26b9eb3bf3
gnu: python-jupyter-client-bootstrap: Fix kernelspec script.
...
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[arguments]:
Add phase 'fix-syntax-error.
Change-Id: Ie160e1ff0152c224bebd581eb266d92ef19b6df8
2025-11-29 12:20:18 +01:00
ad8ce75a78
gnu: r-genomicfeatures: Update to 1.62.0.
...
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.62.0.
[properties]: Update updater-ignored-native-inputs.
[propagated-inputs]: Add r-seqinfo; move r-genomeinfodb from here...
[native-inputs]: ...to here.
Change-Id: I96e66e4bd5ca567208c6c0f37118f5a950781eb3
2025-11-29 12:20:18 +01:00
975b968758
gnu: r-metabocoreutils: Update to 1.18.0.
...
* gnu/packages/bioconductor.scm (r-metabocoreutils): Update to 1.18.0.
[arguments]: Add phase 'testthat-compatibility.
[native-inputs]: Add r-callr.
Change-Id: I4968a77d858e62d81ae394891dc9855510142bab
2025-11-29 12:20:18 +01:00
308d3daee7
gnu: r-biomformat: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.38.0.
[arguments]: Add phase 'testthat-compatibility.
Change-Id: Idb2f673eb9c720c083a6221ebaf3387f158716a5
2025-11-29 12:20:18 +01:00
d86f96e8f3
gnu: r-phyloseq: Update to 1.54.0.
...
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.54.0.
[arguments]: Add phase 'testthat-compatibility.
Change-Id: Id7c69773c1df26b232344d2442f8dd3ca6f50570
2025-11-29 12:20:18 +01:00
c997dff72e
gnu: r-baseline: Add missing inputs.
...
* gnu/packages/cran.scm (r-baseline)[properties]: Record updater-extra-inputs.
[arguments]: Add phase 'fix-lapack.
[inputs]: Add openblas.
[native-inputs]: Add gfortran.
Change-Id: Ic9fd289d6cc7a20331a366564081e82a6b2f4808
2025-11-29 12:20:18 +01:00
e1d7c5b864
gnu: r-mscoreutils: Update to 1.21.0.
...
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.21.0.
[properties]: Record updater-ignored-native-inputs.
[arguments]: Add phase 'disable-bad-tests to disable one test.
Change-Id: I0662daedc00a2e822262d8fe7fdc3b04b90fd216
2025-11-29 12:20:18 +01:00
b2dbef37a7
gnu: r-vcr: Skip one more test.
...
* gnu/packages/cran.scm (r-vcr)[arguments]: Update 'skip-bad-tests phase.
Change-Id: I86b813aeba2febd5198c95b192c5002ad20dc311
2025-11-29 12:20:17 +01:00
4c6951ac69
gnu: r-bamsignals: Update to 1.42.0.
...
* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.42.0.
[arguments]: Add phase 'disable-bad-tests.
[propagated-inputs]: Remove r-zlibbioc.
Change-Id: Iff7edd6821aa637af5875ef50b6cfb08ec181f87
2025-11-29 12:20:17 +01:00
9ddc679a91
gnu: r-biobase: Update to 2.70.0.
...
* gnu/packages/bioconductor.scm (r-biobase): Update to 2.70.0.
[properties]: Update list of ignored native inputs.
Change-Id: I048e40b5c3eec0a3ef479e768ea04ddc179b0357
2025-11-29 12:20:17 +01:00
eada4baa6e
gnu: r-annotationhub: Update to 4.0.0.
...
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 4.0.0.
[properties]: Add r-seqinfo to the ignored native inputs.
[propagated-inputs]: Add r-biocbaseutils; replace r-httr with r-httr2.
Change-Id: If4a6ce0103475312a378d173a635c88e13a364f3
2025-11-29 12:20:17 +01:00
b42f0e2573
gnu: r-escape: Update to 2.6.1.
...
* gnu/packages/bioconductor.scm (r-escape): Update to 2.6.1.
[properties]: Record updater-extra-native-inputs.
[arguments]: Update 'delete-bad-tests phase.
