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Author SHA1 Message Date
Ludovic Courtès 2880dc3046
cpio: Skip test on inode numbers that don't fit on 32 bits. 
Fixes <https://issues.guix.gnu.org/60202>.
Reported by Christopher Baines <mail@cbaines.net>.

* tests/cpio.scm (%test-file): New variable.
("file->cpio-header + write-cpio-header + read-cpio-header"): Use it.
Skip test when the inode number of %TEST-FILE is too big.
 2022-12-20 16:56:03 +01:00
Ludovic Courtès 3f6c5c6f78
doc: Avoid 'match' on the <udev-configuration> record. 
Fixes <https://issues.guix.gnu.org/59907>.
Reported by MANCINI Raffael <Raffael.MANCINI@mnhn.lu>.

* doc/guix.texi (Service Types and Services): Change
'udev-configuration' example to avoid 'match'.
 2022-12-20 16:56:03 +01:00
Ludovic Courtès 680970490c
tests: Adjust 'guix package' test to latest package search metrics. 
With commit bbcd06e56c, the command
"guix package -s '^fileutils$'" would match the 'ocaml-fileutils'
package, because its 'package-upstream-name*' is "fileutils".  Work
around it.

Reported by Vagrant Cascadian.

* tests/guix-package.sh: Change "fileutils" example to use a different
package name.
 2022-12-20 16:56:03 +01:00
Efraim Flashner 7fb27b5441
gnu: seabios: Limit to i686-linux and x86_64-linux. 
* gnu/packages/firmware.scm (seabios)[supported-systems]: New field.
 2022-12-20 17:12:07 +02:00
Efraim Flashner 35530133ae
Revert "gnu: QEMU: Unbundle SeaBIOS." 
This reverts commit 814214c369.

SeaBIOS is only buildable on i686-linux machines and has flags set to
force building for i386 so that it works from x86_64-linux. This commit
breaks qemu and qemu-minimal on all other architectures.
 2022-12-20 17:10:17 +02:00
Greg Hogan fc4eef7506
gnu: openjdk18: Update to 18.0.2. 
* gnu/packages/java.scm (openjdk18): Update to 18.0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:38 +02:00
Greg Hogan a49e4087a1
gnu: openjdk17: Update to 17.0.5. 
* gnu/packages/java.scm (openjdk17): Update to 17.0.5.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:38 +02:00
Greg Hogan 7cf6e66548
gnu: openjdk16: Update to 16.0.2. 
* gnu/packages/java.scm (openjdk16): Update to 16.0.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:38 +02:00
Greg Hogan 0175b93199
gnu: openjdk15: Update to 15.0.9. 
* gnu/packages/java.scm (openjdk15): Update to 15.0.9.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:38 +02:00
Greg Hogan 8a6316ef9e
gnu: openjdk13: Update to 13.0.13. 
* gnu/packages/java.scm (openjdk13): Update to 13.0.13.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:37 +02:00
Efraim Flashner c8ebfa0dd9
gnu: openjdk11: Fix find-files syntax. 
* gnu/packages/java.scm (openjdk11)[source]: Remove extra characters
from find-files invocation.
[arguments]: Remove extra characters from find-files invocations in
multiple phases.
 2022-12-20 17:06:37 +02:00
Greg Hogan f667aeb642
gnu: openjdk11: Update to 11.0.17. 
* gnu/packages/java.scm (openjdk11): Update to 11.0.17.
[source]: Fix source file-name.
[native-inputs]: Add bash.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-12-20 17:06:34 +02:00
Tobias Geerinckx-Rice 1a3d8b9228
gnu: audacity: Update to 3.2.2. 
* gnu/packages/audio.scm (audacity): Update to 3.2.2.
 2022-12-18 01:00:00 +01:00
Tobias Geerinckx-Rice 04665f2673
gnu: audacity: Be less alpha. 
* gnu/packages/audio.scm (audacity)[arguments]: Set AUDACITY_BUILD_LEVEL
in the #:configure-flags.
 2022-12-18 01:00:00 +01:00
Marius Bakke 2f2a9aca4b
gnu: Add ipxe-qemu. 
* gnu/packages/bootloaders.scm (ipxe-qemu): New variable.
 2022-12-20 15:29:11 +01:00
Marius Bakke 040c43d78a
gnu: Add edk2-tools. 
* gnu/packages/firmware.scm (edk2-tools): New variable.
 2022-12-20 15:29:11 +01:00
Nicolas Goaziou e2b8cdde37
gnu: emacs-fzf: Fix version. 
* gnu/packages/emacs-xyz.scm (emacs-fzf)[version]: Set to 0.2.

