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114120 Commits

Author SHA1 Message Date
Ricardo Wurmus 2aa8f2901a gnu: r-paws-customer-engagement: Update to 0.5.0. 
* gnu/packages/cran.scm (r-paws-customer-engagement): Update to 0.5.0.

Change-Id: Ibcde22d17c635d8bfed08bc0464d58be2e87646d
 2024-01-11 11:45:23 +01:00
Ricardo Wurmus c50cdf204f gnu: r-paws-common: Update to 0.7.0. 
* gnu/packages/cran.scm (r-paws-common): Update to 0.7.0.

Change-Id: I3eef5a808b6b0918ffa6b15a01f9d1937301b352
 2024-01-11 11:45:23 +01:00
Ricardo Wurmus 32ce535353 gnu: r-mlr3: Update to 0.17.2. 
* gnu/packages/cran.scm (r-mlr3): Update to 0.17.2.

Change-Id: I873e6c338e99624750da248083b8c650772dc19d
 2024-01-11 11:45:22 +01:00
Ricardo Wurmus a08a55e6ac gnu: r-stanheaders: Update to 2.32.5. 
* gnu/packages/cran.scm (r-stanheaders): Update to 2.32.5.

Change-Id: Ie2cccf037fe7c63d8b3574b1504b378f444fb6b3
 2024-01-11 11:45:22 +01:00
Ricardo Wurmus 51a6d1dd2f gnu: r-patchwork: Update to 1.2.0. 
* gnu/packages/cran.scm (r-patchwork): Update to 1.2.0.

Change-Id: I10574362f942182b47d29d73747355cec2d7111a
 2024-01-11 11:45:22 +01:00
Ricardo Wurmus 309f042a29 gnu: r-gbm: Update to 2.1.9. 
* gnu/packages/cran.scm (r-gbm): Update to 2.1.9.

Change-Id: I2612b6656545b092e8d3ea17c6cf355f5aa0466f
 2024-01-11 11:45:22 +01:00
Ricardo Wurmus 7ed2a46a3d gnu: r-yulab-utils: Update to 0.1.3. 
* gnu/packages/cran.scm (r-yulab-utils): Update to 0.1.3.

Change-Id: Icac6a3048d7c1f6b2dc007027a2acfb34e927930
 2024-01-11 11:45:21 +01:00
Ricardo Wurmus 3f37d72acb gnu: r-compositions: Update to 2.0-7. 
* gnu/packages/cran.scm (r-compositions): Update to 2.0-7.

Change-Id: I79365ad9f61257a1e8feb4697f51db9615845813
 2024-01-11 11:45:21 +01:00
Ricardo Wurmus 2e7f7b8a2f gnu: r-targets: Update to 1.4.1. 
* gnu/packages/cran.scm (r-targets): Update to 1.4.1.

Change-Id: Ifc7b526b2f0b198875111a17568f40f660a1ac9d
 2024-01-11 11:45:21 +01:00
Ricardo Wurmus ab144d871b gnu: r-tarchetypes: Update to 0.7.11. 
* gnu/packages/cran.scm (r-tarchetypes): Update to 0.7.11.

Change-Id: Ia87abdf6690b3db8e43be009e8948777293f0ead
 2024-01-11 11:45:21 +01:00
Ricardo Wurmus 5a655bab8f gnu: r-writexls: Update to 6.5.0. 
* gnu/packages/cran.scm (r-writexls): Update to 6.5.0.

Change-Id: I148760efa41cc8b4c6762638629f79296e61ca7a
 2024-01-11 11:45:20 +01:00
Ricardo Wurmus 10f25e5e73 gnu: r-ggrepel: Update to 0.9.5. 
* gnu/packages/cran.scm (r-ggrepel): Update to 0.9.5.

Change-Id: Ib87cbfacc9f3fce1d1e4bc0d9cbb0fb467522bfb
 2024-01-11 11:45:20 +01:00
Ricardo Wurmus b6b6465da3 gnu: r-rcpp: Update to 1.0.12. 
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.12.

Change-Id: Ia0e182858d8693d00d646bf4f4f38e064674f5bc
 2024-01-11 11:45:20 +01:00
Ricardo Wurmus 7e9cdd4a0b gnu: r-glue: Update to 1.7.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.7.0.

Change-Id: Ic843c657fe483c677af10b7a98bdb654d0441561
 2024-01-11 11:45:20 +01:00
Ricardo Wurmus 273ce26a8c gnu: r-reprex: Update to 2.1.0. 
* gnu/packages/cran.scm (r-reprex): Update to 2.1.0.