[propagated-inputs]: Remove r-aucell, r-biocparallel, r-dplyr,
r-ggpointdensity, r-ggridges, r-gseabase, r-gsva, r-msigdb, r-patchwork,
r-reshape2, r-seuratobject, r-singlecellexperiment, r-stringr, and r-ucell.
[native-inputs]: Add r-biocparallel, r-delayedmatrixstats, r-dplyr, r-fgsea,
r-gseabase, r-gsva, r-seuratobject, and r-singlecellexperiment; remove
r-vdiffr.
Change-Id: I5c99e731996f9fe45eb2e9def1b508fb2b816a49
2025-11-29 12:20:17 +01:00
4bf3222c93
gnu: r-biomart: Update to 2.66.0.
...
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.66.0.
[arguments]: Update 'delete-bad-tests phase.
[propagated-inputs]: Remove r-digest and r-rappdirs.
Change-Id: I13fda0acb06b3147822ec3b324132cf8ae479775
2025-11-29 12:20:17 +01:00
f9e94993b8
gnu: r-biocparallel: Update to 1.44.0.
...
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.44.0.
[arguments]: Adjust phase 'make-reproducible.
Change-Id: I186b4130976be1052db65f38c73837293c32c0f8
2025-11-29 12:20:17 +01:00
6ffc51ff08
gnu: r-s4arrays: Update to 1.8.1.
...
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.8.1.
Change-Id: Iaf7c0dfea9a53efce65f8de0626bb5ce28e9de9d
2025-11-29 12:20:17 +01:00
4c641636e8
gnu: r-biocpkgtools: Update to 1.26.4.
...
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.26.4.
[propagated-inputs]: Remove r-rorcid; add r-httr2.
Change-Id: I6499c36aab5a01a23f901d4c9372f8c5d1a0528b
2025-11-29 12:20:16 +01:00
918295ec6b
gnu: r-tximport: Update to 1.36.1.
...
* gnu/packages/bioconductor.scm (r-tximport): Update to 1.36.1.
Change-Id: Idd97466303b5c4173f322bce2dec5732af10ff01
2025-11-29 12:20:16 +01:00
cf33494417
gnu: Add r-fscache.
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* gnu/packages/cran.scm (r-fscache): New variable.
Change-Id: I0194abcdb241a4d1776c3351b6e53e7d8362bc66
2025-11-29 12:20:16 +01:00
9b6c64c588
gnu: Add r-sqlq.
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* gnu/packages/cran.scm (r-sqlq): New variable.
Change-Id: Iff61b5d647d1fe965164efa7f9510235ac99c7b0
2025-11-29 12:20:16 +01:00
2462a41ccf
gnu: Add r-sched.
...
* gnu/packages/cran.scm (r-sched): New variable.
Change-Id: Ie8e664a0fc44fb6ba7415cb843a47e9494ae9c08
2025-11-29 12:20:16 +01:00
a1c55d15cd
gnu: Add r-immapex.
...
* gnu/packages/bioconductor.scm (r-immapex): New variable.
Change-Id: I90f5240bdf1141f8ecaadb564024a08c5e137273
2025-11-29 12:20:16 +01:00
0f37a94753
gnu: Add r-gcptools.
...
* gnu/packages/bioconductor.scm (r-gcptools): New variable.
Change-Id: Iac41d4a16c15ae32c0655ec86f8f8e70f1aea2de
2025-11-29 12:20:16 +01:00
c5eaf0b436
gnu: Add r-cigarillo.
...
* gnu/packages/bioconductor.scm (r-cigarillo): New variable.
Change-Id: I76d9cda75b9973ff6306075871a62d301675ebce
2025-11-29 12:20:16 +01:00
6e98baa91e
gnu: Add r-convert.
...
* gnu/packages/bioconductor.scm (r-convert): New variable.
Change-Id: Ib8a83b25e93e3971b6d383798290d97597ce1869
2025-11-29 12:20:15 +01:00
f54b8586a6
gnu: Add r-seqinfo.
...
* gnu/packages/bioconductor.scm (r-seqinfo): New variable.
