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Author SHA1 Message Date
Ricardo Wurmus
d72d39eaaf
gnu: r-processx: Update to 3.6.0. 
* gnu/packages/cran.scm (r-processx): Update to 3.6.0.
 2022-06-13 14:21:49 +02:00
Ricardo Wurmus
18fd4e7d70
gnu: r-vcd: Update to 1.4-10. 
* gnu/packages/cran.scm (r-vcd): Update to 1.4-10.
 2022-06-13 14:21:49 +02:00
Ricardo Wurmus
9ccb6b4bee
gnu: r-ipred: Update to 0.9-13. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-13.
 2022-06-13 14:21:49 +02:00
Ricardo Wurmus
8221425e3e
gnu: r-progressr: Update to 0.10.1. 
* gnu/packages/cran.scm (r-progressr): Update to 0.10.1.
 2022-06-13 14:21:48 +02:00
Ricardo Wurmus
38dde27cb3
gnu: r-bdsmatrix: Update to 1.3-6. 
* gnu/packages/cran.scm (r-bdsmatrix): Update to 1.3-6.
 2022-06-13 14:21:48 +02:00
Ricardo Wurmus
c992406b5a
gnu: r-sp: Update to 1.5-0. 
* gnu/packages/cran.scm (r-sp): Update to 1.5-0.
 2022-06-13 14:21:48 +02:00
Ricardo Wurmus
6ffd58142c
gnu: r-proxy: Update to 0.4-27. 
* gnu/packages/cran.scm (r-proxy): Update to 0.4-27.
 2022-06-13 14:21:47 +02:00
Ricardo Wurmus
65464d9027
gnu: r-restrserve: Update to 1.2.0. 
* gnu/packages/cran.scm (r-restrserve): Update to 1.2.0.
 2022-06-13 14:21:47 +02:00
Ricardo Wurmus
ae4c1cb0b3
gnu: r-benchmarkme: Update to 1.0.8. 
* gnu/packages/cran.scm (r-benchmarkme): Update to 1.0.8.
[propagated-inputs]: Add r-stringr.
 2022-06-13 14:21:46 +02:00
Ricardo Wurmus
1917b1f63e
gnu: r-afpt: Update to 1.1.0.2. 
* gnu/packages/cran.scm (r-afpt): Update to 1.1.0.2.
 2022-06-13 14:21:46 +02:00
Ricardo Wurmus
fce6aeba7e
gnu: r-nbpseq: Update to 0.3.1. 
* gnu/packages/bioconductor.scm (r-nbpseq): Update to 0.3.1.
 2022-06-13 14:21:46 +02:00
Ricardo Wurmus
37378829bc
gnu: r-restfulr: Update to 0.0.14. 
* gnu/packages/bioconductor.scm (r-restfulr): Update to 0.0.14.
 2022-06-13 14:21:42 +02:00
Ricardo Wurmus
7846896156
gnu: Add js-mathjax-for-r-mathjaxr. 
* gnu/packages/patches/mathjax-3.1.2-no-a11y.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/javascript.scm (js-mathjax-for-r-mathjaxr): New variable.
 2022-06-13 12:43:31 +02:00
Lars-Dominik Braun
97ebfc8f5c
gnu: python-asyncssh: Update to 2.11.0. 
* gnu/packages/ssh.scm (python-asyncssh)[version]: Update to 2.11.0.
[propagated-inputs]: Add python-typing-extensions.
[native-inputs]: Add python-fido2, python-aiofiles, netcat and
python-pytest.
[arguments]: Disable netcat autodetection. Replace 'check with call
to pytest.
 2022-06-13 12:30:17 +02:00
Artyom V. Poptsov
b40761ca9d
gnu: Add python-langcodes. 
* gnu/packages/python-xyz.scm (python-langcodes): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-13 12:27:35 +02:00
terramorpha
fcad622648
services: guix: Generalize extensions. 
* gnu/services/base.scm (<guix-extension>): New record type.
(guix-extension-merge): New procedure.
(guix-service-type): Honor extensions.
