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85295 Commits

Author SHA1 Message Date
Guillaume Le Vaillant
e0d2f8164e gnu: sbcl: Disable SB-SIMD module. 
SB-SIMD gets enabled only on x86_64 CPUs supporting AVX2 instructions,
and some x86_64 CPUs don't.

Fixes <https://issues.guix.gnu.org/56353>.
Reported by Wensheng Xie <xiewensheng@hotmail.com>.

* gnu/packages/lisp.scm (sbcl)[arguments]: Disable SB-SIMD in the 'build' and
  'build-doc' phases.
 2022-07-03 12:07:31 +02:00
Trevor Richards
f89b581148 gnu: nim: Update to 1.6.6. 
* gnu/packages/nim.scm (nim): Updated to 1.6.6.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-07-03 10:12:24 +01:00
Christopher Baines
12787d532f gnu: propeller-binutils: Remove source patches. 
None of the patches seem to apply. The patches that are not used with binutils
are probably too new for the specific commit used here, and the patches that
were once applied have probably been removed, so just don't apply any patches.

* gnu/packages/embedded.scm (propeller-binutils)[source]: Remove patches that
don't apply.
 2022-07-03 10:11:24 +01:00
Christopher Baines
207ef8758e gnu: java-xpp3: Download source from ci.guix.gnu.org. 
The www.extreme.indiana.edu site is now serving a redirect:

  This site has been deprecated. You can access an archive of this site at
  https://web.archive.org/web/20210225153105/https://www.extreme.indiana.edu/.

Because this isn't a 404, as it probably should be, guix follows this redirect
and gets some content that isn't the file it asked for.

To avoid this incorrect behaviour, switch to using a ci.guix.gnu.org URL for
the file instead.

