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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
Ricardo Wurmus 2c37975fcc
gnu: awscli: Use older version of botocore. 
* gnu/packages/python-web.scm (awscli)[propagated-inputs]: Replace
python-botocore with python-botocore-for-awscli.
 2022-04-12 23:12:22 +02:00
Ricardo Wurmus e8a99abf41
gnu: python-botocore: Update to 1.24.35. 
* gnu/packages/python-xyz.scm (python-botocore): Update to 1.24.35.
 2022-04-12 23:12:22 +02:00
Ricardo Wurmus 8a6c012deb
gnu: python-boto3: Update to 1.21.35. 
* gnu/packages/python-xyz.scm (python-boto3): Update to 1.21.35.
[arguments]: Override 'check phase.
 2022-04-12 23:12:22 +02:00
Ricardo Wurmus 9320410d76
gnu: Add python-botocore-for-awscli. 
* gnu/packages/python-xyz.scm (python-botocore-for-awscli): New variable.
 2022-04-12 23:12:22 +02:00
Ricardo Wurmus 797478f77b
gnu: awscli: Use older pyyaml. 
* gnu/packages/python-web.scm (awscli)[propagated-inputs]: Replace
python-pyyaml with python-pyyaml-for-awscli.
 2022-04-12 23:12:22 +02:00
Ricardo Wurmus 7fcb16e9d4
gnu: Add python-pyyaml-for-awscli. 
* gnu/packages/python-xyz.scm (python-pyyaml-for-awscli): New variable.
 2022-04-12 23:12:22 +02:00
Liliana Marie Prikler 42679e3f81
services: Replace murmur-service-type with mumble-server-service-type. 
* gnu/services/telephony.scm (murmur-configuration, make-murmur-configuration)
(murmur-configuration?, murmur-configuration-package)
(murmur-configuration-user, murmur-configuration-group)
(murmur-configuration-port, murmur-configuration-welcome-text)
(murmur-configuration-server-password)
(murmur-configuration-max-users)
(murmur-configuration-max-user-bandwidth)
(murmur-configuration-database-file)
(murmur-configuration-log-file, murmur-configuration-pid-file)
(murmur-configuration-autoban-attempts)
(murmur-configuration-autoban-timeframe)
(murmur-configuration-autoban-time)
(murmur-configuration-opus-threshold)
(murmur-configuration-channel-nesting-limit)
(murmur-configuration-channelname-regex)
(murmur-configuration-username-regex)
(murmur-configuration-test-message-length)
(murmur-configuration-image-message-length)
(murmur-configuration-cert-required?)
(murmur-configuration-remember-channel?)
(murmur-configuration-allow-html?)
(murmur-configuration-allow-ping?)
(murmur-configuration-bonjour?)
(murmur-configuration-send-version?)
(murmur-configuration-log-days)
(murmur-configuration-obfuscate-ips?)
(murmur-configuration-ssl-cert murmur-configuration-ssl-key)
(murmur-configuration-ssl-dh-params murmur-configuration-ssl-ciphers)
(murmur-configuration-public-registration)
(murmur-configuration-file)
(murmur-public-registration-configuration)
(make-murmur-public-registration-configuration)
(murmur-public-registration-configuration?)
(murmur-public-registration-configuration-name)
(murmur-public-registration-configuration-url)
(murmur-public-registration-configuration-password)
(murmur-public-registration-configuration-hostname)
(murmur-service-type): Add deprecation alias and rename to ...
(mumble-server-configuration, make-mumble-server-configuration)
(mumble-server-configuration?, mumble-server-configuration-package)
(mumble-server-configuration-user, mumble-server-configuration-group)
(mumble-server-configuration-port, mumble-server-configuration-welcome-text)
(mumble-server-configuration-server-password)
(mumble-server-configuration-max-users)
(mumble-server-configuration-max-user-bandwidth)
(mumble-server-configuration-database-file)
(mumble-server-configuration-log-file, mumble-server-configuration-pid-file)
(mumble-server-configuration-autoban-attempts)
(mumble-server-configuration-autoban-timeframe)
(mumble-server-configuration-autoban-time)
(mumble-server-configuration-opus-threshold)
(mumble-server-configuration-channel-nesting-limit)
(mumble-server-configuration-channelname-regex)
(mumble-server-configuration-username-regex)
(mumble-server-configuration-test-message-length)
(mumble-server-configuration-image-message-length)
(mumble-server-configuration-cert-required?)
(mumble-server-configuration-remember-channel?)
(mumble-server-configuration-allow-html?)
(mumble-server-configuration-allow-ping?)
(mumble-server-configuration-bonjour?)
(mumble-server-configuration-send-version?)
(mumble-server-configuration-log-days)
(mumble-server-configuration-obfuscate-ips?)
(mumble-server-configuration-ssl-cert mumble-server-configuration-ssl-key)
(mumble-server-configuration-ssl-dh-params) (mumble-server-configuration-ssl-ciphers)
(mumble-server-configuration-public-registration)
(mumble-server-configuration-file)
(mumble-server-public-registration-configuration)
(make-mumble-server-public-registration-configuration)
(mumble-server-public-registration-configuration?)
(mumble-server-public-registration-configuration-name)
(mumble-server-public-registration-configuration-url)
(mumble-server-public-registration-configuration-password)
(mumble-server-public-registration-configuration-hostname)
(mumble-server-service-type): ... these.
* doc/guix.texi ("Murmur (VoIP server)"): Rename to ...
("Mumble server"): ... this.  Adjust documentation accordingly.
 2022-04-12 20:32:32 +02:00
Liliana Marie Prikler 9ab158a457
guix: Add define-deprecated/public-alias. 
* guix/deprecation.scm (define-deprecated/public-alias): New variable.
 2022-04-12 20:32:32 +02:00
Liliana Marie Prikler 1be7f43756
gnu: libressl: Update to 3.3.6. 
* gnu/packages/tls.scm (libressl): Update to 3.3.6.
 2022-04-12 20:32:31 +02:00
Roman Riabenko b0f477b8a3
gnu: games: Add robotfindskitten. 
* gnu/packages/games.scm (robotfindskitten): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-04-12 20:31:33 +02:00
Ricardo Wurmus 8550976832
gnu: r-rbowtie: Fix build on architectures other than x86_64. 
* gnu/packages/bioconductor.scm (r-rbowtie)[arguments]: Disable use of popcnt
on systems other than x86_64.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus dabd0d793c
gnu: r-rlrsim: Update to 3.1-8. 
* gnu/packages/statistics.scm (r-rlrsim): Update to 3.1-8.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus 59e94c9bee
gnu: r-norm: Update to 1.0-10.0. 
* gnu/packages/statistics.scm (r-norm): Update to 1.0-10.0.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus a12b85175b
gnu: r-puniform: Update to 0.2.5. 
* gnu/packages/statistics.scm (r-puniform): Update to 0.2.5.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus 7b23d24b89
gnu: r-cairo: Update to 1.5-15. 
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-15.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus a5b0f1db21
gnu: r-tsne: Update to 0.1-3.1. 
* gnu/packages/statistics.scm (r-tsne): Update to 0.1-3.1.
 2022-04-12 16:00:01 +02:00
Ricardo Wurmus d3daace423
gnu: r-lme4: Update to 1.1-29. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-29.
 2022-04-12 16:00:01 +02:00