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Author SHA1 Message Date
Mădălin Ionel Patrașcu 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
Ricardo Wurmus cb115ba722
gnu: pigx-sars-cov-2: Fix build. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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). 
* 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. 
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'. 
* gnu/services/herd.scm (wait-for-service): New procedure.
 2022-05-28 23:23:36 +02:00
Ricardo Wurmus 66bfe55848
gnu: Add r-msdata. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.0.
 2022-05-28 23:19:44 +02:00