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Author SHA1 Message Date
Zheng Junjie
126a2e8cb4
Partial revert "gnu: bootstrap: %bootstrap-glibc: Also fix libm.so." 
This partially reverts commit 204fe1b1f0.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: I921984ef5eff58792ffc17b64675db6a8e79695c
 2024-12-05 01:13:02 +08:00
Zheng Junjie
7b64a96326
Partial revert "gnu: make-bootstrap: Update gcc-static to gcc-14, for the 64bit Hurd." 
This partially reverts commit ec8a5ec15f.

This part accidentally triggered a world rebuild for non-x86 architectures.

Change-Id: Id2f9bcbcda8dc86ea407e9a7857a854dc1a742b5
 2024-12-05 01:13:02 +08:00
Ricardo Wurmus
e00ca95e08
gnu: Add r-ggupset. 
* gnu/packages/cran.scm (r-ggupset): New variable.

Change-Id: I044fff58b66dbb56e6b7fb1ebcb5353e7ab3d1f7
 2024-12-04 16:25:20 +01:00
Ricardo Wurmus
3cfd6e11a4
gnu: Add skewer. 
* gnu/packages/bioinformatics.scm (skewer): New variable.

Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a
 2024-12-04 16:21:07 +01:00
Sharlatan Hellseher
0c1dddd90f
gnu: packages/python-science: Update copyright header. 
* gnu/packages/python-science.scm: Update copyright header for Antero
Mejr <antero@mailbox.org> .

Change-Id: I4153d51d74f7de1629d5a7851346021b77e7352d
 2024-12-04 14:38:09 +00:00
Antero Mejr
16c71b7fe3
gnu: Add python-scikit-surprise. 
* gnu/packages/python-science.scm (python-scikit-surprise): New variable.

Change-Id: I9b5e13f0c985f34bb0bd759e76ebd27221a340a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2024-12-04 14:28:10 +00:00
Janneke Nieuwenhuizen
1c4a00820a
gnu: ikiwiki: Fix build by disabling a test. 
* gnu/packages/web.scm (ikiwiki)[arguments]: In stage "pre-check", disable
failing "t/t.po" test.

Change-Id: I4fc1240512b4d3df3ece837521116aee5746e181
 2024-12-04 10:15:24 +01:00
John Kehayias
3e2442de52
Revert "news: Add entry for the Guix survey." 
This reverts commit cd26d76fed.  See discussion
at <https://issues.guix.gnu.org/74549>.  Let's keep news.scm to direct user
impact/software (or at least not set a different precedent here).

Change-Id: I1a72474ad3c79bc59100979f35f0216f68f4e88e
 2024-12-04 00:49:27 -05:00
Ekaitz Zarraga
9001514e24
doc: contributing: Remove --base=auto 
* doc/contributing.texi(Sending a Patch Series): Remove --base=auto from
  examples

Change-Id: Idd421f9d6b592d6a314edfaa66404dee4c1b2241
 2024-12-03 22:43:10 +01:00
Ekaitz Zarraga
7b46b8db9a
doc: Explain git format-patch revision format 
* doc/contributing.texi(Sending a Patch Series): Add a note about
`git format-patch` revision format and link to git documentation.

Change-Id: Ie08f85dc19e3804165fb184664b74e85a804d7c4
 2024-12-03 22:42:54 +01:00
Ricardo Wurmus
595fb0ade7
gnu: r-rcdt: Add missing input. 
* gnu/packages/cran.scm (r-rcdt)[native-inputs]: Add r-testthat.

Change-Id: Ic5358aee6d5174052266dc01b81f618edf931cd2
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
8c97926a01
import/cran: Enhance import pattern. 
* guix/import/cran.scm (import-pattern): Comment; capture direct namespace
imports as well as silent imports.

Change-Id: Ia54035d6f230d695aa950adb3e691cbce4f2d416
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
1261bf83b8
import/cran: Also add set-HOME phase when R.cache exists. 
* guix/import/cran.scm (phases-for-inputs): Add "R.cache" to the list.

Change-Id: Ia65beb7cd535de10b024d108a97db0169045fe1f
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
46badc09bd
gnu: r-msnid: Disable vignettes. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Disable vignettes.

Change-Id: I47dc4cf5b6d80699d4f22b2b92382ada7ca3322a
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
2f4814e95c
gnu: r-pcaexplorer: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-pcaexplorer)[native-inputs]: Add
r-airway and r-org-hs-eg-db.

