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2023-11-15gnu: slurm: Add 23.02.6.Ludovic Courtès
* gnu/packages/parallel.scm (slurm): Update to 23.02.6. (slurm-22.05): New variable.
2023-11-15gnu: opensm: Use gexps.Ludovic Courtès
* gnu/packages/fabric-management.scm (opensm)[arguments]: Use gexps.
2023-11-15gnu: opensm: Use the right version string for the doc directory.Ludovic Courtès
Previously, when built with ‘--with-latest=opensm’, the package would install its documentation under a directory with the wrong version string. * gnu/packages/fabric-management.scm (opensm)[arguments]: Use the name and version of THIS-PACKAGE.
2023-11-14gnu: soci: Add PIE flag.Ricardo Wurmus
* gnu/packages/databases.scm (soci)[arguments]: Set CMAKE_CXX_FLAGS to add -fPIE. Change-Id: I79527759d0d35833168f5106a9d6f372375a8ebe
2023-11-14gnu: agda-1lab: Update to 549fdb1c948a975e90e70f871993a4a4239aa280.Josselin Poiret
* gnu/packages/agda.scm (agda-1lab): Update to 549fdb1c948a975e90e70f871993a4a4239aa280. Change-Id: Iad77350fea5a6378e836cbd18c1f4a51bd5a5f0e
2023-11-14gnu: agda-cubical: Update to 0.6.Josselin Poiret
* gnu/packages/agda.scm (agda-cubical): Update to 0.6. Change-Id: I1d6edc44755260e505985fb974c632ec6fff2b49
2023-11-14gnu: agda-categories: Adapt to agda-stdlib 1.7.3.Josselin Poiret
* gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch: New patch. * gnu/packages/agda.scm (agda-categories)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Register it. Change-Id: I25f16d55f14465a1dae882fd8ec47a95f8598e5c
2023-11-14gnu: agda-stdlib: Update to 1.7.3.Josselin Poiret
* gnu/packages/agda.scm (agda-stdlib): Update to 1.7.3. Change-Id: Ic941073814a6a2150d470fc05218dc8d19954445
2023-11-14gnu: agda: Update to 2.6.4.Josselin Poiret
* gnu/packages/agda.scm (agda): Update to 2.6.4. Also build with optimizations and cluster counting support. * gnu/packages/patches/agda-use-sphinx-5.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. Change-Id: I98a66678ec401b9201d9fd3a0f606fff9767b4bc
2023-11-14gnu: Add ghc-text-icu.Josselin Poiret
* gnu/packages/haskell-xyz.scm (ghc-text-icu): New variable. Change-Id: I553f1fef4e76aeea6d09901917fd5d6032c23d46
2023-11-14gnu: emacs-denote: Update to 2.1.0.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-denote): Update to 2.1.0. Change-Id: I4d0f585604ef049480842b4c052edd1aef300e15
2023-11-14gnu: emacs-org: Update to 9.6.12.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.6.12. Change-Id: I0d2b063526f24b7104fcbab972f212e279060f27
2023-11-14gnu: emacs-package-lint: Update to 0.21.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-package-lint): Update to 0.21. Change-Id: I82e28b8e1c211389e99f1947c5c7ddfcba893612
2023-11-14gnu: emacs-compat: Update to 29.1.4.4.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-compat): Update to 29.1.4.4. Change-Id: I11705cb0c2b50bb445711bfdfdb142557aa58b04
2023-11-14gnu: emacs-flycheck-grammalecte: Improve package style.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte)[arguments]Use G-expressions. <#:exclude>: Remove non-existing excluded file. <#:emacs>: Use EMACS-NO-X. <#:phases>: Use G-expressions. Change-Id: Ic5a3c5e3f5271e75cd369cdd40ce210d7c2b859b
2023-11-14gnu: emacs-flycheck-grammalecte: Update to 2.4.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Update to 2.4. Change-Id: I372e3e55534606dba6fed2c2d2f00dc27dc76c0e
2023-11-14gnu: insight-toolkit-4.12: Fix building.Efraim Flashner
* gnu/packages/image-processing.scm (insight-toolkit-4.12)[arguments]: Add a configure-flag to build with c++14. Change-Id: I5e7a0a3ed47e4e3f25611147f8e66c58a1bf8a8c
2023-11-14gnu: ffmpeg-2.8: Update to 2.8.22.Efraim Flashner
* gnu/packages/video.scm (ffmpeg-2.8): Update to 2.8.22. Change-Id: I4ab83a07f60692aa43d04a81dd227b56a95a1d74
2023-11-14gnu: ffmpeg-3.4: Update to 3.4.13.Efraim Flashner
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.13. Change-Id: I9ef7b61dcdeab96d4021150fb57b3739a61376d0
2023-11-14gnu: ffmpeg-5: Update to 5.1.4.Efraim Flashner
* gnu/packages/video.scm (ffmpeg-5): Update to 5.1.4. Change-Id: I4ea8faa3bcee2e34287af4461d078850de17154f
2023-11-11gnu: appstream: Update to 0.16.4.Liliana Marie Prikler
* gnu/packages/freedesktop.scm (appstream): Update to 0.16.4. [arguments]<#:configure-flags>: Add “-Dsystemd=false”. <#:phases>: Adjust accordingly. Change-Id: I9c22cbd10681666c20e848dbc1e52ca08431d984
2023-11-11gnu: libxmlb: Update to 0.3.14.Liliana Marie Prikler
* gnu/packages/xml.scm (libxmlb): Update to 0.3.14. Change-Id: I8571b3f46a5528d04cc2ea013ff2ab0ef4ba19da
2023-11-11gnu: gtk: Update to 4.12.3.Liliana Marie Prikler
* gnu/packages/gtk.scm (gtk): Update to 4.12.3. [source]: Remove snippet. [arguments]<#:configure-flags>: Add “--no-suite=headless”. <#:phases>: Also patch text-color tests in gsk/nodeparser. Change-Id: Iedabfd12ae4f60f02ea21f427b85aeb6b17d03d6
2023-11-04Merge branch 'master' into gnome-teamLiliana Marie Prikler
Change-Id: I88d3789460d1a89917451d80405d89a2824006ac
