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* gnu: mpfrcx: Update to 0.6.1.Andreas Enge2021-04-29
| | | | * gnu/packages/algebra.scm (mpfrcx): Update to 0.6.1.
* gnu: bigloo: Update to 4.3g.Guillaume Le Vaillant2021-04-29
| | | | | | | * gnu/packages/scheme.scm (bigloo): Update to 4.3g. [source]: Remove bundled libunistring and pcre. [arguments]: Add 'fix-gmp-detection' phase. Add options to 'configure' phase to throw an error when gmp is not found.
* gnu: Update bedtools to 2.30.0.Roel Janssen2021-04-29
| | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0, [inputs]: Use latest samtools.
* gnu: Update samtools to 1.12.Roel Janssen2021-04-29
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
* gnu: Update bcftools to 1.12.Roel Janssen2021-04-29
| | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
* gnu: htslib: Update to 1.12.Roel Janssen2021-04-29
| | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
* gnu: kmscon: Fix layout setup.Mathieu Othacehe2021-04-29
| | | | | | | | | | | | | | | | | Kmscon may discover multiple inputs, corresponding to multiple devices. This means that the uxkb_dev_keymap_update function may be called multiple times, and the FIFO is registered on each input poll loop. When a new layout is written on the FIFO by the installer, the first input picking up the message, will apply the new layout. However, that input may not be the input that the user is currently using. To fix it, register the FIFO on the first input poll loop, but apply the new layout on all the inputs in the uxkb_keymap_update_handler function. * gnu/packages/patches/kmscon-runtime-keymap-switch.patch (uxkb_keymap_update_handler): Apply the new layout to all the inputs. (input_new_dev): Register the FIFO fd only on the first input poll loop.
* gnu: Add r-qpcr.Ricardo Wurmus2021-04-29
| | | | * gnu/packages/cran.scm (r-qpcr): New variable.
* gnu: git-annex: Update to 8.20210428.Kyle Meyer2021-04-29
| | | | | | * gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210428. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: oil: Update to 0.8.10.Ryan Prior2021-04-29
| | | | | | * gnu/packages/shells.scm (oil): Update to 0.8.10. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add python-hissp.BonfaceKilz2021-04-29
| | | | | | * gnu/packages/python-xyz.scm (python-hissp): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: xaos: Update to 4.2.1.Kei Kebreau2021-04-29
| | | | | * gnu/packages/maths.scm (xaos): Update to 4.2.1. [arguments]: Patch call to "lrelease" in XaoS.pro.
* gnu: linux-libre-arm64-generic@5.10: Add eDP panel, audio and batteryVagrant Cascadian2021-04-28
| | | | | | | support for Pinebook Pro. * gnu/packages/linux.scm (linux-libre-5.10-source): Add pinebook pro lcd patch. (linux-libre-arm64-generic-5.10): Add audio and battery modules.
* gnu: linux-libre-arm64-generic: Add eDP panel, battery and audioVagrant Cascadian2021-04-28
| | | | | | | | | | | support for Pinebook Pro. * gnu/packages/linux.scm (linux-libre-5.11-source): Add Pinebook Pro lcd patch. (linux-libre-arm64-generic): Enable audio and battery modules for Pinebook Pro. * gnu/packages/patches/linux-libre-arm64-generic-pinebook-lcd.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patch.
* gnu: emacs-hyperbole: Install images and help files.Xinglu Chen2021-04-29
| | | | | | | * gnu/packages/emacs-xyz.scm (emacs-hyperbole)[arguments]: Include help file and install images for the manual. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
* gnu: emacs-corfu: Update to 0.4.Xinglu Chen2021-04-29
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.4. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
* gnu: isc-dhcp: Update bundled BIND to 9.11.31 [security fixes].Leo Famulari2021-04-28
| | | | | | Fixes CVE-2021-{25214,25215,25216]. * gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.31.
* gnu: bind: Update to 9.16.15 [fixes CVE-2021-25214, CVE-2021-25215, ↵Tobias Geerinckx-Rice2021-04-28
| | | | | | CVE-2021-25216]. * gnu/packages/dns.scm (isc-bind): Update to 9.16.15.
* gnu: linux-libre 4.4: Update to 4.4.268.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.268. (linux-libre-4.4-pristine-source): Update hash.
* gnu: linux-libre 4.9: Update to 4.9.268.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.268. (linux-libre-4.9-pristine-source): Update hash.
* gnu: linux-libre 4.14: Update to 4.14.232.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.232. (linux-libre-4.14-pristine-source): Update hash.
* gnu: linux-libre 4.19: Update to 4.19.189.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.189. (linux-libre-4.19-pristine-source): Update hash.
* gnu: linux-libre 5.4: Update to 5.4.115.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.115. (linux-libre-5.4-pristine-source): Update hash.
* gnu: linux-libre 5.10: Update to 5.10.33.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.33. (linux-libre-5.10-pristine-source): Update hash.
* gnu: linux-libre: Update to 5.11.17.Leo Famulari2021-04-28
| | | | | * gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.17. (linux-libre-5.11-pristine-source): Update hash.
* gnu: pigx-bsseq: Update to 0.1.3.Ricardo Wurmus2021-04-28
| | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3. [inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
* gnu: ustr: Don't use vsnprintf.Tobias Geerinckx-Rice2021-04-28
| | | | | | | | This follows up on 1059d1570b7078e6a83e067577b42ed24ee25b55, which caused new tests failures on non-cross builds. * gnu/packages/textutils.scm (ustr)[arguments]: Return "0" for ./autoconf_vsnprintf.
