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2021-12-03gnu: Remove python2-biom-format.Ricardo Wurmus
There are no users of this variant, and the current version of biom-format does not support Python 2. * gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable. (python-biom-format)[properties]: Remove field.
2021-12-03gnu: r-flowclust: Add gsl.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally committed comment character.
2021-12-03gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.Mark H Weaver
This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20. * gnu/packages/patches/icecat-78-makeicecat.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2021-12-03gnu: cuirass: Update to 1.1.0-6.df8837c.Mathieu Othacehe
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
2021-12-03gnu: python-pandocfilters: Update to 1.5.0.jgart
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03gnu: icecat: Fix CVE-2021-43527.Mark H Weaver
* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat-source): Apply it.
2021-12-03gnu: nss: Fix CVE-2021-43527 via graft.Mark H Weaver
* gnu/packages/patches/nss-CVE-2021-43527.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/nss.scm (nss/fixed): New variable (nss)[replacement]: New field.
2021-12-02gnu: openjdk16: Use MAKE-FILE-WRITABLE.Ricardo Wurmus
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
2021-12-02gnu: Add openjdk17.Arne Babenhauserheide
* gnu/packages/java.scm (openjdk17): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-02doc: Give more details about generating patches with base commit information.Leo Famulari
* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
2021-12-02gnu: python2-decorator: Downgrade to 4.3.0Ricardo Wurmus
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0. (python-decorator)[properties]: Add python2-variant.
2021-12-02gnu: ribodiff: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase.
2021-12-02gnu: ribodiff: Disable broken test.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test.
2021-12-02gnu: python2-statsmodels: Downgrade to 0.9.0.Ricardo Wurmus
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
2021-12-02gnu: khmer: Fix build with Python 3.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility.
2021-12-02gnu: python-biom-format: Update to 2.1.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10. [source]: Simplify snippet. [arguments]: Add phase 'relax; remove trailing #T from other build phases. [propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with python-pandas.
2021-12-02gnu: Add trayer-srg.jgart
* gnu/packages/wm.scm (trayer-srg): New variable. Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com> Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: pardre: Update to 2.2.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests.
2021-12-02gnu: pardre: Use C++ bindings for MPI.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++.
2021-12-02gnu: Add openmpi-c++.Ricardo Wurmus
* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-12-02gnu: Add libconfini.Liliana Marie Prikler
* gnu/packages/cpp.scm (libconfini): New variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: shotcut: Update to 21.10.31.Vinicius Monego
* gnu/packages/video.scm (shotcut): Update to 21.10.31. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: kdenlive: Update to 21.08.3.Vinicius Monego
* gnu/packages/kde.scm (kdenlive): Update to 21.08.3. [arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are currently disabled. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: mlt: Update to 7.2.0.Vinicius Monego
* gnu/packages/video.scm (mlt): Update to 7.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: ccls: Update to 0.20210330.jgart
* gnu/packages/cpp.scm (ccls): Update to 0.20210330. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: guile-udev: Update to 0.2.0Artyom V. Poptsov
* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-02gnu: python-ipython: Update to 7.20.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
2021-12-02gnu: python-ipython: Remove trailing #T.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T from build phases.
2021-12-02gnu: yggdrasil: Simplify build phases.Efraim Flashner
* gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom 'build phase reusing go-build-system 'build phase. Remove custom 'install phase.
2021-12-02gnu: go-golang-zx2c4-com-wireguard: Fix downloading source.Efraim Flashner
* gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]: Adjust commit string in git-reference.
2021-12-02gnu: go-github-com-vividcortex-ewma: Adjust import-path.Efraim Flashner
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma)[arguments]: Adjust import-path to location other go packages expect it to be.
2021-12-02gnu: guix: Update to 8cc099b.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to 8cc099b.
2021-12-02gnu: Add python-mygene.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
2021-12-02gnu: Add python-biothings-client.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
2021-12-02gnu: Add r-scdblfinder.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scdblfinder): New variable.
