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2026-06-25bioinformatics: Add igor.Ghislain Vaillant1-0/+22
* guix-science/packages/bioinformatics.scm (igor): New variable. * patches/igor-fix-missing-return.patch: Add patch for igor.
2026-05-29machine-learning: Update python-ray patch for Python 3.12.Ricardo Wurmus1-0/+106
Python 3.12 removed distutils. This commit moves all substitutions of WORKSPACE into a patch file and patches out the CI dependency buildkite, which relied on distutils. * guix-science/packages/machine-learning.scm (python-ray/wheel)[arguments]: Move substitutions for WORKSPACE into a patch file. [source]: Reference that patch file here. * patches/python-ray.patch: New file.
2026-05-16rstudio: rstudio-server: Update to 2026.04.0+526.Ricardo Wurmus8-82/+163
* patches/rstudio-server-install.patch: Update file. * patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch, patches/rstudio-server-multi-version/0002-launchAndTrackSession-Configure-R-version-from-activ.patch, patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch, patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch, patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch, patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch, patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch: Update to latest version. * guix-science/packages/rstudio.scm (dtl-for-rstudio, utfcpp-for-rstudio): New variables. (rstudio-server): Update to 2026.04.0+526. [arguments]: Do not use #:OUT-OF-SOURCE?, add extra configure flags; update generated cmake files; rename phase 'unpack-dictionary to 'unpack-extras and unpack GWT sources; update patching in 'patch-paths; update location of script in 'generate-server-options. [native-inputs]: Replace openjdk11:jdk with openjdk:jdk; add googletest and r-here; add origin for gwt sources. [inputs]: Replace boost-1.88 with boost; add dtl-for-rstudio, libgit2, and utfcpp-for-rstudio.
2026-04-13rstudio: rstudio-server: Update to 2025.05.1+513.Ricardo Wurmus2-49/+136
* patches/rstudio-server-panmirror.patch: Delete file. * patches/rstudio-server-install.patch: Update to changes in 2025.05.1+513. * guix-science/packages/rstudio-node.scm: Replace file with newly generated contents. * guix-science/packages/rstudio.scm (js-panmirror): Update to 0.1.0. (gsl-lite-for-rstudio, rapidjson-for-rstudio, hunspell-for-rstudio, yaml-cpp-for-rstudio): New variables. (rstudio-server): Update to 2025.05.1+513. [source]: Remove rstudio-server-panmirror.patch. [arguments]: Disable copilot support; add phase 'find-hunspell-and-rapidjson; update phase 'patch-paths to patch search for system libraries; add phase 'patch-rapidjson. [native-inputs]: Add libexpected and pkg-config. [inputs]: Replace boost-1.83 with boost-1.88; replace yaml-cpp with yaml-cpp-for-rstudio; add fmt-11, gsl-lite-for-rstudio, hunspell-for-rstudio, rapidjson-for-rstudio, and websocketpp-next.
2026-03-26jasp: Remove broken package.Romain GARBAGE2-78/+0
Fixes #566. * guix-science/packages/jasp.scm: Remove file. * patches/jasp-0.14.0.0-includes.patch: Remove file. * patches/jasp-0.14.0.0-noupdate.patch: Remove file.
2026-03-16rstudio: Use older sources for desktop variant.Ricardo Wurmus1-0/+38
Newer versions require Electron. * patches/rstudio-desktop-install.patch: New file. * guix-science/packages/rstudio.scm (rstudio): Do not inherit from rstudio-server; use sources at version 2023.12.1.
2026-03-16gnu: rstudio-server: Update to 2024.12.1+563.Ricardo Wurmus9-46/+77
* guix-science/packages/rstudio.scm (rstudio-server): Update to 2024.12.1+563. [arguments]: Adjust patches. * patches/rstudio-server-install.patch: New file. * patches/rstudio-server-panmirror.patch: New file. * patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch, patches/rstudio-server-multi-version/0002-launchAndTrackSession-Configure-R-version-from-activ.patch, patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch, patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch, patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch, patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch, patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch: Port to latest version.
2026-03-12algebra: composyx: Update to 1.5.0.MARAIT Gilles1-14/+0
* guix-science/packages/algebra.scm (composyx) [source]: Update to 1.5.0. * patches/composyx-chameleon-1.4.patch: Remove. Signed-off-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>
2026-03-06algebra: composyx: Fix package after Chameleon upgrade.Romain GARBAGE1-0/+14
Chameleon upgrade caused an API breakage in Composyx. * guix-science/packages/algebra.scm (composyx): Fix API breakage from Chameleon. * patches/composyx-chameleon-1.4.patch: New file.
