6400f08d07
gnu: Add python-paramz.
...
* gnu/packages/python-science.scm (python-paramz): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
6dacd15381
gnu: Add python-climin.
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* gnu/packages/python-science.scm (python-climin): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
3d1b2bc740
gnu: wla-dx: Update to 10.1.
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* gnu/packages/assembly.scm (wla-dx): Update to 10.1.
[native-inputs]: Use new style.
[arguments]: Add custom 'check phase to run run_tests.sh.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29 23:56:05 +02:00
40530ffd15
store: Record cache lookups in 'references/cached'.
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* guix/store.scm (references/cached): Add call to
'record-cache-lookup!'.
2022-05-29 23:56:01 +02:00
98e2f4fbeb
gnu: openjdk: Update to 17.0.3.
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* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
2022-05-29 22:57:19 +02:00
d1f4b6dc83
gnu: python-translate-toolkit: Update to 3.6.2.
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* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to
3.6.2.
2022-05-29 22:20:15 +02:00
31a9d8677c
gnu: python-user-agents: Update to 2.2.0.
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* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
2022-05-29 21:30:45 +02:00
92a83f38b5
gnu: python-ua-parser: Update to 0.10.0.
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* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
2022-05-29 21:30:16 +02:00
e8b2219152
gnu: lagrange: Update to 1.13.6.
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* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6.
[source]: Adjust snippet to remove another bundled library.
2022-05-29 19:26:47 +03:00
9cd22702b8
gnu: wget: Update to 1.21.3.
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* gnu/packages/wget.scm (wget): Update to 1.21.3.
2022-05-29 16:31:59 +03:00
1ed40eee39
gnu: mutt: Update to 2.2.5.
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* gnu/packages/mail.scm (mutt): Update to 2.2.5.
2022-05-29 16:31:59 +03:00
46ed423e28
gnu: git-annex: Update to 10.20220525.
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* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
2022-05-29 16:31:59 +03:00
e4fe344a5c
gnu: nmap: Honor tests? flag.
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* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor
the #:tests? flag.
2022-05-29 16:31:09 +03:00
50970a28b7
gnu: wgetpaste: Remove trailing #t from phases.
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* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from
phases.
2022-05-29 16:31:09 +03:00
c62be7d530
gnu: wgetpaste: Add missing input.
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* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
2022-05-29 16:23:48 +03:00
69af8a6837
gnu: telescope: Update to 0.8.1.
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* gnu/packages/web-browsers.scm (telescope): Update to 0.8.1.
[home-page]: Update to new upstream home-page.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-29 16:10:34 +03:00
d540e686ef
gnu: Add pbuilder.
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* gnu/packages/debian.scm (pbuilder): New variable.
2022-05-29 16:01:02 +03:00
b456086c65
gnu: apostrophe: Build with correct webkitgtk.
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* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-29 15:53:48 +03:00
e640da33f3
Merge branch 'wip-r'
2022-05-29 11:49:03 +02:00
89e9262012
gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993.
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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
2022-05-29 11:44:09 +02:00
926fcb488b
gnu: clang-from-llvm: Fix building on riscv64-linux.
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* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for
riscv64-linux add configure-flags and make-flags to ensure linking with
'-latomic'.
2022-05-29 08:46:17 +03:00
a5f4c03df1
gnu: Add r-scmap.
...
* gnu/packages/bioconductor.scm (r-scmap): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29 00:43:05 +02:00
cb115ba722
gnu: pigx-sars-cov-2: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
2022-05-29 00:39:19 +02:00
df3e5cfa05
gnu: pigx-bsseq: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
2022-05-29 00:34:29 +02:00
b64f4a1245
gnu: pigx-scrnaseq: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
2022-05-29 00:29:19 +02:00
add551f651
gnu: pigx-chipseq: Fix build.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
2022-05-29 00:18:48 +02:00
a4b90009c7
gnu: Add r-googlevis.
