Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
add551f651
gnu: pigx-chipseq: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
2022-05-29 00:18:48 +02:00
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Ludovic Courtès
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
Ludovic Courtès
b04ae71def
services: herd: Add 'wait-for-service'.
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* gnu/services/herd.scm (wait-for-service): New procedure.
2022-05-28 23:23:36 +02:00
Ricardo Wurmus
66bfe55848
gnu: Add r-msdata.
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* gnu/packages/bioconductor.scm (r-msdata): New variable.
2022-05-28 23:19:48 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
9d538de266
gnu: r-curatedtcgadata: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
1c4d0fc9a9
gnu: r-gagedata: Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
c56b553e97
gnu: r-affydata: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
e06ee7a745
gnu: r-all: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
15e10974ef
gnu: r-hsmmsinglecell: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
3ff4e48e85
gnu: r-pasilla: Update to 1.24.0.
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* 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
Ricardo Wurmus
4f2ac5f19f
gnu: r-genomationdata: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
d24b0702b6
gnu: r-genelendatabase: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
7a58c9af46
gnu: r-copyhelper: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
e437cf10a4
gnu: r-chromstardata: Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
2022-05-28 23:19:47 +02:00
Ricardo Wurmus
1413f9f214
gnu: r-celldex: Update to 1.6.0.
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* gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
3ce819d563
gnu: r-biscuiteerdata: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
ccb66a16a0
gnu: r-arrmdata: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
9db43e4979
gnu: r-aneufinderdata: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
c89eb68ede
gnu: r-adductdata: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
7feae8098c
gnu: r-pfam-db: Update to 3.15.0.
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* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
8ee1246a38
gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4.
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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
3d93251ea5
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update to 1.4.3.
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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): Update to 1.4.3.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
549a9e6f6a
gnu: r-leidenbase: Update to 0.1.9.
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* gnu/packages/bioconductor.scm (r-leidenbase): Update to 0.1.9.
2022-05-28 23:19:46 +02:00
Ricardo Wurmus
319fa58dac
gnu: r-phyloseq: Update to 1.40.0.
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* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.40.0.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
e0be852a1e
gnu: r-tximeta: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.0.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
e290d834d9
gnu: r-tricycle: Update to 1.4.0.
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* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.4.0.
[propagated-inputs]: Add r-ggnewscale.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
5ec7143f69
gnu: r-tcgabiolinks: Update to 2.24.1.
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* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.1.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
a4f03b0a55
gnu: r-biscuiteer: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.10.0.
[propagated-inputs]: Add r-iranges.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
6f31f4618a
gnu: r-omnipathr: Update to 3.4.0.
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* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.4.0.
[propagated-inputs]: Add r-withr.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
b1c215755a
gnu: r-dmrseq: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.16.0.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
4ab8327ba4
gnu: r-bsseq: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.32.0.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
397bdc4329
gnu: r-biotmle: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.20.0.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
4b3f9a16f2
gnu: r-biotip: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-biotip): Update to 1.10.0.
[propagated-inputs]: Remove r-hmisc; add r-scran.
2022-05-28 23:19:45 +02:00
Ricardo Wurmus
e8e3d333f0
gnu: r-bioqc: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.24.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
dba6a33e3d
gnu: r-bionetstat: Update to 1.16.0.
...
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
8fe9bcf0a4
gnu: r-bionet: Update to 1.56.0.
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* gnu/packages/bioconductor.scm (r-bionet): Update to 1.56.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
f5262fa4ed
gnu: r-bionero: Update to 1.4.0.
...
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.4.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
3391ff6ddb
gnu: r-biomvrcns: Update to 1.36.0.
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* gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.36.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
7fe83026b7
gnu: r-biomvcclass: Update to 1.64.0.
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* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.64.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
a3a8109fe8
gnu: r-mvcclass: Update to 1.70.0.
...
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.70.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
eb18527e5f
gnu: r-biomformat: Update to 1.24.0.
...
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.24.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
12ee563b41
gnu: r-biodb: Update to 1.4.0.
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* gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.0.
2022-05-28 23:19:44 +02:00
Ricardo Wurmus
259c003f02
gnu: r-biocdockermanager: Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.8.0.
2022-05-28 23:19:43 +02:00
