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2024-01-21gnu: Add r-netgsa.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-netgsa): New variable. Change-Id: I79b842854db80bbacdb8ff4c9fccfabdfc04d779
2024-01-21gnu: Add r-glassofast.Ricardo Wurmus
* gnu/packages/cran.scm (r-glassofast): New variable. Change-Id: I6ec7a1f8d4391d7d93f23789f448476b866e4687
2024-01-21gnu: Add r-rcy3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rcy3): New variable. Change-Id: Ia295e8a174f65c8378ae83bdc1dde2877a48ff45
2024-01-21gnu: torbrowser: Add support for language localisation.Clément Lassieur
* gnu/packages/gnuzilla.scm (all-mozilla-locales): Export it. * gnu/packages/tor.scm (%torbrowser-locales, translation-base-browser, translation-tor-browser): New variables. (torbrowser)[arguments]: In ‘setenv’ phase, set MOZ_CHROME_MULTILOCALE. Add ‘copy-firefox-locales’, ‘copy-basebrowser-locales’, ‘copy-torbrowser-locales’ and ‘build-locales’ phases. Change-Id: Ia5b28fa5d885f24140893dc270e57e83b0250c67
2024-01-21gnu: r-cytolib: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.14.1. [source]: Do not unbundle included boost. [arguments]: Remove. [inputs]: Remove boost. Change-Id: Ibe26b9df3f73e67fb9f53676a2c27a5aed714895
2024-01-20gnu: python-pandera: Fix build.Troy Figiel
* gnu/packages/python-science.scm (python-pandera): Fix build. [source]: Delete tests/modin directory. [native-inputs]: Remove python-modin. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-20gnu: python-pandas-stubs: Update to 1.5.3.230321.Troy Figiel
* gnu/packages/python-science.scm (python-pandas-stubs): Update to 1.5.3.230321. [arguments]<#:test-flags>: Ignore tests that require a version of python-pyarrow with ORC integration. [native-inputs]: Add python-odfpy. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-20gnu: xorg-server-xwayland: Update to 23.2.4 [security fixes].Kaelyn Takata
Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886, CVE-2024-0409, and CVE-2024-0408. See the X.Org security advisory <https://lists.x.org/archives/xorg/2024-January/061525.html> for more information. * gnu/packages/xorg.scm (xorg-server-xwayland): Update to 23.2.4. Change-Id: Ie6343d34652ba0caf00940775b5b227dd9bc05bc Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
2024-01-20gnu: xorg-server: Update to 21.1.11 [security fixes].Kaelyn Takata
Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886, CVE-2024-0409, and CVE-2024-0408. See the X.Org security advisory <https://lists.x.org/archives/xorg/2024-January/061525.html> for more information. Copyright line updated as followup to commits 3080abba40c819933d1857abe4abaaa3cf65baab and 158502e40d800407f1bd697dd5dd0437086730bf. * gnu/packages/xorg.scm (xorg-server): Update to 21.1.11. Change-Id: I07cb273e2a504f94f8f26624d26ad79c6e92f109 Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
2024-01-20gnu: gnutls: Update to 3.8.3 [security-fixes].Jack Hill
Fixes CVE-2024-0553 and CVE-2024-0567. gnu/packages/tls.scm (gnutls-3.8.2): Rename to ... (gnutls/fixed): ... this. Update to 3.8.3. (gnutls): Rename replacement to gnutls/fixed. Change-Id: Ic44b3b0481ffd51cdc42a2d71a598f001b43c6f7 Signed-off-by: John Kehayias <john.kehayias@protonmail.com> Co-authored-by: John Kehayias <john.kehayias@protonmail.com>
2024-01-20gnu: Add python-manimpango.Wamm K. D
* gnu/packages/python-xyz.scm (python-manimpango): New variable. Co-authored-by: Troy Figiel <troy@troyfigiel.com> Change-Id: I80effb2412e7c35ddf69c0d3ff6e2f052f282840 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-20gnu: r-org-hs-eg-db: Update to 3.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.18.0. Change-Id: Iaba83a413858a95e81b6488a2f8cde648f0bdeed
2024-01-20gnu: Add r-methylclockdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-methylclockdata): New variable. Change-Id: Id76373a9aec8276dcfd1ec3428d2ce9c81cc51d2
