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Author SHA1 Message Date
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 a252ab6f88
gnu: Fix patch location. 
This is a follow-up to commit db7488a7fb.

* gnu/local.mk (dist_patch_DATA): Restore "packages/" prefix.

Change-Id: I1f8e420e75c3f4e1927dac935c2de337fd1306eb
 2024-01-10 22:07:57 +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 e541f9593f
Authorize Oleg (Sharlatan)'s key. 
* .guix-authorizations (sharlatan): Register PGP key fingerprint.

Change-Id: I0d20e50a37971237721964852a404c5cf136f0be
 2024-01-09 23:08:17 -05:00
Maxim Cournoyer 58ab25a2ce
tests: telephony: Fix typo. 
* gnu/tests/telephony.scm: Fix typo.

Series-to: 65371@debbugs.gnu.org
Series-postfix: telephony-team
Series-version: 2

Change-Id: I3eb048b8cdd1335c45ffb61b08425a18a2e7a4b2
 2024-01-09 22:10:14 -05:00
Wojtek Kosior 693a4785be
tests: telephony: Fix VPATH builds. 
* gnu/tests/telephony.scm (%jami-account-content-sexp): New variable.  Compute
its value with `read` instead of using `include`.
* gnu/tests/data/jami-dummy-account.dat (%jami-account-content-sexp): Remove
variable.  Make the file contain just the S-expression.

Change-Id: I8d37aaf7b739f5f39715bfb8a9b8c9536385fd09
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2024-01-09 22:10:13 -05:00
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
Maxim Cournoyer 202b16e31a
gnu: pjproject-jami: Update and relocate. 
* gnu/packages/jami.scm (pjproject-jami): Move to...
* gnu/packages/telephony.scm (pjproject-jami): ... here.  Update to latest
commit.
[arguments]: Use same configure flags as done in Jami/DhtNet projects.

Change-Id: I638364ebc94f17762ee072311b5fe439b7c6f837
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer 88f294cc14
gnu: Add dhtnet. 
* gnu/packages/networking.scm (dhtnet): New variable.

Change-Id: I91cc3541f476c8614be35b1ae7cb1740690f685a
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer 79bd3c685f
gnu: opendht: Update to 3.1.7. 
* gnu/packages/networking.scm (opendht): Update to 3.1.7.
[arguments]: Add a new relax-test-timeouts phase.

Change-Id: Ida7fe021599e9c469e49f6540a908e80b7264241
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer edb03ceb60
gnu: msgpack: Deprecate with msgpack-c. 
* gnu/packages/serialization.scm (msgpack-c): New variable.
(msgpack-cxx): New variable.
(msgpack): Rename to...
(msgpack-3): ... this, and inherit from msgpack-c.
* gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c
phase.
[inputs]: Replace msgpack with msgpack-c.
* gnu/packages/terminals.scm (tmate)
[inputs]: Replace msgpack with msgpack-3.
* gnu/packages/networking.scm (opendht)
[propagated-inputs]: Replace msgpack with msgpack-cxx.
* gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer 504b46cd87
gnu: libnatpmp: Update to 20230423-0.6a850fd. 
* gnu/packages/networking.scm (libnatpmp): Update to 20230423-0.6a850fd.
[source]: Fetch from git.
[build-system]: Use cmake-build-system.
[arguments]: Add patch-build-system and fix-version phases.  Reinstate
configure and check phase, but set #:tests? to #f.  New #:configure-flags
argument.
[native-inputs]: Add which.
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer 0860b612f2
gnu: restinio: Update to 0.7.1. 
* gnu/packages/networking.scm (restinio): Update to 0.7.1.
[arguments] <configure-flags>: Remove RESTINIO_FIND_DEPS,
RESTINIO_USE_EXTERNAL_HTTP_PARSER and RESTINIO_USE_EXTERNAL_SOBJECTIZER
configure flags.  Add -DRESTINIO_DEP_LLHTTP=system, -DRESTINIO_DEP_FMT=system,
-DRESTINIO_DEP_EXPECTED_LITE=system and -DRESTINIO_WITH_SOBJECTIZER=OFF.
<phases>: Add use-system-catch2.
[native-inputs]: Remove clara.  Replace catch2 with catch2-3.
[propagated-inputs]: Replace http-parser with llhttp.
(restinio-0.6): New variable.
(opendht) [propagated-inputs]: Replace restinio with restinio-0.6.

Change-Id: Id69fde5e2c476d7e44b8dd6e065c489314707c31
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer 6f20c8df0e
gnu: Add xdiff. 
* gnu/packages/version-control.scm (xdiff): New variable.
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer 39bd088e75
gnu: Add llhttp. 
* gnu/packages/web.scm (llhttp): New variable.

Change-Id: I3c0475ff6d86a16f51d8870577808ce97ee66a92
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer 0ec349078f
gnu: Add expected-lite. 
* gnu/packages/cpp.scm (expected-lite): New variable.

Change-Id: I5a21dd631e1f2a3c97b920efcdca69f2537b42da
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer 45d07a0b01
gnu: catch2-3: Update to 3.5.1. 
* gnu/packages/check.scm (catch2-3.3): Rename to...
(catch2-3): ... this.  Update to 3.5.1.
* gnu/packages/logging.scm (spdlog) [native-inputs]: Rename catch2-3.3 to
catch2-3.
* gnu/packages/potassco.scm (clingo) [inputs]: Likewise.

Change-Id: Ied7724597ff4c6371dc4fedc10452ae870d23933
 2024-01-09 22:10:10 -05:00
Maxim Cournoyer 1e35c18c86
gnu: asio: Update to 1.28.0. 
* gnu/packages/networking.scm (asio): Update to 1.28.0.

Change-Id: I517fb9c6c52c5b5e5c41c5760c06eca6750d3765
 2024-01-09 22:10:10 -05:00
Maxim Cournoyer 9e9e373751
gnu: libnatpmp: Update home page. 
* gnu/packages/networking.scm (libnatpmp) [home-page]: Update.
 2024-01-09 22:10:10 -05:00