Last tagged version and Version keyword from main file differ. We use the
highest one (the tag).
 2022-12-20 15:27:50 +01:00
Ricardo Wurmus 4651d380b4
gnu: p2c: Update to 2.02. 
* gnu/packages/pascal.scm (p2c): Update to 2.02.
[arguments]: Use gexp.
[native-inputs]: Add unzip.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus fd4ca4a266
gnu: r-kegggraph: Update to 1.58.3. 
* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.58.3.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus cfa8d448bc
gnu: r-scran: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.26.1.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus 71c115fd94
gnu: r-scuttle: Update to 1.8.3. 
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.3.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus c4cbfa40d8
gnu: r-chromvar: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.20.1.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus 68701917b8
gnu: r-s4vectors: Update to 0.36.1. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.36.1.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus e895da0406
gnu: r-preprocesscore: Update to 1.60.1. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.1.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus 18468f775e
gnu: r-biocviews: Update to 1.66.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.66.1.
[native-inputs]: Add r-knitr.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus fc617e70e6
gnu: r-rcistarget: Update to 1.18.2. 
* gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.18.2.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus 031dbcbd0e
gnu: r-opencyto: Update to 2.10.1. 
* gnu/packages/bioconductor.scm (r-opencyto): Update to 2.10.1.
[propagated-inputs]: Remove r-clue, r-flowstats, r-gtools, r-ks, r-lattice, r-mass,
r-plyr, r-r-utils, r-rcpp, and r-rrcov; add r-bh and r-cpp11.
 2022-12-20 12:09:34 +01:00
Ricardo Wurmus 7edcbf84bf
gnu: r-ggcyto: Update to 1.26.4. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.26.4.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 5ac36a82e8
gnu: r-rsubread: Update to 2.12.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.12.2.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 90b10b37e8
gnu: r-iclusterplus: Update to 1.34.2. 
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.34.2.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 7f45db2df8
gnu: r-aucell: Update to 1.20.2. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.20.2.
[propagated-inputs]: Add r-matrix.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus da24c1c949
gnu: r-clusterexperiment: Update to 2.18.1. 
* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.18.1.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 2e10df101f
gnu: r-enrichplot: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.18.3.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 7205384533
gnu: r-sigpathway: Update to 1.66.1. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.66.1.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus ceffbc313f
gnu: r-linnorm: Update to 2.22.1. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.22.1.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 2eb81c0888
gnu: r-lpsymphony: Update to 1.26.2. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.2.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus b51001141b
gnu: r-dnacopy: Update to 1.72.2. 
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.2.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 96508fa43a
gnu: r-glmgampoi: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.10.1.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus c47fd0c47c
gnu: r-diffbind: Update to 3.8.3. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.8.3.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus a13f5a52d0
gnu: r-oligo: Update to 1.62.1. 
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.1.
 2022-12-20 12:09:33 +01:00
Ricardo Wurmus 9e18e3a372
gnu: r-tximport: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-tximport): Update to 1.26.1.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus dc6f9ab3ab
gnu: r-scmap: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.20.1.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus 5fc338637b
gnu: r-lfa: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-lfa): Update to 1.28.1.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus 53fb765c85
gnu: r-impute: Update to 1.72.2. 
* gnu/packages/bioconductor.scm (r-impute): Update to 1.72.2.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus b035f07cc2
gnu: r-genomicranges: Update to 1.50.2. 
* gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.50.2.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus a4362f4599
gnu: r-genomicfeatures: Update to 1.50.3. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.3.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus 86fcb20aa8
gnu: r-genomeinfodb: Update to 1.34.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.4.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus a71a89ac39
gnu: r-genefilter: Update to 1.80.2. 
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.2.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus 6af97fcc0e
gnu: r-edger: Update to 3.40.1. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.40.1.
 2022-12-20 12:09:32 +01:00
Ricardo Wurmus db6ae57157
gnu: r-deseq2: Update to 1.38.2. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.2.
[propagated-inputs]: Remove r-genefilter; add r-matrixstats.
 2022-12-20 12:09:32 +01:00