2024-01-20gnu: Add r-experimenthubdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-experimenthubdata): New variable. Change-Id: I5faf26f483898b162bc1f863a4aceb6f46c52c18
2024-01-20gnu: Add r-jaspar2016.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-jaspar2016): New variable. Change-Id: Ib2970791207b426c39bd0226e01107a35fec0bb2
2024-01-20gnu: Add r-genomicstate.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicstate): New variable. Change-Id: I1b86c8e849af7b69b5fa9ea2a0e43b4e3e1850b2
2024-01-20gnu: Add r-shinymeta.Ricardo Wurmus
* gnu/packages/cran.scm (r-shinymeta): New variable. Change-Id: I35e1c032283cdc010e4551c0d33f9d4202d9deee
2024-01-20gnu: Add r-ensdb-hsapiens-v79.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ensdb-hsapiens-v79): New variable. Change-Id: I773615df66194ddb195f013f7000d175ac07d095
2024-01-19gnu: Add rust-rustc-demangle-capi-0.1.Maxim Cournoyer
* gnu/packages/crates-io.scm (rust-rustc-demangle-capi-0.1): New variable. Change-Id: I98afb19ed4bdbcb9107a1ab30af49b055802b8b0 Reviewed-by: Efraim Flashner <efraim@flashner.co.il> Change-Id: Ifeaefa5a377600320c3fd2a637aefaf29707e3b7
2024-01-19gnu: guile-hall: Update to 0.4.1-1.7558ba9.Maxim Cournoyer
* gnu/packages/guile-xyz.scm (guile-hall): Update to 0.4.1-1.7558ba9. [arguments] <modules>: Remove (ice-9 match) and (ice-9 ftw) modules. Add (guix build guile-build-system). <phases>: Use gexps. Streamline hall-wrap-binaries phase. [native-inputs]: Add guile-3.0 and gettext-minimal. [propagated-inputs]: Delete field, moving guile-config to... [inputs]: ... here. Add bash-minimal and guile-lib. Change-Id: Idef796dc3ba9ca3fa4df8114efe91af7c5cf7be0
2024-01-19gnu: reuse: Update to 3.0.1.Maxim Cournoyer
* gnu/packages/license.scm (reuse): Update to 3.0.1. [arguments]: New field. Change-Id: Ibbc5ae8cfa0e0e62b6c64bd90387022e88f9c933
2024-01-19gnu: symengine: Update to 0.11.2.Vinicius Monego
* gnu/packages/algebra.scm (symengine): Update to 0.11.2. Change-Id: I34c24dd8591e306a7740f0a3d51077aceec67fab
2024-01-19gnu: python-metpy: Update to 1.6.1.Vinicius Monego
* gnu/packages/geo.scm (python-metpy): Update to 1.6.1. Change-Id: Id8d8d6db3e31307242e56c494b6dee7c2ffab8f1
2024-01-19gnu: python-deepxde: Update to 1.10.1.Vinicius Monego
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.1. Change-Id: If3515735d4adee8a2f1e9460d6ccb72c6ce26321
2024-01-19gnu: python-mapie: Update to 0.8.2.Vinicius Monego
* gnu/packages/statistics.scm (python-mapie): Update to 0.8.2. Change-Id: I82098caa8ed5d3bf68eec9f374f600d203d6b178
2024-01-19gnu: libngspice: Update to 42.Vinicius Monego
* gnu/packages/engineering.scm (libngspice, ngspice): Update to 42. Change-Id: Ib7b72724f8f46ce376bd6517cb2652c870edcb0d
2024-01-19gnu: darktable: Update to 4.6.0.Vinicius Monego
* gnu/packages/photo.scm (darktable): Update to 4.6.0. Change-Id: Ic64b02e8d191ba91fde1b95b9bcb4321a471dcba
2024-01-19gnu: darktable: Enable more optional features.Vinicius Monego
* gnu/packages/photo.scm (darktable)[inputs]: Add libjxl, portmidi. Change-Id: I7747dfc2e88379a13182590f87514951bdd70e0c
2024-01-19gnu: darktable: Build with GCC.Vinicius Monego
* gnu/packages/photo.scm (darktable)[arguments][#:phases]: Delete the 'prepare-build-environment phase. [native-inputs]: Remove clang. Add gcc-13. Change-Id: Ia0dc1c6a717ccd00cd31d378aa51ce63fbf1806a
2024-01-19gnu: gmic: Update to 3.3.3.Vinicius Monego
gmic was integrated into Krita 5+. * gnu/packages/image-processing.scm (gmic, gmic-qt): Update to 3.3.3. (gmic-qt-krita): Delete variable. Change-Id: I44e33b570bcf3e1df3eba5eb9ede1f333f8a177a
2024-01-19gnu: labplot: Update to 2.10.1.Vinicius Monego
* gnu/packages/kde.scm (labplot): Update to 2.10.1. [source]<origin>: Update URI. Change-Id: I03d24410304fb14daa20f7a75f6947caed63ab84
2024-01-19gnu: python-symengine: Update to 0.11.0.Vinicius Monego
* gnu/packages/python-xyz.scm (python-symengine): Update to 0.11.0. [native-inputs]: Replace python-cython with python-cython-3. Change-Id: Ieab464491e3df6e2bdb5b552cbf48ebf67ff81e4