* doc/guix.texi (Base Services): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-13 12:27:35 +02:00
Ludovic Courtès
8918ce6d16
gnu: racket: Avoid use of (ice-9 exceptions). 
Fixes <https://issues.guix.gnu.org/54546>.
Reported by Giovanni Biscuolo <g@xelera.eu>
and Michael Chirillo <michael.a.chirillo@gmail.com>.

* gnu/packages/racket.scm (racket): Rewrite in terms of SRFI-34/35
instead of (ice-9 exceptions).
 2022-06-13 12:27:34 +02:00
Ludovic Courtès
2a2856d5cc
challenge: Actually delete nars that have been extracted. 
Fixes <https://issues.guix.gnu.org/55809>.
Reported by Vagrant Cascadian <vagrant@reproducible-builds.org>.

* guix/scripts/challenge.scm (make-directory-writable): New procedure.
(call-with-mismatches)[restore-file*]: New procedure.
Use it instead of 'restore-file'.
 2022-06-13 12:27:34 +02:00
Guillaume Le Vaillant
c318f4fcb1
gnu: txr: Update to 277. 
* gnu/packages/lisp.scm (txr): Update to 277.
  [inputs]: Add zlib.
 2022-06-13 11:06:57 +02:00
Ludovic Courtès
6aa457fed1
Merge branch 'staging' 2022-06-13 08:57:51 +02:00
Marius Bakke
d4482e9a9e
gnu: ungoogled-chromium: Update to 102.0.5005.115-1. 
* gnu/packages/chromium.scm (%chromium-version): Set to 102.0.5005.115.
(%ungoogled-revision): Set to 1.
(%ungoogled-origin, ungoogled-chromium): Update hash.
 2022-06-13 00:44:12 +02:00
Marius Bakke
bcd9866eb4
gnu: LLVM, Clang, LLD: Update to 14.0.5. 
* gnu/packages/llvm.scm (llvm-14, clang-14, lld-14): Update to 14.0.5.
(%llvm-monorepo-hashes, %llvm-patches): Adjust accordingly.
 2022-06-13 00:44:12 +02:00
Marius Bakke
d3d00b1b4f
gnu: uBlock Origin: Update to 1.43.0. 
* gnu/packages/browser-extensions.scm (ublock-origin): Update to 1.43.0.
 2022-06-13 00:44:12 +02:00
Ricardo Wurmus
0006a9a83a
gnu: Add r-deconvr. 
* gnu/packages/bioconductor.scm (r-deconvr): New variable.
 2022-06-12 22:51:23 +02:00
Ricardo Wurmus
eec1724ea6
gnu: Add r-rsq. 
* gnu/packages/cran.scm (r-rsq): New variable.
 2022-06-12 22:51:23 +02:00
Ludovic Courtès
622545de6c
Merge branch 'master' into staging 2022-06-12 22:49:47 +02:00
jgart
9c036f2dfb
gnu: Add emacs-corfu-doc-terminal. 
* gnu/packages/emacs-xyz.scm (emacs-corfu-doc-terminal): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-06-12 13:19:24 +02:00
jgart
a473d74ff1
gnu: Add emacs-corfu-terminal. 
* gnu/packages/emacs-xyz.scm (emacs-corfu-terminal): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-06-12 13:19:23 +02:00
Efraim Flashner
e22b55f0b9
gnu: llvm-14: Fix configure-flags for cross-compiling. 
* gnu/packages/llvm.scm (llvm-14)[arguments]: Fix syntax error in
configure-flags when cross-compiling llvm.
 2022-06-12 13:50:47 +03:00
Efraim Flashner
3cbef19a90
gnu: zig: Limit to 64bit systems. 
* gnu/packages/zig.scm (zig)[supported-systems]: New field.
 2022-06-12 13:50:47 +03:00
Efraim Flashner
2a34333d0c
guix: packages: Add %32bit-supported-systems, %64bit-supported-systems. 
* guix/packages.scm (%32bit-supported-systems,
%64bit-supported-systems): New variables.