Change-Id: I084c1b55480e58e4be10cfd7917f2f3846841f84
2025-11-29 12:20:15 +01:00
1a97739bda
guix: Update Bioconductor version to 3.22.
...
* guix/build-system/r.scm (bioconductor-uri): Update to 3.22.
* guix/import/cran.scm (%bioconductor-version): Set to 3.22.
Change-Id: I53c6b0d1ddc37faad90492103b7d02c210f945d7
2025-11-29 12:20:15 +01:00
8b7a0cdc98
gnu: r-extrafont: Add test input.
...
* gnu/packages/cran.scm (r-extrafont)[native-inputs]: Add r-testthat.
Change-Id: I8d629cbbde3a8668681ad3e8d556d496f9e1744f
2025-11-29 12:20:15 +01:00
e8609b3805
gnu: r-extrafontdb: Add test input.
...
* gnu/packages/cran.scm (r-extrafontdb)[native-inputs]: Add r-testthat.
Change-Id: I8e5a77dbee00f03ba2bf0ce447d1a8f578f98c50
2025-11-29 12:20:15 +01:00
fe8a55c0f1
gnu: r-rttf2pt1: Add test inputs.
...
* gnu/packages/cran.scm (r-rttf2pt1)[native-inputs]: Add r-testthat and
r-withr.
Change-Id: I3c5781fb53c03a5ed3bc817212a0a8fe881057e5
2025-11-29 12:20:15 +01:00
3b5f808fea
gnu: r-readr: Update to 2.1.6.
...
* gnu/packages/statistics.scm (r-readr): Update to 2.1.6.
[native-inputs]: Add r-dplyr, r-spelling, and r-withr.
Change-Id: I4be3fe4c30747a282cb03a1e825074d5cd2583f2
2025-11-29 12:20:15 +01:00
98059912dd
gnu: r-duckdb: Update to 1.4.2.
...
* gnu/packages/duckdb.scm (r-duckdb): Update to 1.4.2.
Change-Id: I7f8c65d1e994906a27dc05610934d4136e1afa50
2025-11-29 12:20:15 +01:00
e8224f3e81
gnu: r-paws-common: Update to 0.8.6.
...
* gnu/packages/cran.scm (r-paws-common): Update to 0.8.6.
Change-Id: I4e5c8365d652ab63c7ea99f9d02523a555274d8e
2025-11-29 12:20:15 +01:00
93ef3bbcb8
gnu: r-downlit: Update to 0.4.5.
...
* gnu/packages/cran.scm (r-downlit): Update to 0.4.5.
[native-inputs]: Add r-htmltools, r-knitr, r-mass, r-rmarkdown, and r-xml2.
Change-Id: Iee0654344931fecf951d8b5416339fcb9203e990
2025-11-29 12:20:14 +01:00
b9351be9d9
gnu: r-mlr3cluster: Update to 0.1.12.
...
* gnu/packages/cran.scm (r-mlr3cluster): Update to 0.1.12.
Change-Id: Ib49a5abc91b5db0c7544d2ed8e83bb2a33b6278c
2025-11-29 12:20:14 +01:00
3532391ccc
gnu: r-locpol: Update to 0.9.0.
...
* gnu/packages/cran.scm (r-locpol): Update to 0.9.0.
Change-Id: I738d5a9a8cec2a65a3f9006b9f019000db6f5514
2025-11-29 12:20:14 +01:00
36fba42be4
gnu: r-qtl: Update to 1.72.
...
* gnu/packages/cran.scm (r-qtl): Update to 1.72.
Change-Id: Id4d13b3ec65a692c0c36963a7dc44131235ab24e
2025-11-29 12:20:14 +01:00
bf3b1a041e
gnu: r-slider: Update to 0.3.3.
...
* gnu/packages/cran.scm (r-slider): Update to 0.3.3.
Change-Id: Id51f0dbd6e9ff7dafce8715975fb1fcae5d808b0
2025-11-29 12:20:14 +01:00
c2abe13b8f
gnu: r-warp: Update to 0.2.2.
...
* gnu/packages/cran.scm (r-warp): Update to 0.2.2.
