0dd06bd0c
gnu: Add r-xcir. 
* gnu/packages/bioconductor.scm (r-xcir): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 14:53:17 +02:00
Ludovic Courtès
16372cb347
gnu: sundials: Remove input labels. 
* gnu/packages/maths.scm (sundials)[native-inputs, inputs]: Remove labels.
(sundials-openmpi)[inputs]: Remove labels.
 2022-04-14 14:48:21 +02:00
Ludovic Courtès
61bcd648ca
gnu: sundials: Update to 6.1.1. 
* gnu/packages/maths.scm (sundials): Update to 6.1.1.
[inputs]: Add PETSC.
(sundials-openmpi)[inputs]: Remove PETSC.
[arguments]: Remove now unnecessary flags.  Change "MPI_ENABLE" to "ENABLE_MPI".
 2022-04-14 14:48:21 +02:00
Ludovic Courtès
5f74169e8e
daemon: Support systemd-style socket activation. 
* nix/nix-daemon/guix-daemon.cc (SD_LISTEN_FDS_START): New macro.
(systemd_activation_sockets): New function.
(main): Use it.  Remove obsolete 'printMsg' call.
* doc/guix.texi (Invoking guix-daemon): Document socket activation.
 2022-04-14 14:48:20 +02:00
Ludovic Courtès
b9233cb9a8
publish: Support systemd-style socket activation. 
* guix/scripts/publish.scm (systemd-socket): New procedure.
(guix-publish): Add 'style' variable.  Adjust startup message depending
on whether STYLE is 'systemd.
* doc/guix.texi (Invoking guix publish): Mention socket activation.
 2022-04-14 14:48:20 +02:00
Ludovic Courtès
17c6d00b57
publish: Use SRFI-71 instead of SRFI-11. 
* guix/scripts/publish.scm (make-request-handler): Use 'let' instead of
'let-values'.
 2022-04-14 14:48:20 +02:00
Ludovic Courtès
1f82602153
gnu: guile-fibers@1.1: Support cross-compilation. 
Fixes <https://issues.guix.gnu.org/54793>.
Reported by Mathieu Othacehe <othacehe@gnu.org>.

* gnu/packages/guile-xyz.scm (guile-fibers-1.1)[arguments]: Add
'support-cross-compilation' phase.
 2022-04-14 14:48:20 +02:00
Ludovic Courtès
c9cded0955
style: Correctly read dots in pairs and improper lists. 
Until now dots were read as symbols.

* guix/scripts/style.scm (read-with-comments)[dot]: New variable.
[dot?, reverse/dot]: New procedures.
Use 'reverse/dot' instead of 'reverse' when reading lists.
* tests/style.scm ("read-with-comments: dot notation")
("((a . 1) (b . 2))", "(a b c . boom)"): New tests.
 2022-04-14 14:48:20 +02:00
Ricardo Wurmus
919cecd00b
gnu: r-illuminahumanmethylation450kanno-ilmn12-hg19: Move to annotation section. 
* gnu/packages/bioconductor.scm (r-illuminahumanmethylation450kanno-ilmn12-hg19):
Move this variable up to the annotation section.
 2022-04-14 13:38:30 +02:00
Ricardo Wurmus
03009f2a2b
gnu: r-snplocs-hsapiens-dbsnp144-grch37: Move to annotation section. 
* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): Move
this variable up to the annotation section.
 2022-04-14 13:37:23 +02:00
Ricardo Wurmus
c8a6e4abbc
gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics). 
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
 2022-04-14 13:35:22 +02:00
Ricardo Wurmus
aafd0d2309
gnu: r-absseq: Move out of experiments section. 
* gnu/packages/bioconductor.scm (r-absseq): Move definition out of experiments
section.
 2022-04-14 13:34:11 +02:00
Ricardo Wurmus
ed3697c040
gnu: r-abarray: Move out of experiments section. 
* gnu/packages/bioconductor.scm (r-abarray): Move definition out of
experiments section.
 2022-04-14 13:32:52 +02:00
Ricardo Wurmus
67941709e2
gnu: r-aneufinder: Move to packages section. 
* gnu/packages/bioconductor.scm (r-aneufinder): Move this definition out of
the section for Bioconductor experiments packages.
 2022-04-14 13:31:33 +02:00
Mădălin Ionel Patrașcu
cab6657094
gnu: Add r-absseq. 
* gnu/packages/bioconductor.scm (r-absseq): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 13:29:48 +02:00
Mădălin Ionel Patrașcu
a436582124
gnu: Add r-abarray. 
* gnu/packages/bioconductor.scm (r-abarray): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 13:20:07 +02:00
Mădălin Ionel Patrașcu
1b2b1c30e2
gnu: Add r-acde. 
* gnu/packages/bioconductor.scm (r-acde): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 13:18:07 +02:00
Mădălin Ionel Patrașcu
dd9d26bce6
gnu: Add r-wppi. 
* gnu/packages/bioconductor.scm (r-wppi): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 12:47:24 +02:00
Mădălin Ionel Patrașcu
55be5fc400
gnu: Add r-acme. 
* gnu/packages/bioconductor.scm (r-acme): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 12:33:27 +02:00
Mădălin Ionel Patrașcu
08df30f232
gnu: Add r-acgh. 
* gnu/packages/bioconductor.scm (r-acgh): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 11:59:15 +02:00
Attila Lendvai
50046194a2
gnu: libfprint: Fix build, add python for the tests. 
* gnu/packages/freedesktop.scm (libfprint)[native-inputs]: Add python-minimal
as it's needed by the tests.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 11:54:11 +02:00
Mădălin Ionel Patrașcu
839241501a
gnu: Add r-ace. 
* gnu/packages/bioconductor.scm (r-ace): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 11:50:34 +02:00
Mădălin Ionel Patrașcu
7d990e775e
gnu: r-catalyst: Update description. 
* gnu/packages/bioconductor.scm (r-catalyst)[description]: Add Texinfo markup
and clarify a sentence.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-14 11:43:24 +02:00
Ricardo Wurmus
d85146c9df
gnu: r-tcgabiolinks: Update to 2.22.4. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.22.4.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
5acc125305
gnu: r-omnipathr: Update to 3.2.8. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.8.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
2def20d3ae
gnu: r-bgeedb: Update to 2.20.1. 
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.1.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
c7cb92e494
gnu: r-gviz: Update to 1.38.4. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.4.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
3c7e190eea
gnu: r-catalyst: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
3e07fbf32a
gnu: r-mscoreutils: Update to 1.6.2. 
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.2.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
40735701a8
gnu: r-singler: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
2a71a7b961
gnu: r-s4vectors: Update to 0.32.4. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.4.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
51ddaf48e8
gnu: r-experimenthub: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
c9e925d444
gnu: r-universalmotif: Update to 1.12.4. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.4.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
eadb1f53e9
gnu: r-variancepartition: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.1.
[propagated-inputs]: Add r-aod, r-rdpack, and r-rhpcblasctl.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
9950ed71fc
gnu: r-cytolib: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.2.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
0861d4fff5
gnu: r-rsubread: Update to 2.8.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.2.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
cb30400097
gnu: r-ropls: Update to 1.26.4. 
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.4.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
0c478f50f2
gnu: r-birewire: Update to 3.26.5. 
* gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.5.
[propagated-inputs]: Remove r-tsne; add r-rtsne.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
b446be46ba
gnu: r-biocfilecache: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.1.
 2022-04-14 11:29:39 +02:00