2024-01-19gnu: Add r-trnadbimport.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-trnadbimport): New variable. Change-Id: I5a232b50c08ef999f691566ccf5c0fbaf0eb21ea
2024-01-19gnu: Add r-trna.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-trna): New variable. Change-Id: Ifce902910fa75ddc471d8a25cc974307c19fd1d0
2024-01-19gnu: Add r-modstrings.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-modstrings): New variable. Change-Id: Ia61816213a7d128ab50a9ae2b2c8879e6ac00499
2024-01-19gnu: Add r-structstrings.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-structstrings): New variable. Change-Id: I9759520a03ee8178432591c48bf56fb25a379f27
2024-01-19gnu: Add python-mediapy.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-mediapy): New variable. Change-Id: I2e55c018670053c662ae2d896feefab3b505b139
2024-01-19gnu: Add r-flames.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flames): New variable. Change-Id: I551a8f9d7de16e2281898b9541572dd244aadc36
2024-01-19gnu: kubo: Update to 0.16.0.Artyom V. Poptsov
* gnu/packages/ipfs.scm (kubo): Update to 0.16.0. [arguments]: Use go-1.18. [home-page]: Set to "https://ipfs.tech". Change-Id: I06239354b0c9c23294d5aeac6d01f67636d5d3a5 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-19gnu: emacs-evil-quickscope: Skip failing test.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-evil-quickscope) [arguments]: Use gexps. Add disable-failing-tests phase. Change-Id: If372531778eab6e3fc164a2f63b98d6775193114
2024-01-19gnu: emacs-shx: Fix test failure.Maxim Cournoyer
* gnu/packages/patches/emacs-shx-byte-compilation-test.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/emacs-xyz.scm (emacs-shx): Apply it. Change-Id: I6d8edd3b50f99f1c4cd495216caf9648dfee4ea3
2024-01-19gnu: emacs-org-journal: Disable failing tests.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-org-journal) [arguments]: Add disable-failing-tests phase. Change-Id: I466cb46613a7048ccbda66cd7855001a04871891
2024-01-19gnu: emacs-ess: Disable flaky "command-without-trailing-newline-test" test.Maxim Cournoyer
* gnu/packages/statistics.scm [arguments]: Add new disable-etests syntax in 'skip-failing-tests phase, and use it to disable the 'command-without-trailing-newline-test' test. Change-Id: I99f52685691d86dc633fe6061f9ef3332159eb4e
2024-01-19gnu: wfmash: Update to 0.12.5.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5. (source): Use git-fetch. Update git repository URL. (arguments): In check phase, symlink to "../source/data" and change wfmash invocation arguments. (home-page): Update URL. Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
2024-01-19gnu: python-graph-tool: Update to 2.59.Greg Hogan
* gnu/packages/graph.scm (python-graph-tool): Update to 2.59. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: I08ecb5fe76183fa980fedf2408fc1df93ebbc63d
2024-01-19gnu: guix-build-coordinator: Update to 0-95.dc04b74.Christopher Baines
* gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-95.dc04b74. Change-Id: I89d968e72188428d40906a7d55533dfd25c7ec25
2024-01-19gnu: bffe: Update to 0-3.1c12da4.Christopher Baines
* gnu/packages/package-management.scm (bffe): Update to 0-3.1c12da4. Change-Id: I90a4231961aed434c2b4ffa07189b85e108b5c46
2024-01-19gnu: nsq: Fix build on i686-linux.Sharlatan Hellseher
As seen in https://ci.guix.gnu.org/build/3329277/details * gnu/packages/high-availability.scm (nsq)[arguments]<#:phases>{check}: Skip '-race' option during tests on i686-linux. Change-Id: I952d7187443835d5fbcb74f0ae09b923bd6bdb29
2024-01-18gnu: Add emacs-vhdl-mode.Cayetano Santos
* gnu/packages/emacs-xyz.scm (emacs-vhdl-mode): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Change-Id: I7e261fc25ae011c20f22e1078ae40bacff3a6947
2024-01-18gnu: Add emacs-pde.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-pde): New variable. Change-Id: Icab5d8acf9d441bb4a832a82e75432d64cc77ba7
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