Change-Id: Id559bea8cd4308058a06158e74d3e13d7f645572
 2024-12-03 17:00:01 +01:00
Ricardo Wurmus
0b64bb6ee5
gnu: Add r-airway. 
* gnu/packages/bioconductor.scm (r-airway): New variable.

Change-Id: I521c1bf868566f80997c8ba80609fd5709a95694
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
dedc157d71
gnu: r-reportingtools: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-reportingtools)[native-inputs]: Add
r-all, r-genefilter, r-hgu95av2-db, r-org-hs-eg-db, r-org-mm-eg-db,
r-org-sc-sgd-db, r-pasilla, and r-shiny.
[properties]: Tell updater to ignore r-gsealm.

Change-Id: I9512bbc7a96c328ee05e15bc898969494dca4be0
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
f8bbfe1ea9
gnu: Add r-faahko. 
* gnu/packages/bioconductor.scm (r-faahko): New variable.

Change-Id: I70cd662bdd202ac78f5f25235fb7b9b9e7d60b37
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
9e72ac0e0c
gnu: r-xcms: Disable tests. 
* gnu/packages/bioconductor.scm (r-xcms)[arguments]: Disable tests.
[properties]: Tell updater to ignore r-faahko.
[native-inputs]: Add r-msdata.

Change-Id: I2ee167828534a4046d15d740f6f25d8eff9d589f
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
68c1fab64f
gnu: r-httpgd: Disable tests. 
* gnu/packages/statistics.scm (r-httpgd)[arguments]: Disable tests.
[synopsis]: Use lower case and remove extraneous quotes.

Change-Id: I25e69987b6c647d14cc51ba01ba2fcfb1163c568
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
8035314cb1
gnu: r-mcmc: Disable vignettes. 
* gnu/packages/cran.scm (r-mcmc)[arguments]: Disable vignettes.

Change-Id: I0453d3a812d8e5fea52ab38d16e82f9c5ea439ac
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
014b08cbc8
gnu: r-biodb: Disable tests. 
* gnu/packages/bioconductor.scm (r-biodb)[arguments]: Disable tests.

Change-Id: I40746a3fbfad0801058b7f34182edc358a863fa2
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
b97678925a
gnu: discrover: Add missing input. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-etoolbox.

Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
1084879b45
gnu: r-rtk: Add missing input. 
* gnu/packages/cran.scm (r-rtk)[native-inputs]: Add r-testthat.

Change-Id: I22bd9756036270cf9e60fcdf1b09f8be8aace74d
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
01a5b0eb53
gnu: r-assertive: Add missing input. 
* gnu/packages/cran.scm (r-assertive)[native-inputs]: Add r-testthat.

Change-Id: I0119786699e4353b9254f4a4858a2b0820a85e31
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
a2cfd9f8c9
gnu: r-assertive-data: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data)[native-inputs]: Add r-testthat.

Change-Id: Ie47c9aaa6dc8f9bf3f627555bde01eff38b58b7f
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
1a3c5d25ac
gnu: r-assertive-data-uk: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data-uk)[native-inputs]: Add r-testthat.

Change-Id: I9a388538bc3a7b8192132da7139eb6d37ba785c6
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
f2dcb38d11
gnu: r-assertive-data-us: Add missing input. 
* gnu/packages/cran.scm (r-assertive-data-us)[native-inputs]: Add r-testthat.

Change-Id: Ib2e5540aa6fb409cf807b51871eb80f87d221c5b
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
56fd1386ff
gnu: r-assertive-datetimes: Add missing input. 
* gnu/packages/cran.scm (r-assertive-datetimes)[native-inputs]: Add
r-testthat.

Change-Id: I41cf25fde0519a2552e2bfabf88325c9790b9598
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
483ea05d47
gnu: r-assertive-code: Add missing input. 
* gnu/packages/cran.scm (r-assertive-code)[native-inputs]: Add r-testthat.

Change-Id: Iab971756002abbe84f7472092db82f62eb9acc55
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
78ce99acf5
gnu: r-assertive-strings: Add missing input. 
* gnu/packages/cran.scm (r-assertive-strings)[native-inputs]: Add r-testthat.

Change-Id: Ib4f6eb638105f7d1aaa54972176b8d66704ed2a4
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
8f7196cbae
gnu: r-rcas: Add missing inputs 
* gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager.
[arguments]: Add phases 'skip-bad-tests and 'set-HOME.

Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
eb04b8ca59
gnu: r-affyplm: Add missing inputs and disable tests. 
* gnu/packages/bioconductor.scm (r-affyplm)[native-inputs]: Add r-affydata and
r-hgu95av2cdf.
[arguments]: Disable tests.
[properties]: Tell updater to keep extra input.

