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Author SHA1 Message Date
Ricardo Wurmus
40735701a8
gnu: r-singler: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
2a71a7b961
gnu: r-s4vectors: Update to 0.32.4. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.4.
 2022-04-14 11:29:40 +02:00
Ricardo Wurmus
51ddaf48e8
gnu: r-experimenthub: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
c9e925d444
gnu: r-universalmotif: Update to 1.12.4. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.4.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
eadb1f53e9
gnu: r-variancepartition: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.1.
[propagated-inputs]: Add r-aod, r-rdpack, and r-rhpcblasctl.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
9950ed71fc
gnu: r-cytolib: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.2.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
0861d4fff5
gnu: r-rsubread: Update to 2.8.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.2.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
cb30400097
gnu: r-ropls: Update to 1.26.4. 
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.4.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
0c478f50f2
gnu: r-birewire: Update to 3.26.5. 
* gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.5.
[propagated-inputs]: Remove r-tsne; add r-rtsne.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
b446be46ba
gnu: r-biocfilecache: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
5576a98b6a
gnu: r-massspecwavelet: Update to 1.60.1. 
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.60.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
6f2d89fb40
gnu: r-atacseqqc: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.18.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
88ed3fc340
gnu: r-genomicscores: Update to 2.6.1. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.6.1.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
e129f579f5
gnu: r-clusterprofiler: Update to 4.2.2. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.2.2.
 2022-04-14 11:29:39 +02:00
Ricardo Wurmus
21037105ac
gnu: r-enrichplot: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.14.2.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
f8a38e8380
gnu: r-geoquery: Update to 2.62.2. 
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.62.2.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
fe6a8b4338
gnu: r-karyoploter: Update to 1.20.3. 
* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.20.3.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
84c0ec875c
gnu: r-destiny: Update to 3.8.1. 
* gnu/packages/bioconductor.scm (r-destiny): Update to 3.8.1.
[native-inputs]: Add r-knitr.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
d625f52bca
gnu: r-chippeakanno: Update to 3.28.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.28.1.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
f7d7ba3613
gnu: r-diffbind: Update to 3.4.11. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.4.11.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
cf46f2c331
gnu: r-systempiper: Update to 2.0.8. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.0.8.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
43053e08da
gnu: r-stringdb: Update to 2.6.5. 
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.6.5.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
a3ddba54fd
gnu: r-slingshot: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.2.1.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
6dad28d221
gnu: r-rhdf5: Update to 2.38.1. 
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.38.1.
 2022-04-14 11:29:38 +02:00
Ricardo Wurmus
30027f837d
gnu: r-regioner: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.26.1.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
06d13cf4b0
gnu: r-msnbase: Update to 2.20.4. 
* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.20.4.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
e586613384
gnu: r-mutationalpatterns: Update to 3.4.1. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.4.1.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
78f7de977a
gnu: r-limma: Update to 3.50.3. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.50.3.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
68c1c989b6
gnu: r-genomicfeatures: Update to 1.46.5. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.46.5.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
455636fecd
gnu: r-genomeinfodb: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.30.1.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
9000c8acc2
gnu: r-ensembldb: Update to 2.18.4. 
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.18.4.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
e4816bcaed
gnu: r-biomart: Update to 2.50.3. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.3.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
ac67d0a467
gnu: r-annotationhub: Update to 3.2.2. 
* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.2.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
4353404e21
gnu: Add r-aod. 
* gnu/packages/cran.scm (r-aod): New variable.
 2022-04-14 11:29:37 +02:00
Ricardo Wurmus
f6bc281cd7
gnu: r-tricycle: Move out of annotation packages. 
* gnu/packages/bioconductor.scm (r-tricycle): Move definition out of the
section containing annotation packages.
 2022-04-14 06:55:20 +02:00
Efraim Flashner
5743d50583
gnu: gama: Update to 2.18. 
* gnu/packages/gps.scm (gama): Update to 2.18.
 2022-04-13 23:53:18 +03:00
Eric Bavier
b5e32d9620
gnu: idris: Fixes test failure. 
* gnu/packages/patches/idris-test-ffi008.patch: New file.
* gnu/packages/idris.scm (source): Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2022-04-13 09:48:04 -05:00
Leo Famulari
8d82d817bc
gnu: nginx: Update to 1.21.6. 
* gnu/packages/web.scm (nginx): Update to 1.21.6.
(nginx-documentation): Update to 1.21.6-2829-1ecf0e0526da.
 2022-04-13 10:30:21 -04:00
Foo Chuan Wei
4996104189
gnu: Add cl-simple-routes. 
* gnu/packages/lisp-xyz.scm (cl-simple-routes, ecl-simple-routes,
  sbcl-simple-routes): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-13 13:42:35 +02:00
Ricardo Wurmus
fc89b50b7b
gnu: awscli: Do not propagate inputs. 
* gnu/packages/python-web.scm (awscli)[propagated-inputs]: Move all inputs
from here...
[inputs]: ...to here.
 2022-04-13 09:26:47 +02:00
Ricardo Wurmus
21cd4c704e
gnu: awscli: Use PyYAML 6. 
This should be fine because all uses of yaml.load supply the now mandatory
loader argument.