Change-Id: I3c5e7f79cd7b6171ae9ec4562ce8866455f05ae6
 2024-01-11 11:45:19 +01:00
Ricardo Wurmus 16aa6d4fc3 gnu: r-astsa: Update to 2.1. 
* gnu/packages/cran.scm (r-astsa): Update to 2.1.

Change-Id: Ia3ceb05742c9acdd8fbb117f342d526bf7ee1bc1
 2024-01-11 11:45:19 +01:00
Ricardo Wurmus 2383da330d gnu: r-ggpp: Update to 0.5.6. 
* gnu/packages/cran.scm (r-ggpp): Update to 0.5.6.

Change-Id: Ib9a5bb2ff59381f301f481e189a196706cdbb928
 2024-01-11 11:45:19 +01:00
Ricardo Wurmus e007e93b63 gnu: r-zcompositions: Update to 1.5.0-1. 
* gnu/packages/cran.scm (r-zcompositions): Update to 1.5.0-1.

Change-Id: I472ebcf9f2d3f1d401f19b4a67b27bb892249cac
 2024-01-11 11:45:19 +01:00
Ricardo Wurmus 5d855222a4 gnu: r-castor: Update to 1.8.0. 
* gnu/packages/cran.scm (r-castor): Update to 1.8.0.
[propagated-inputs]: Add r-jsonlite.

Change-Id: I00ffcf5cbcd4badf644ec2572421c6df31792670
 2024-01-11 11:45:18 +01:00
Ricardo Wurmus 1f37c81400 gnu: r-rcurl: Update to 1.98-1.14. 
* gnu/packages/statistics.scm (r-rcurl): Update to 1.98-1.14.
[native-inputs]: Move libxml2 from here...
[inputs]: ...to here.

Change-Id: Ib1b3326a997c7f56053715682b43606b3153c140
 2024-01-11 11:44:33 +01:00
Ricardo Wurmus 1f452641c5 gnu: r-rstan: Update to 2.32.5. 
* gnu/packages/cran.scm (r-rstan): Update to 2.32.5.
[properties]: Tell updater to leave tzdata-for-tests.

Change-Id: I8a12fdea4a0197fae1610826be9ccb856c25afb7
 2024-01-11 11:43:51 +01:00
Ricardo Wurmus 10be2ba0e5 gnu: r-topicmodels: Update to 0.2-16. 
* gnu/packages/cran.scm (r-topicmodels): Update to 0.2-16.
[properties]: Tell updater not to remove GSL from inputs.

Change-Id: I7940d546af32240b3a45bc64f7b1b2361ea8bf0f
 2024-01-11 11:32:01 +01:00
Ricardo Wurmus 5e7d139461 gnu: r-rpostgresql: Update to 0.7-6. 
* gnu/packages/cran.scm (r-rpostgresql): Update to  0.7-6.
[properties]: Tell updater not to remove postgresql input.

Change-Id: Id88180f2781022b1554286f4beee85183ff474ac
 2024-01-11 11:18:06 +01:00
Ricardo Wurmus b52234c016 gnu: r-readr: Update to 2.1.5. 
* gnu/packages/statistics.scm (r-readr): Update to 2.1.5.

Change-Id: If3329e6b01db9fb457491ac44cdbbc97b0ec7c7c
 2024-01-11 11:15:18 +01:00
Ricardo Wurmus 6341dddcb9 gnu: python-afdko: Disable failing test. 
* gnu/packages/fontutils.scm (python-afdko)[arguments]: Disable
test_alt_missing_glyph.

Change-Id: I49f9d27f61955fe2bf9dd9d5cf22499e813ff3d0
 2024-01-11 08:09:38 +01:00
Guillaume Le Vaillant f122f2bead gnu: sbcl: Fix riscv build. 
* gnu/packages/patches/sbcl-fix-riscv-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/lisp.scm (sbcl)[source]: Use it.

Change-Id: I63f1b9a7a7b6f3a1961d0a0cb31189b74a60abc3
 2024-01-10 22:57:43 +01:00
Ricardo Wurmus 3bf2465faa gnu: openjdk11: Fix time bomb in ‘GenerateCurrencyData.java’. 
Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f424.

* gnu/packages/java.scm (openjdk11)[source]: Add patch.

Change-Id: I5ff53b8dd90598721a6c3814980c6553013b347c
 2024-01-10 22:26:23 +01:00
Ricardo Wurmus d255944400 gnu: openjdk10: Simplify. 
* gnu/packages/java.scm (openjdk10)[arguments]: Remove trailing #T from build
phase.