Change-Id: I05778ba527078d46e955a752a2b1af075508fdf0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
0e1b5c7d44
gnu: Add r-hgu95av2cdf. 
* gnu/packages/bioconductor.scm (r-hgu95av2cdf): New variable.

Change-Id: I12095d54198b563a81c0d3967699016fef0f2de0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
a18bc29ee0
gnu: r-assertive-files: Add missing input. 
* gnu/packages/cran.scm (r-assertive-files)[native-inputs]: Add r-testthat.
[arguments]: Add phases 'set-HOME.

Change-Id: Icd6d2dc145b31b25fcad1c0482ba87928165c7f7
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
bf177fb732
gnu: r-assertive-types: Add missing input. 
* gnu/packages/cran.scm (r-assertive-types)[native-inputs]: Add r-testthat.

Change-Id: I58ef096504602989de101b744362b115fcb67f27
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
ee88301053
gnu: Remove r-bioconcotk. 
This package has been removed from Bioconductor and tests depend on a package
that has also been removed.

* gnu/packages/bioconductor.scm (r-bioconcotk): Remove variable.

Change-Id: If444fb7a10aea71a5339b4a488683148c84bb236
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
4b0c460719
gnu: r-bigmelon: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-bigmelon)[native-inputs]: Add
r-biocstyle and r-knitr.

Change-Id: Ie24831140e5b38d330435231d8ea976a060b4800
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
436869bdf9
gnu: r-chipexoqual: Add missing input. 
* gnu/packages/bioconductor.scm (r-chipexoqual)[native-inputs]: Add
r-chipexoqualexample.

Change-Id: I68e5ac7ce3d0c00cfc1838ef7d6b4e2e5410bb50
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
5f8f7435a2
gnu: Add r-chipexoqualexample. 
* gnu/packages/bioconductor.scm (r-chipexoqualexample): New variable.

Change-Id: I181bb085e441d056d886d4110a46668d92cd39f4
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
85c3a9385f
gnu: r-chk: Add missing input. 
* gnu/packages/cran.scm (r-chk)[native-inputs]: Add tzdata-for-tests.
[properties]: Tell updater to keep it.

Change-Id: I86058064135869dadb79d490f16a8b7ea5fd4661
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
9ba40c620c
gnu: r-btools: Disable tests. 
* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests.

Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
dcd3f1660d
gnu: r-genomicstate: Disable tests. 
* gnu/packages/bioconductor.scm (r-genomicstate)[arguments]: Disable tests.

Change-Id: Ia2a43c0b20af344e74306f88c3306c6bd40267b0
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
7a3d88efa9
gnu: r-googlesheets: Add missing inputs. 
* gnu/packages/statistics.scm (r-googlesheets)[native-inputs]: Add r-knitr and
r-testthat.

Change-Id: I8ac8ec40c9bbcdb01509dc199b4937e95563aad6
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
38e85d78ad
gnu: r-gqtlstats: Add missing input and disable tests. 
* gnu/packages/bioconductor.scm (r-gqtlstats)[native-inputs]: Add r-runit.
[arguments]: Disable tests.

Change-Id: I1b11251e88826970d16f32a1304a92f9c4923bd5
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
91b5e69b29
gnu: r-gostats: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-gostats)[native-inputs]: Add r-biocgenerics
and r-hgu95av2-db.

Change-Id: I4e5ee933154dc102efe4c034f993c959b2924671
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
803f1f6401
gnu: r-mumin: Add missing inputs. 
* gnu/packages/statistics.scm (r-mumin)[native-inputs]: Add r-mgcv and
r-survival.

Change-Id: Id5b1a558af6020018d1fbdc88179682681bd625c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
b0e2aa61e7
gnu: r-nabor: Add missing input. 
* gnu/packages/cran.scm (r-nabor)[native-inputs]: Add r-rann.

Change-Id: Ie177502c2f902a6d4e76a94a2d2d30537c747df6
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
169c4e612b
gnu: r-msnbase: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-msnbase)[native-inputs]: Add r-msdata,
r-rpx, r-summarizedexperiment, and r-xml.
[arguments]: Add phases 'set-HOME and 'delete-bad-tests.
[properties]: Tell updater to avoid a dependency cycle.

Change-Id: I49f6ec0c516f610785c3e79e0d4a4ad74a9ac38c
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
594d64569d
gnu: Add r-prolocdata. 
* gnu/packages/bioconductor.scm (r-prolocdata): New variable.

Change-Id: Iac4da738f793e2a746d1ef8a17251a3b27c2e599
 2024-12-03 16:59:58 +01:00