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Author SHA1 Message Date
Ricardo Wurmus
c11b92a8aa
gnu: Add r-singlet. 
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
 2023-06-02 21:18:26 +02:00
Ricardo Wurmus
76eda50717
gnu: Add r-rcppml/devel. 
* gnu/packages/machine-learning.scm (r-rcppml/devel): New variable.
 2023-06-02 19:54:27 +02:00
Navid Afkhami
f09944461f
gnu: Add python-cell2cell. 
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-02 19:54:27 +02:00
Ludovic Courtès
69dfdb7bd1
environment: Fix unbound-variable bug with '--symlink'. 
Fixes <https://issues.guix.gnu.org/63845>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.

* guix/scripts/environment.scm (launch-environment/container): Reference
'evaluate-populate-directive' before calling 'call-with-container'.
 2023-06-02 16:57:17 +02:00
Jean-Pierre De Jesus DIAZ
7469d9c106
gnu: Add coccinelle. 
* gnu/packages/patchutils.scm (coccinelle): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:41 +02:00
Jean-Pierre De Jesus DIAZ
5461ff1e54
gnu: Add ocaml-pyml. 
* gnu/packages/ocaml.ml (ocaml-pyml): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:39 +02:00
Jean-Pierre De Jesus DIAZ
4017fae4e0
gnu: Add ocaml-stdcompat. 
* gnu/packages/ocaml.scm (ocaml-stdcompat): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:34 +02:00
Jean-Pierre De Jesus DIAZ
bb7f978e60
gnu: Add ocaml-parmap. 
* gnu/packages/ocaml.scm (ocaml-parmap): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:29 +02:00
Greg Hogan
d756564db5
gnu: Add tmux-plugin-mem-cpu-load. 
* gnu/packages/tmux.scm (tmux-plugin-mem-cpu-load): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:25:44 +02:00
Brian Cully
dbbc7e9461
services: Error in MODIFY-SERVICES when services don't exist 
This patch causes MODIFY-SERVICES to raise an error if a reference is made to
a service which isn't in its service list. This it to help users notice if
they have an invalid rule, which is currently silently ignored.

* gnu/services.scm (%delete-service):  new procedure
(%apply-clauses): new syntax rule
(%modify-service): remove syntax rule

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:23:03 +02:00
Brian Cully
ae707b62e7
tests: Check for service existence in MODIFY-SERVICES 
* tests/services.scm ("modify-services: delete non-existing service")
("modify-services: change value for non-existing service"): New tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:16:12 +02:00
Brian Cully
09fcf261c1
tests: Add tests for MODIFY-SERVICES procedure 
* tests/services.scm ("modify-services: do nothing")
("modify-services: delete service")
("modify-services: change value"): New tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:16:07 +02:00
Ludovic Courtès
decf5fed65
gnu: cuirass: Update to b825967. 
Fixes a regression introduced with the guile-squee update in
63e5975cac (which brings
non-blocking/asynchronous 'exec-query') whereby Cuirass would call
'exec-query' whereby another command was being processed.

* gnu/packages/ci.scm (cuirass): Update to b825967.
 2023-06-02 16:13:35 +02:00
Greg Hogan
7d7dcc3600
gnu: python-ipython-documentation: Update dependencies. 
* gnu/packages/python-xyz.scm (python-ipython-documentation)
[native-inputs]: Add python-ipykernel.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:43 +02:00
Greg Hogan
f1af4fbeec
gnu: python-ipython-documentation: Remove patches. 
* gnu/packages/python-xyz.scm (python-ipython-documentation)[source]:
Remove upstreamed patches.
* gnu/packages/patches/python-ipython-documentation-chars.patch,
gnu/packages/patches/python-ipython-documentation-repro.patch:
Delete files.
* gnu/local.mk: Remove files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:39 +02:00
Greg Hogan
53c47c4f28
gnu: python-docrepr: Fix tests. 
* gnu/packages/patches/python-docrepr-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/documentation.scm (python-docrepr)[source]<patches>: Use
  it here.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:28 +02:00
Denis 'GNUtoo' Carikli
c3f9445144
gnu: cpp-mustache: Update to 5.0 to fix build. 
* gnu/packages/cpp.scm (cpp-mustache): Update to 5.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:05:25 +02:00
Ludovic Courtès
48c7e71cd7
gnu: gcc-boot0: Do not use 'coreutils-boot0' on GNU/Hurd. 
Fixes <https://issues.guix.gnu.org/63789>.
Reported by Janneke Nieuwenhuizen <janneke@gnu.org>.