* gnu: giac: Update to 1.7.0-3.Nicolas Goaziou2021-04-28
| | | | * gnu/packages/algebra.scm (giac): Update to 1.7.0-3.
* gnu: python-pikepdf: Update to 2.11.4.Nicolas Goaziou2021-04-28
| | | | * gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.11.4.
* gnu: emacs-auctex: Update to 13.0.10.Nicolas Goaziou2021-04-28
| | | | * gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.0.10.
* gnu: ustr: Cross-compile.Tobias Geerinckx-Rice2021-04-28
| | | | | | | Also fix <http://issues.guix.gnu.org/48084>. * gnu/packages/text-utils.scm (ustr)[arguments]: Use CC-FOR-TARGET. Add a new 'fix-cross-compilation phase.
* gnu: less: Update to 581.2.Tobias Geerinckx-Rice2021-04-28
| | | | * gnu/packages/less.scm (less): Update to 581.2.
* gnu: iproute2: Update to 5.12.0.Tobias Geerinckx-Rice2021-04-28
| | | | * gnu/packages/linux.scm (iproute2): Update to 5.12.0.
* gnu: folly: Update to 2021.04.26.00.Tobias Geerinckx-Rice2021-04-28
| | | | * gnu/packages/cpp.scm (folly): Update to 2021.04.26.00.
* gnu: xsimd: Update to 7.5.0.Tobias Geerinckx-Rice2021-04-28
| | | | * gnu/packages/cpp.scm (xsimd): Update to 7.5.0.
* gnu: fcitx-qt5: Update to 1.2.6.Tobias Geerinckx-Rice2021-04-28
| | | | * gnu/packages/fcitx.scm (fcitx-qt5): Update to 1.2.6.
* gnu: ungoogled-chromium: Update to 90.0.4430.93.Marius Bakke2021-04-28
| | | | | | | | | | | | | | | | | | | * gnu/packages/patches/ungoogled-chromium-system-nspr.patch, gnu/packages/patches/ungoogled-chromium-system-opus.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 90. (debian-patch): Make REVISION optional, default to %DEBIAN-REVISION. (%chromium-version): New variable. (%ungoogled-revision): Set to 90.0.4430.85-1-11-g3184907. (%debian-revision): Set to debian/90.0.4430.85-1. (%debian-patches): Add more patches; update hashes. (%ungoogled-origin): Update hash. (%guix-patches): Remove obsolete patches. (libvpx/chromium): Update to 1.9.0-147-g61edec1ef. (ungoogled-chromium)[version]: Base on %CHROMIUM-REVISION and the last component of %UNGOOGLED-REVISION, a 'git describe --long' style ID. [arguments]: Add build_with_flite_lib in #:configure-flags. Add openjpeg substitution in #:phases.
* gnu: uBlock Origin: Update to 1.35.0.Marius Bakke2021-04-28
| | | | | * gnu/packages/browser-extensions.scm (uassets): Update to edfb13aae. (ublock-origin): Update to 1.35.0.
* gnu: LLVM, Clang: Add 12.0.0.Marius Bakke2021-04-28
| | | | | | | | * gnu/packages/patches/clang-12-tools-extra-directory.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/llvm.scm (llvm-12, clang-runtime-12, clang-12, clang-toolchain-12): New variables. (llvm-11): Inherit from LLVM-12.
* gnu: Add lofreq.Ricardo Wurmus2021-04-28
| | | | * gnu/packages/bioinformatics.scm (lofreq): New variable.
* gnu: kraken2: Replace references to rsync.Ricardo Wurmus2021-04-28
| | | | | | * gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync. [arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to avoid repeating "scripts".
* gnu: global: Fix cross compiling.Efraim Flashner2021-04-28
| | | | | | | Coreutils was removed during patch review erroneously. Reported by Maxime Devos <maximedevos@telenet.be>. * gnu/packages/code.scm (global)[inputs]: Add coreutils.
* gnu: global: Fix globash.luhui2021-04-28
| | | | | | * gnu/packages/code.scm (global)[arguments]: Add 'fix-globash phase. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add python-pyliftover.Ricardo Wurmus2021-04-28
| | | | * gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
* gnu: keepassxc: Wrap binary with wrap-qt-program.Efraim Flashner2021-04-28
| | | | | * gnu/packages/password-utils.scm (keepassxc)[arguments]: Import qt-utils module. Replace custom 'wrap-bin phase with 'wrap-qt phase.
* gnu: slurm: Link plugins with libslurm.Ricardo Wurmus2021-04-28
| | | | | | * gnu/packages/parallel.scm (slurm)[arguments]: Add phase patch-plugin-linker-flags to link plugins with libslurm; run autoconf phase after this new phase.
* gnu: krona-tools: Install download scripts.Ricardo Wurmus2021-04-28
| | | | | * gnu/packages/web.scm (krona-tools)[inputs]: Add curl and make. [arguments]: Patch and install update scripts to /share.
* gnu: krona-tools: Update to 2.8.Ricardo Wurmus2021-04-28
| | | | * gnu/packages/web.scm (krona-tools): Update to 2.8.
* gnu: Add mmc-utils.Leo Famulari2021-04-28
| | | | * gnu/packages/disk.scm (mmc-utils): New variable.
* gnu: Add gdc-11.Efraim Flashner2021-04-27
| | | | * gnu/packages/gcc.scm (gdc-11): New variable.
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