(%supported-systems): Rewrite using %32bit-supported-systems,
%64bit-supported-systems.
 2022-06-12 13:50:43 +03:00
Ricardo Wurmus
541823b318
gnu: r-hdf5array: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.24.1.
 2022-06-12 11:16:30 +02:00
Ricardo Wurmus
a12ec47cbd
gnu: r-universalmotif: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.14.1.
 2022-06-12 11:16:30 +02:00
Ricardo Wurmus
a76b657d93
gnu: r-rsubread: Update to 2.10.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.2.
 2022-06-12 11:16:30 +02:00
Ricardo Wurmus
41435e0e1c
gnu: r-clusterprofiler: Update to 4.4.2. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.2.
 2022-06-12 11:16:29 +02:00
Ricardo Wurmus
640b45d73c
gnu: r-monocle: Update to 2.24.1. 
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.24.1.
 2022-06-12 11:16:29 +02:00
Ricardo Wurmus
8ed8c8b8da
gnu: r-chippeakanno: Update to 3.30.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.30.1.
 2022-06-12 11:16:29 +02:00
Ricardo Wurmus
46aab4d33d
gnu: r-zellkonverter: Update to 1.6.2. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.2.
 2022-06-12 11:16:28 +02:00
Ricardo Wurmus
7a344aa9e2
gnu: r-keggrest: Update to 1.36.2. 
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.2.
 2022-06-12 11:16:28 +02:00
Ricardo Wurmus
1ecac84c73
gnu: r-genomicfeatures: Update to 1.48.3. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.3.
 2022-06-12 11:16:28 +02:00
Ricardo Wurmus
15e26f97d9
gnu: r-biocparallel: Update to 1.30.3. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.30.3.
[propagated-inputs]: Add r-codetools.
 2022-06-12 11:16:28 +02:00
Ricardo Wurmus
f5899fe58b
gnu: r-deepsnv: Update to 1.42.1. 
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.42.1.
 2022-06-12 11:16:23 +02:00
Julien Lepiller
965d54e344
gnu: java-plexus-component-metadata: Fix package. 
* gnu/packages/java.scm (java-plexus-component-metadata): Apply fix for
  newer jdom.
 2022-06-12 09:07:17 +02:00
Ludovic Courtès
091eb323ba
Merge branch 'master' into staging 2022-06-08 14:53:16 +02:00
jgart via Guix-patches via
0c5299200f
gnu: Add emacs-pyimport. 
* gnu/packages/emacs-xyz.scm (emacs-pyimport): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-06-08 00:14:41 +02:00
Stefan Reichör
7fbf02b854
gnu: Add emacs-toodoo. 
* gnu/packages/emacs-xyz.scm (emacs-toodoo): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-06-08 00:09:04 +02:00
Thomas Albers
1ba8c74de3
gnu: Add emacs-opencl-mode. 
* gnu/packages/emacs-xyz.scm (emacs-opencl-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2022-06-08 00:02:53 +02:00
Ludovic Courtès
05fef7bfc6
gnu: timescaledb: Adjust test preparation to PostgreSQL 13.6. 
The previous method of making a union with symlinks would work with 13.4
but not with 13.6, which has an extra 'canonicalize_path' call in
'find_my_exec'.

* gnu/packages/databases.scm (timescaledb)[arguments]: In
'prepare-tests', pass #:symlink argument to 'union-build'.
 2022-06-07 23:58:16 +02:00
Ludovic Courtès
b422687cbd
gnu: postgresql@10: Fix manual compilation. 
This is a followup to f0227a18c2.

* gnu/packages/databases.scm (postgresql-10)[native-inputs]: New field.
 2022-06-05 17:00:18 +02:00
Ludovic Courtès
5035be651a
gnu: docbook-sgml: Add 4.2. 
* gnu/packages/docbook.scm (docbook-sgml-4.2, docbook-sgml-4.1): New
variables.
(docbook-sgml): Make an alias to 'docbook-sgml-4.1'.
 2022-06-05 17:00:18 +02:00