2023-11-04gnu: passff-host: Add explicit references to inputs and remove some.Clément Lassieur
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and ‘gnu-make’ inputs, which were only used by the Makefile and install_host_app.sh. Instead of running install_host_app.sh (through ‘make’) which does a few text substitutions, do the text substitutions with Scheme code. This simplifies things and avoids unnecessary native inputs. * gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to copy-build-system. [arguments]: Copy passff.json and passff.py. Do text substitutions on them rather than running make. Refer to ‘password-store’ and ‘python’ through inputs rather than directly. [inputs]: Add PASSWORD-STORE and PYTHON. Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
2023-11-04gnu: password-store: Add missing ‘tail’ input.Clément Lassieur
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to the list of requisites. [inputs]: Add COREUTILS. Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
2023-11-03gnu: Add r-ggbreak.Afkhami, Navid
* gnu/packages/cran.scm (r-ggbreak): New variable. Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03gnu: python-pymc: Update to 5.9.1.Vinicius Monego
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1. Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
2023-11-03gnu: python-pytensor: Update to 2.17.3.Vinicius Monego
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3. Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
2023-11-03gnu: python-deepxde: Update to 1.10.0.Vinicius Monego
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0. Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
2023-11-03gnu: Add python-emcee.Vinicius Monego
* gnu/packages/statistics.scm (python-emcee): New variable.
2023-11-03gnu: Add python-salib.Vinicius Monego
* gnu/packages/python-science.scm (python-salib): New variable.
2023-11-03gnu: python-openturns: Update to 1.21.1.Vinicius Monego
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
2023-11-03gnu: python-opentsne: Update to 1.0.0.Vinicius Monego
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
2023-11-03gnu: symengine: Update to 0.11.1.Vinicius Monego
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
2023-11-03gnu: r-gdata: Remove Excel from description.Ricardo Wurmus
gdata 3.0.0 has removed support for reading Excel files. * gnu/packages/statistics.scm (r-gdata)[description]: Update it. Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
2023-11-03gnu: Remove r-sigpathway.Ricardo Wurmus
This package has been removed with the release of Bioconductor 3.18. * gnu/packages/bioconductor.scm (r-sigpathway): Remove variable. Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
2023-11-03gnu: r-rhdf5filters: Simplify.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove 'use-system-libraries phase and pass configure flags to disable bundled libraries. Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
2023-11-03gnu: r-spams: Build with C++11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11. Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
2023-11-03gnu: Remove r-genomegraphs.Ricardo Wurmus
This package had been removed from Bioconductor with release 3.11. * gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable. Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
2023-11-03gnu: Remove r-wavetiling.Ricardo Wurmus
This package had been removed from Bioconductor since release 3.12. * gnu/packages/bioconductor.scm (r-wavetiling): Remove variable. Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
2023-11-03gnu: r-mpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add MPO.sqlite. Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
2023-11-03gnu: r-readwriter: Update to 0.3.2-1.12d32cb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb. Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
2023-11-03gnu: r-hpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add HPO.sqlite. Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
2023-11-03gnu: r-rhdf5lib: Adjust modifications to Makevars.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch. Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
2023-11-03gnu: r-phyloseq: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0. Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
2023-11-03gnu: r-tximeta: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0. Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
2023-11-03gnu: r-tricycle: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0. Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
2023-11-03gnu: r-tcgabiolinks: Update to 2.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0. Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
2023-11-03gnu: r-biscuiteer: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0. Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
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