* gnu/packages/xml.scm (java-xpp3)[source]: Switch the uri to ci.guix.gnu.org.
 2022-07-03 10:11:24 +01:00
Efraim Flashner
c145e51844 gnu: curl: Skip failing test on 32-bit architectures. 
* gnu/packages/curl.scm (curl-7.84.0)[arguments]: Use custom
'skip-failing-tests phase on all 32-bit architectures.
 2022-07-03 10:07:46 +03:00
Efraim Flashner
89fe091bb4 gnu: curl: Fix build on some systems. 
* gnu/packages/curl.scm (curl-7.84.0)[source]: Add patch to work around
implicit function declaration.
* gnu/packages/patches/curl-easy-lock.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2022-07-03 10:07:38 +03:00
muradm
cec5a522e1 gnu: Add sqls 0.2.18. 
* gnu/packages/databases (sqls): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-07-03 01:41:07 +02:00
muradm
eed4494da7 gnu: Add go-github-com-sourcegraph-jsonrpc2 0.1.0. 
* gnu/packages/golang.scm (go-github-com-sourcegraph-jsonrpc2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-07-03 01:41:07 +02:00
muradm
9b6226bcda gnu: Add go-github-com-gorilla-websocket 1.5.0. 
* gnu/packages/golang.scm (go-github-com-gorilla-websocket): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-07-03 01:41:06 +02:00
Ricardo Wurmus
4745be8514 gnu: r-ifultools: Patch in removed macros to fix build. 
* gnu/packages/cran.scm (r-ifultools)[arguments]: Define removed compatibility
macros.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
a0142125e6 gnu: r-with-tests: Update to 4.2.1. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.2.1.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
3bb39fc370 gnu: r-tcgabiolinks: Update to 2.24.3. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.3.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
af06365a3e gnu: r-bionetstat: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.1.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
26981da96b gnu: r-bgeedb: Update to 2.22.3. 
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.3.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
5f03154c15 gnu: r-ggbio: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.1.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
11f30bfa3d gnu: r-rsubread: Update to 2.10.4. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.4.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
0a5a06ed24 gnu: r-biosigner: Update to 1.24.2. 
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
fbb6489abd gnu: r-ropls: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.2.
[propagated-inputs]: Add r-multiassayexperiment and r-summarizedexperiment.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
4aabb20226 gnu: r-genomicscores: Update to 2.8.2. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.2.
[propagated-inputs]: Add r-httr.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
b7a5534e61 gnu: r-clusterprofiler: Update to 4.4.4. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.4.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
a17b7aabfd gnu: r-batchelor: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.3.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
7ff0669cee gnu: r-matrixgenerics: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.1.
 2022-07-02 23:56:10 +02:00
Ricardo Wurmus
605eda07df gnu: r-zellkonverter: Update to 1.6.3. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.3.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
febec55f57 gnu: r-simplifyenrichment: Update to 1.6.1. 
* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.1.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
c4113d3035 gnu: r-rtracklayer: Update to 1.56.1. 
* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.1.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
5298b57d56 gnu: r-organismdbi: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.1.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
4e6026031a gnu: r-limma: Update to 3.52.2. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.2.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
103d4d918f gnu: r-ensembldb: Update to 2.20.2. 
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.2.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
5888776c87 gnu: r-gld: Update to 2.6.5. 
* gnu/packages/statistics.scm (r-gld): Update to 2.6.5.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
1f6de97557 gnu: r-clubsandwich: Update to 0.5.7. 
* gnu/packages/statistics.scm (r-clubsandwich): Update to 0.5.7.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
f6c9920f62 gnu: r-ranger: Update to 0.14.1. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.14.1.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
9360df02d1 gnu: r-car: Update to 3.1-0. 
* gnu/packages/statistics.scm (r-car): Update to 3.1-0.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
2998060a53 gnu: r-gtools: Update to 3.9.2.2. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.9.2.2.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
e9f9791b14 gnu: r-r-rsp: Update to 0.45.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.45.0.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
7d7712c9a0 gnu: r-r-utils: Update to 2.12.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.12.0.
 2022-07-02 23:56:09 +02:00
Ricardo Wurmus
c37911f090 gnu: r-r-methodss3: Update to 1.8.2. 
* gnu/packages/statistics.scm (r-r-methodss3): Update to 1.8.2.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
eae36e7aed gnu: r-rcpparmadillo: Update to 0.11.2.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.11.2.0.0.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
a12211cd93 gnu: r-dbplyr: Update to 2.2.1. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.2.1.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
1e57895c5c gnu: r-rlang: Update to 1.0.3. 
* gnu/packages/statistics.scm (r-rlang): Update to 1.0.3.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
2ddb659da1 gnu: r-dbi: Update to 1.1.3. 
* gnu/packages/statistics.scm (r-dbi): Update to 1.1.3.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
54c86cf5f8 gnu: r-nlme: Update to 3.1-158. 
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-158.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
764938a242 gnu: r-spacetime: Update to 1.2-8. 
* gnu/packages/cran.scm (r-spacetime): Update to 1.2-8.
[native-inputs]: Add r-knitr.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
621a3350c4 gnu: r-pkgdown: Update to 2.0.5. 
* gnu/packages/cran.scm (r-pkgdown): Update to 2.0.5.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
3b656f1caf gnu: r-downlit: Update to 0.4.1. 
* gnu/packages/cran.scm (r-downlit): Update to 0.4.1.
[propagated-inputs]: Add r-withr.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
b16b702db7 gnu: r-clustree: Update to 0.5.0. 
* gnu/packages/cran.scm (r-clustree): Update to 0.5.0.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
6e5a09f701 gnu: r-phangorn: Update to 2.9.0. 
* gnu/packages/cran.scm (r-phangorn): Update to 2.9.0.
[propagated-inputs]: Add r-generics.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
b427be3510 gnu: r-parsnip: Update to 1.0.0. 
* gnu/packages/cran.scm (r-parsnip): Update to 1.0.0.
[propagated-inputs]: Add r-pillar.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
0a33bc0cba gnu: r-tidyposterior: Update to 1.0.0. 
* gnu/packages/cran.scm (r-tidyposterior): Update to 1.0.0.
 2022-07-02 23:56:08 +02:00
Ricardo Wurmus
2b09daaf71 gnu: r-dials: Update to 1.0.0. 
* gnu/packages/cran.scm (r-dials): Update to 1.0.0.
[propagated-inputs]: Add r-pillar.
 2022-07-02 23:56:07 +02:00
Ricardo Wurmus
1c01ab0a84 gnu: r-rsample: Update to 1.0.0. 
* gnu/packages/cran.scm (r-rsample): Update to 1.0.0.
[propagated-inputs]: Remove r-lifecycle; add r-glue and r-pillar.
 2022-07-02 23:56:07 +02:00