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* gnu/packages/cran.scm (r-googlevis): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29 00:01:47 +02:00
371a83b764
scripts/import: Use pretty printer from (guix scripts style).
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* guix/scripts/import.scm (guix-import): Use pretty-print-with-comments.
(newline-rewriting-port): Remove procedure.
2022-05-29 00:01:46 +02:00
f383838a09
services: elogind: When started by dbus-daemon, wait for the Shepherd service.
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Fixes <https://issues.guix.gnu.org/55444 >.
Previously shepherd and dbus-daemon would race to start elogind. In
some cases (for instance if one logs in quickly enough on the tty),
dbus-daemon would "win" and start elogind before shepherd has had a
chance to do it. Consequently, shepherd would fail to start elogind and
mark it as stopped and disabled, in turn preventing services that depend
on it such as 'xorg-server' from starting.
* gnu/services/desktop.scm (elogind-dbus-service): Rewrite to refer to a
wrapper that waits for the 'elogind' Shepherd service.
2022-05-28 23:23:36 +02:00
b04ae71def
services: herd: Add 'wait-for-service'.
...
* gnu/services/herd.scm (wait-for-service): New procedure.
2022-05-28 23:23:36 +02:00
66bfe55848
gnu: Add r-msdata.
...
* gnu/packages/bioconductor.scm (r-msdata): New variable.
2022-05-28 23:19:48 +02:00
79158a5624
gnu: r-tcgabiolinksgui-data: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
2022-05-28 23:19:48 +02:00
9d538de266
gnu: r-curatedtcgadata: Update to 1.18.0.
...
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
2022-05-28 23:19:47 +02:00
1c4d0fc9a9
gnu: r-gagedata: Update to 2.34.0.
...
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
2022-05-28 23:19:47 +02:00
c56b553e97
gnu: r-affydata: Update to 1.44.0.
...
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
2022-05-28 23:19:47 +02:00
e06ee7a745
gnu: r-all: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
2022-05-28 23:19:47 +02:00
15e10974ef
gnu: r-hsmmsinglecell: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
2022-05-28 23:19:47 +02:00
3ff4e48e85
gnu: r-pasilla: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0.
[propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown.
[native-inputs]: Add r-knitr.
2022-05-28 23:19:47 +02:00
4f2ac5f19f
gnu: r-genomationdata: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
d24b0702b6
gnu: r-genelendatabase: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
2022-05-28 23:19:47 +02:00
7a58c9af46
gnu: r-copyhelper: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
e437cf10a4
gnu: r-chromstardata: Update to 1.22.0.
...
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
2022-05-28 23:19:47 +02:00
1413f9f214
gnu: r-celldex: Update to 1.6.0.
...
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
2022-05-28 23:19:46 +02:00
3ce819d563
gnu: r-biscuiteerdata: Update to 1.10.0.
...
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
2022-05-28 23:19:46 +02:00
ccb66a16a0
gnu: r-arrmdata: Update to 1.32.0.
...
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
2022-05-28 23:19:46 +02:00
9db43e4979
gnu: r-aneufinderdata: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
2022-05-28 23:19:46 +02:00
c89eb68ede
gnu: r-adductdata: Update to 1.12.0.
...
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
2022-05-28 23:19:46 +02:00
7feae8098c
gnu: r-pfam-db: Update to 3.15.0.
...
* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0.
2022-05-28 23:19:46 +02:00
5efae7b049
gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.15.0.
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* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.15.0.
[propagated-inputs]: Add r-annotationdbi.
2022-05-28 23:19:46 +02:00
8ee1246a38
gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4.
...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4.
2022-05-28 23:19:46 +02:00
Wiktor Zelazny
Felix Gruber
Ludovic Courtès
Danny Milosavljevic
Julien Lepiller
Efraim Flashner
cage
Rene Saavedra
Ricardo Wurmus
Mădălin Ionel Patrașcu