Change-Id: Icdb082b250704fe6de3a5e4323f29fa5db8446c7
 2024-01-10 22:10:15 +01:00
Ricardo Wurmus fc891f004a gnu: openjdk10: Fix time bomb in ‘GenerateCurrencyData.java’. 
Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f424.

* gnu/packages/java.scm (openjdk10)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb2.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: I42fc14d305883f672cd6764a0ee6462852e41a5b
 2024-01-10 22:09:49 +01:00
Ricardo Wurmus cf11f07588 gnu: openjdk9: Simplify. 
* gnu/packages/java.scm (openjdk9)[source]: Remove BEGIN.
[arguments]: Delete trailing #T from build phases.

Change-Id: If011dc595c1b9b0d79fd5bb727a8680d1ad4d100
 2024-01-10 21:54:16 +01:00
Ricardo Wurmus db7488a7fb gnu: openjdk9: Fix time bomb in ‘GenerateCurrencyData.java’. 
Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f424.

* gnu/packages/java.scm (openjdk9)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: I45ca1fe5bad922307eba64d46a330a8f233c0f55
 2024-01-10 21:52:33 +01:00
Ricardo Wurmus 6c453e04b8 gnu: python-distributed: Disable breaking test. 
This test times out since the merge of the mesa-updates branch.

* gnu/packages/python-science.scm (python-distributed)[arguments]: Disable
test_tell_workers_when_peers_have_left.

Change-Id: Ib65b971a3a821ea13d36a4be60658ffc366ca6ac
 2024-01-10 20:35:28 +01:00
nafkhamdc c1fda6cf61 gnu: Add r-jaspar2020. 
* gnu/packages/bioconductor.scm (r-jaspar2020): New variable.

Change-Id: I84f0fc2a7defc5d179ffc24aa1f30177cb3b3060
 2024-01-10 18:39:13 +01:00
nafkhamdc feab3943c1 gnu: Add r-dsb. 
* gnu/packages/bioconductor.scm (r-dsb): New variable.

Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd
 2024-01-10 18:39:13 +01:00
nafkhamdc db75afb4c5 gnu: r-signac: Update to 1.12.0-1.8ecdde2. 
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.12.0-1.8ecdde2.

Change-Id: Ib852f7a23768383fc62d60577f2aaa893c509317
 2024-01-10 18:39:13 +01:00
nafkhamdc 2ec29a8c11 gnu: Add r-escape. 
* gnu/packages/bioconductor.scm (r-escape): New variable.

Change-Id: Ia308f9c90fa81c3304f97daa4f56ae4cd722d5cc
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus 6688e9f4bd gnu: Add python-telomerecat. 
* gnu/packages/bioinformatics.scm (python-telomerecat): New variable.

Change-Id: Ice4cd367cab677466630f44f6900fc38e3be350c
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus 16a277e0a9 gnu: Add python-parabam. 
* gnu/packages/bioinformatics.scm (python-parabam): New variable.

Change-Id: I66ccf5fd0647f908f1cefd38f0d92e589a81683b
 2024-01-10 18:39:13 +01:00
Ludovic Courtès 5c0f77f424 gnu: icedtea: Fix time bomb in ‘GenerateCurrencyData.java’. 
Fixes <https://issues.guix.gnu.org/68333>.

* gnu/packages/java.scm (icedtea-7)[drop]: Add optional ‘patches’
parameter and honor it.
[native-inputs]: Add patch for “jdk-drop”.
(icedtea-8): Likewise.
* gnu/packages/patches/jdk-currency-time-bomb.patch,
gnu/packages/patches/jdk-currency-time-bomb2.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.

Change-Id: I3b4cf562ce4bedb87ce0e7c289e431fbb0dbb6f8
 2024-01-10 16:42:03 +01:00
Zheng Junjie a126e8120d gnu: mesa: Fix cross-compilation. 
* gnu/packages/gl.scm(mesa)[arguments]<#:phases>: When cross-compiling, force
the use of the cmake method to find llvm.

Change-Id: I27f6f4d9d71028c15588eeade48d3a918c042b9c
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-10 15:29:11 +01:00
Zheng Junjie 6401efb554 gnu: yaml-cpp: Update to 0.8.0. 
* gnu/packages/serialization.scm (yaml-cpp): Update to 0.8.0.