* gnu/packages/python-web.scm (awscli)[arguments]: Add phase
'use-recent-pyyaml.
[propagated-inputs]: Replace python-pyyaml-for-awscli with python-pyyaml.
 2022-04-13 09:25:13 +02:00
Maxim Cournoyer
7bd5394bf8
gnu: wpewebkit: Update to 2.36.0. 
* gnu/packages/webkit.scm (%webkit-version): New variable.
(wpewebkit): Update to 2.36.0, rewriting package to inherit from webkitgtk.
(webkitgtk)[source]: Use %webkit-version, and adjust definition to match that
of wpewebkit.
 2022-04-12 23:18:12 -04:00
Maxim Cournoyer
4ec7aac483
gnu: webkitgtk: Update to 2.36.0 and enable extra features. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.36.0.
[source]: Remove the webkitgtk-bind-all-fonts.patch and
webkitgtk-canonicalize-paths.patch patches.
[arguments]: Use gexp.
[tests?]: Update comment.
[build-type]: Add explanatory comment.
[configure-flags]: Enable gamepad support,  remove nonexistent
USE_SYSTEMD option and enable mini-browser.
[phases]{do-not-disable-new-dtags}: New phase.
{help-cmake-find-elogind}: Likewise.
{patch-gtk-doc-scan}: Simplify to avoid for-each.  Locate docbookx.dtd via
search-input-file.
{embed-absolute-wpebackend-reference}: Use search-input-file.
[native-inputs]: Use new style.
[inputs]: Likewise.  Add elogind and libmanette.
[description]: Adjust indentation.
(webkitgtk-with-libsoup2): Re-format comment, fixing spacing.
[configure-flags]: Use gexp.
[propagated-inputs]: Use modify-inputs to replace libsoup with
libsoup-minimal-2.
* gnu/packages/patches/webkitgtk-bind-all-fonts.patch: Delete file.
* gnu/packages/patches/webkitgtk-canonicalize-paths.patch: Likewise.
* gnu/local.mk: De-register them.
 2022-04-12 23:18:12 -04:00
Maxim Cournoyer
322e23e600
gnu: woff2: Propagate brotli. 
* gnu/packages/fontutils.scm (woff2)[phases]: Delete trailing #t.
[inputs]: Move brotli to ...
[propagated-inputs]: ... here.
 2022-04-12 23:18:12 -04:00
Leo Famulari
a62f0f6d85
gnu: linux-libre 4.9: Update to 4.9.310. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.310.
(linux-libre-4.9-pristine-source): Update hash.
 2022-04-12 22:39:16 -04:00
terramorpha
950f3e4f98
gnu: Add smtpmail. 
* gnu/packages/mail.scm (smtpmail): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-04-12 23:55:14 +02:00
Olivier Dion
1885f8035a
gnu: Add librseq. 
* gnu/packages/engineering.scm (librseq): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-04-12 23:42:40 +02:00
Leo Nikkilä
e1f0c88ea2
shepherd: Add #:supplementary-groups. 
To support the argument introduced in Shepherd 0.9.0 when defining
container-bound services.

* gnu/build/shepherd.scm (exec-command*)
(make-forkexec-constructor/container): Add '#:supplementary-groups'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-04-12 23:40:44 +02:00
Andrew Tropin
8805c7eab1
home: shepherd: Prevent launching the second instance. 
Fixes <https://issues.guix.gnu.org/54545>.

* gnu/home/services/shepherd.scm (launch-shepherd-gexp): Launch shepherd
if and only if its socket file does not already exist.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-04-12 23:30:09 +02:00
Ricardo Wurmus
6a69e41c17
gnu: python-moto: Update to 3.1.4. 
* gnu/packages/python-xyz.scm (python-moto): Update to 3.1.4.
[arguments]: Adjust disabled tests.
[native-inputs]: Remove python-parameterized; add python-graphql-core.
[propagated-inputs]: Remove python-boto, python-idna, python-mock, and
python-six; add python-importlib-metadata and python-markupsafe.
 2022-04-12 23:12:22 +02:00