2026-03-05rstudio: rstudio-server: Update to 2023.12.1+402.Ricardo Wurmus1-0/+38
* patches/rstudio-server-install.patch: New file. * guix-science/packages/rstudio.scm (rstudio-server) [source]: Fetch from upstream repository; add patch. [arguments]: Drop unnecessary configure flag; set RSTUDIO_NODE_VERSION; add phase 'create-os-release; update phase 'patch-paths to address node locations; use THIS-PACKAGE-INPUT where possible. [native-inputs]: Drop labels. [inputs]: Drop labels; add node.
2026-02-25rstudio: Fix build of rstudio-server-multi-version.Ricardo Wurmus8-126/+129
The patches from the upstream fork were outdated and did not actually work for version 2023.06.1+524. * patches/rstudio-server-multi-version: Update patches from upstream. * guix-science/packages/rstudio.scm (rstudio-server-multi-version) [source]: Replace patches. [arguments]: Add phase 'patch-gwt-build. [native-inputs]: Add python-wrapper and python-lxml.
2026-02-04rstudio: js-panmirror: Move patch to patches folder.Simon Tournier1-0/+56
* guix-science/packages/rstudio.scm (js-panmirror): Change patch location. * js-panmirror-no-pinyin.patch: Move to patches/ folder.
2026-02-04jasp: jasp: Move patch to patches folder.Simon Tournier2-0/+78
* guix-science/packages/jasp.scm (jasp): Change patch location. * jasp-0.14.0.0-noupdate.patch, jasp-0.14.0.0-includes.patch: Move to patches/ folder.
2026-02-04grid-engine: grid-engine-core: Move patch to patches folder.Simon Tournier2-0/+240
* guix-science/packages/grid-engine.scm (grid-engine-core): Change patch location. * grid-engine-core-openssl-1.1.patch, grid-engine-core-extern_qualifier.patch: Move to patches/ folder.
2026-02-04bioinformatics: cgp-cavemanwrapper: Move patch to patches folder.Simon Tournier1-0/+54
* guix-science/packages/bioinformatics.scm (cgp-cavemanwrapper): Change patch location. * cgp-cavemanwrapper-fix-script.patch: Move to patches/ folder.
2026-01-28chemistry: Add python-deepmd.Romain GARBAGE1-0/+14
* guix-science/packages/chemistry.scm (python-deepmd): New variable. * patches/python-deepmd-remove-unsupported-key.patch: New file.
2026-01-19databases: Add redox.Romain GARBAGE2-0/+83
* guix-science/packages/databases.scm: New file. (redox): New variable. * patches/redox-generate-pkg-config-file.patch: New file. * patches/redox-install-pkg-config-file.patch: New file.
2026-01-19cpp: Add cpp-docopt.Romain GARBAGE1-0/+53
* guix-science/packages/cpp.scm (cpp-docopt): New variable.
2025-11-07hpc-runtime: Add starpu.Romain GARBAGE1-0/+26
* guix-science/packages/hpc-runtime.scm: New file. (starpu): New variable. * patches/starpu-skip-apps.patch: New file.
2025-11-04benchmark: Add netlib-hpl.Romain GARBAGE1-0/+20
* guix-science/packages/benchmark.scm (netlib-hpl): New variable.
2025-04-18patches: Update rstudio-server-multi-version patches.Ricardo Wurmus7-86/+104
Replace the patches with newer versions suitable for version 2023.06.1+524 of rstudio-server. * patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch, patches/rstudio-server-multi-version/0002-sessionProcessConfig-Configure-R-version-from-active.patch, patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch, patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch, patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch, patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch, patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch: Replace.
2025-04-18rstudio: Backport upstream patch for R 4.5.0.Ricardo Wurmus1-0/+61
* patches/rstudio-server-r-4.5.0.patch: Add patch. * guix-science/packages/rstudio.scm (rstudio-server)[source]: Apply it.
2024-01-12bazel: bazel-6: Add patch.Ricardo Wurmus1-0/+45
* patches/bazel-recreate-markers.patch: New file. * guix-science/packages/bazel.scm (bazel-6)[source]: Add patch.
2023-10-12guix-science: Add Bazel.Ricardo Wurmus2-0/+585
* guix-science/packages/bazel.scm: New file. * patches/bazel-mock-repos.patch, patches/bazel-workspace.patch: New patches.
2021-09-24patches: Update rstudio-server-multi-version patches.Ricardo Wurmus7-42/+60
The changes have been rebased on top of version 1.4.1717 and include a bug fix. Previous versions would fail to look up the user's active sessions (and thus fail to restore a previously set version of R) when rserver did not run as the same user account as the rsession process (e.g. root).
2021-05-03guix-science: Add rstudio-server-multi-version.Ricardo Wurmus7-0/+681
* guix-science/packages/rstudio.scm (rstudio-server-multi-version): New variable. * patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch, patches/rstudio-server-multi-version/0002-sessionProcessConfig-Configure-R-version-from-active.patch, patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch, patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch, patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch, patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch, patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch: New files.
generated by cgit v1.2.3 (git 2.25.1) at 2026-09-03 05:31:45 +0000