Change-Id: I927111f2d103dbb30ff336b64dd4ab90c22312a0
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-10 15:25:45 +01:00
Guillaume Le Vaillant 749c3e016a Merge branch 'master' into lisp-team 
Change-Id: I6c2ce53e782a00861c3adf01c2505099daef7728
 2024-01-10 14:04:40 +01:00
Andre A. Gomes 537768018e gnu: Add cl-stripe. 
* gnu/packages/lisp-xyz.scm (sbcl-stripe): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: Ideeff671b8577bcfceb241a86624ac26f1d077f7
 2024-01-10 10:53:01 +01:00
Andre A. Gomes d34fe10018 gnu: nyxt: Update to 3.11.0. 
* gnu/packages/web-browsers.scm (nyxt): Update to 3.11.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2024-01-10 10:13:42 +01:00
Andre A. Gomes d8ddf42712 gnu: cl-prompter: Update to 0.1.1-0.7890ed5. 
* gnu/packages/lisp-xyz.scm (sbcl-prompter): Update to 0.1.1-0.7890ed5.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: I65a7d23d4a889c1d7c4821e83b8ea3a56701a5c8
 2024-01-10 10:09:56 +01:00
Maxim Cournoyer c5fb46685f gnu: jami-docs: Update to 0.0.0-2.a48997d. 
* gnu/packages/jami.scm (jami-docs): Update to 0.0.0-2.a48997d.

Change-Id: I0c6ee456dec6251a66d1566c855069f3ecf2e44e
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer 8237f4e997 gnu: jami: Update to 20231222.2. 
* gnu/packages/jami.scm (%jami-version): Rename to...
(%jami-nightly-version): ... this.  Update to 20231222.2.
(%jami-daemon-commit): New variable.
(%jami-sources): Delete variable.
(libjami) Adjust source to use %jami-nightly-version, %jami-daemon-commit.
[source]: Fetch from git.  Apply libjami-ac-config-files.patch.
[arguments] <make-flags>: Skip ut_media_player test.
<phases>: Add extend-scheduler-test-timeout and extend-scheduler-test-timeout
phases.
[inputs]: Replace dbus-c++ with sdbus-c++.
Add dhtnet.  Replace libgit2 with libgit2-1.6.
(jami): Set version to %jami-nightly-version.
[source]: Fetch from git.  Apply new jami-qml-tests-discovery.patch,
jami-skip-tests-requiring-internet.patch and jami-unbundle-dependencies.patch
patches.
[arguments] <configure-flags>: Add -DWITH_DAEMON_SUBMODULE=OFF.
<phases>: Delete change-directory/maybe.
Adjust check phase.  Add fake-x11-environment,
copy-3rdparty-source-dependencies and disable-problematic-tests phases.
[inputs]: Add md4c and tidy-html.
* gnu/packages/patches/jami-qml-tests-discovery.patch: New file.
* gnu/packages/patches/libjami-ac-config-files.patch: Likewise.
* gnu/packages/patches/jami-skip-tests-requiring-internet.patch: Likewise.
* gnu/packages/patches/jami-unbundle-dependencies.patch: Likewise.
* gnu/packages/patches/jami-libjami-headers-search.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/patches/jami-disable-integration-tests.patch: Adjust patch.

Series-changes: 2
 - Update Jami to latest nightly version (20231222.2)

Change-Id: If30f1178bdfa29c4ea3e54dbb7997e360788adae
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer d9c9b97e93 gnu: Add sortfilterproxymodel. 
* gnu/packages/jami.scm (sortfilterproxymodel): New variable.

Change-Id: I7c46fce26d5fcdc98e8646e65dd119155a8b9287
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer de002b93db gnu: ffmpeg-jami: Relocate to (gnu packages video). 
To avoid Guile module dependency cycles, inherited packages must be defined in
the same module.  Use this opportunity to simplify the patches applying
mechanism, versioning custom patches the same as for other packages.

* gnu/packages/patches/ffmpeg-jami-change-RTCP-ratio.patch: New file.
* gnu/packages/patches/ffmpeg-jami-rtp_ext_abs_send_time.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusdec-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-reload-packet-loss-at-encode.patch:
Likewise.
* gnu/packages/patches/ffmpeg-jami-remove-mjpeg-log.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-screen-sharing-x11-fix.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Register them.
* gnu/packages/jami.scm (jami-apply-custom-patches): Delete procedure.
(%ffmpeg-default-configure-flags): Delete variable.
(ffmpeg-compose-configure-flags): Delete procedure.
(ffmpeg-jami): Move to...
* gnu/packages/video.scm (ffmpeg-jami): ... here.  Apply patches to origin and
repatriate configure flags.

Change-Id: Id374fae18240cd76b224915d80b61422635ccb77
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer 5a38120c67 gnu: ffmpeg-jami: Update configure flags. 
* gnu/packages/jami.scm (%ffmpeg-default-configure-flags): Add new flags.

Change-Id: I1bac70e7b0ec58c46348a7138f7260b40cdf79f8
 2024-01-09 22:10:12 -05:00