2021-12-02Revert "gnu: godot: Update to 3.4."Leo Famulari
This reverts commit dd4365efa1c6fb609de9bd7cd10f9c82e064aed4. We reverted this commit because it broke the operation of the only package in Guix that depends on Godot, SuperStarfighter: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=52233#20
2021-12-02gnu: cl-tooter: Update to 1.0.0-3.ec97bee.cage
* gnu/packages/lisp-xyz.scm (cl-tooter): Update to 1.0.0-3.ec97bee. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-02gnu: cl-i18n: Update to 0.5.1-1.4216fe9.cage
* gnu/packages/lisp-xyz.scm (cl-i18n): Update to 0.5.1-1.4216fe9. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-02gnu: godot: Update to 3.4.Andy Tai
* gnu/packages/game-development.scm (godot): Update to 3.4. [source]: Add new bundled dependencies to the origin snippet. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-01gnu: linux-libre 4.19: Update to 4.19.219.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.219. (linux-libre-4.19-pristine-source): Update hash.
2021-12-01gnu: linux-libre 5.4: Update to 5.4.163.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.163. (linux-libre-5.4-pristine-source): Update hash.
2021-12-01gnu: linux-libre 5.10: Update to 5.10.83.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.83. (linux-libre-5.10-pristine-source): Update hash.
2021-12-01gnu: linux-libre: Update to 5.15.6.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.6. (linux-libre-5.15-pristine-source): Update hash.
2021-12-02gnu: Remove couger.Ricardo Wurmus
This package has been moved to the Guix Past channel. * gnu/packages/bioinformatics.scm (couger): Remove variable.
2021-12-02gnu: randomjungle: Fix compatibility errors.Ricardo Wurmus
* gnu/packages/machine-learning.scm (randomjungle)[arguments]: Add build phase 'fix-compatibility-errors to patch type errors.
2021-12-01news: Add entry about Icedove 91.Jonathan Brielmaier
* etc/news.scm: New entry.
2021-12-01gnu: icecat: Remove leftovers of release 78.Jonathan Brielmaier
No longer required as icedove is now based on the 91 branch. * gnu/packages/gnuzilla.scm (mozilla-78-compare-locales): Remove. (all-mozilla-78-locales): Remove. (%icecat-78-version): Remove. (icecat-78-source): Remove.
2021-12-01gnu: icedove: Update to 91.3.2.Jonathan Brielmaier
The profile folder moved from `~/.icedove` to `~/.thunderbird`. You may need to migrate (copy) your profile over. * gnu/packages/gnuzilla.scm (icedove): Update to 91.3.2. [source]: Switch back to icecat-source. [arguments]: `obj-x86_64-pc-linux-gnu` folder is now generated during build, so it can't deleted in front. Remove surounding `'` from MOZ_DEDICATED_PROFILES to follow source code. MOZ_APP_BASENAME and MOZ_APP_DISPLAYNAME are no longer set in `comm/mail/confvars.sh`. Update path of `customizeToolbar.js`. Delete `'bootstrap` phase and no longer set AUTOCONF variable as the autoconf build part was removed. Set MACH_USE_SYSTEM_PYTHON and MOZ_APP_NAME, the latter is the binary name. `--enable-calendar` flag got removed. Use bundled NSS until core-updates merge. [inputs]: Update to `icu4c-69` and `nspr-4.32`. Use bundled NSS for now. [native-inputs]: Switch to comm-esr91 branch. Remove autoconf, add m4. Update rust and cargo to 1.51. Use `rust-cbindgen-0.19`.
2021-12-01gnu: Add nspr@4.32.Jonathan Brielmaier
Required for icecat/icedove 91. * gnu/packages/nss.scm (nspr-4.32): New variable.
2021-12-01gnu: emacs-citar: Remove unnecessary input.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-citar)[propagated-inputs]: Remove emacs-helm-bibtex.
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