* gnu/packages/commencement.scm (gcc-boot0)[source]: Use
'%bootstrap-coreutils&co' when on GNU/Hurd.
 2023-06-02 15:47:28 +02:00
Ludovic Courtès
0a8f53d61b
read-print: Add 'package/inherit' special form. 
* guix/read-print.scm (%special-forms): Add 'package/inherit'.
 2023-06-02 15:47:27 +02:00
Ludovic Courtès
acef4cecf9
ci: Reify the timestamps of evaluations. 
* guix/ci.scm (<evaluation>)[start-time, checkout-time,
completion-time]: New fields.
 2023-06-02 15:47:27 +02:00
Arvid Krein
a7d9cd742c
gnu: Add pcsc-cyberjack. 
* gnu/packages/security-token.scm (pcsc-cyberjack): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-06-02 19:24:21 +08:00
Peter Polidoro
7307b05abd
gnu: kicad: Update to 7.0.5. 
* gnu/packages/engineering.scm (kicad): Update to 7.0.5.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-06-02 13:13:23 +02:00
Ricardo Wurmus
41b6f213c1
gnu: r-tcgabiolinks: Update to 2.28.2. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.2.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
6d194c1ba8
gnu: r-biocthis: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
302b916b2b
gnu: r-basilisk-utils: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
6d54b5cc23
gnu: r-megadepth: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.10.0.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
0beada7cb0
gnu: r-s4arrays: Update to 1.0.4. 
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.4.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
f06bd3e740
gnu: r-biocviews: Update to 1.68.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.68.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
438d2b80f7
gnu: r-rsubread: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.14.2.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus
08e1e36942
gnu: r-treeio: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.24.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
93350d89a2
gnu: r-apeglm: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.22.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
e6faedd0c9
gnu: r-zellkonverter: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.10.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
071c31583b
gnu: r-scmap: Update to 1.22.3. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
2a35673351
gnu: r-limma: Update to 3.56.1. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
21342c3bcf
gnu: r-edger: Update to 3.42.4. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.4.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
15ffd4014e
gnu: r-biostrings: Update to 2.68.1. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.68.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
9e9e21dc46
gnu: r-biocparallel: Update to 1.34.2. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
6693480b46
gnu: r-densvis: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
3b20a9e600
gnu: r-delayedarray: Update to 0.26.3. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
f947aa3ac9
gnu: r-dearseq: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
ca0c012d4a
gnu: r-bambu: Update to 3.2.3. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus
83bd8d51c3
gnu: r-alpine: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-alpine): Update to 1.26.0.
 2023-06-02 12:53:13 +02:00
Ricardo Wurmus
f4639380ae
gnu: r-anvil: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.3.
 2023-06-02 12:53:13 +02:00
Ricardo Wurmus
c2f0ce73a7
import/cran: string->license: Add another case for GPLv3+. 
* guix/import/cran.scm (string->license): Translate "GPL (>=3)" to gpl3+.
 2023-06-02 12:52:22 +02:00
Ricardo Wurmus
4f7efc8db9
gnu: r-biocviews: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them.
 2023-06-02 12:51:15 +02:00
Ricardo Wurmus
52546a4512
gnu: r-biocparallel: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort
them.
 2023-06-02 12:50:47 +02:00
Ricardo Wurmus
cbbb619ddb
import/cran: Libraries should not use CRAN-GUIX-NAME. 
* guix/import/cran.scm (source-dir->dependencies): Do not use CRAN-GUIX-NAME
when processing result of NEEDED-LIBRARIES-IN-DIRECTORY.
 2023-06-02 12:49:25 +02:00
Ricardo Wurmus
67183e25ad
import/cran: Also search Makevars file for libraries. 
* guix/import/cran.scm (needed-libraries-in-directory): Look at Makevars in
addition to Makevars.in for libraries.
 2023-06-02 12:48:42 +02:00
Ricardo Wurmus
bb27e3b8b1
gnu: r-dismo: Replace bundled jars. 
Fixes <https://issues.guix.gnu.org/63783>.

* gnu/packages/cran.scm (r-dismo)[source]: Delete bundled jars.
[inputs]: Add java-maxent.
[native-inputs]: Add JDK and zip.
[arguments]: Add phases 'build-jars and 'strip-jar-timestamps.
 2023-06-02 11:34:17 +02:00
Ricardo Wurmus
341b4b2a97
gnu: Add java-maxent. 
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
 2023-06-02 11:34:17 +02:00