[native-inputs]: Add r-withr.
[properties]: Record updater-extra-native-inputs.
Change-Id: I34259c20df4f50505f31abd9d0cb768dd591494e
2025-11-29 12:20:14 +01:00
a7c3a9cba8
gnu: r-lobstr: Update to 1.1.3.
...
* gnu/packages/cran.scm (r-lobstr): Update to 1.1.3.
Change-Id: I055205206321b92ef994d47b1b80b2a6f06501fb
2025-11-29 12:20:14 +01:00
b72bc202a5
gnu: r-spatstat-geom: Update to 3.6-1.
...
* gnu/packages/cran.scm (r-spatstat-geom): Update to 3.6-1.
Change-Id: I595fd49b1f988e7afd60c19e60862de2445f7654
2025-11-29 12:20:14 +01:00
8a9b10754d
gnu: r-spatstat-univar: Update to 3.1-5.
...
* gnu/packages/cran.scm (r-spatstat-univar): Update to 3.1-5.
Change-Id: Id6e618991f0fd7921b24029440431912c40cc5ea
2025-11-29 12:20:13 +01:00
abe7e2d34a
gnu: r-bridgesampling: Update to 1.2-1.
...
* gnu/packages/cran.scm (r-bridgesampling): Update to 1.2-1.
[native-inputs]: Add r-cmdstanr, r-mcmcpack, r-rcpp, and r-rstan.
Change-Id: I5e2153752c81b7f93ab651c9cc47ea94c0928566
2025-11-29 12:20:13 +01:00
3b652c53fd
gnu: r-rsconnect: Update to 1.6.2.
...
* gnu/packages/cran.scm (r-rsconnect): Update to 1.6.2.
Change-Id: I130aa67a4f74976a746df89b1d1cc9c69cd32c6b
2025-11-29 12:20:13 +01:00
86b67fee09
gnu: r-xml2: Update to 1.5.0.
...
* gnu/packages/cran.scm (r-xml2): Update to 1.5.0.
Change-Id: I3d6310cf5aa4b505a54f13f939d928a4b7c08b72
2025-11-29 12:20:13 +01:00
73d1898d69
gnu: r-ggpointdensity: Update to 0.2.1.
...
* gnu/packages/cran.scm (r-ggpointdensity): Update to 0.2.1.
[propagated-inputs]: Add r-mass.
Change-Id: I11d53befd0a93bdced2119d7ec0981a36c7e0c1f
2025-11-29 12:20:13 +01:00
ab5fa5d9e8
gnu: r-xkcd: Update to 0.1.0.
...
* gnu/packages/cran.scm (r-xkcd): Update to 0.1.0.
[propagated-inputs]: Add r-rlang.
Change-Id: I76b047d46f0782c73088881f14580b7f02a9a6b3
2025-11-29 12:20:13 +01:00
7fb6d6c65e
gnu: r-future: Update to 1.68.0.
...
* gnu/packages/cran.scm (r-future): Update to 1.68.0.
Change-Id: I8b89791ac957821c83bf68f57bbb35265194e686
2025-11-29 12:20:13 +01:00
dcfb30ad9a
gnu: r-rgl: Update to 1.3.31.
...
* gnu/packages/cran.scm (r-rgl): Update to 1.3.31.
Change-Id: I2e7ee1a913a27b1d0aa176c2ee096b44bbab1aa0
2025-11-29 12:20:13 +01:00
f3f7186a35
gnu: r-biocmanager: Update to 1.30.27.
...
* gnu/packages/cran.scm (r-biocmanager): Update to 1.30.27.
Change-Id: Ic9c27b9222327fda1219874b844cdade54cc3a67
2025-11-29 12:20:12 +01:00
3e2aa9a827
gnu: r-gert: Update to 2.2.0.
...
* gnu/packages/cran.scm (r-gert): Update to 2.2.0.
[inputs]: Add pcre2.
Change-Id: Ia5d0d56b4047dc40cf99d79f3fcf075ac58ea420
2025-11-29 12:20:12 +01:00
Ricardo Wurmus