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2021-04-29gnu: htslib: Update to 1.12....* gnu/packages/bioinformatics.scm (htslib): Update to 1.12. Roel Janssen
2021-04-29gnu: kmscon: Fix layout setup....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. Mathieu Othacehe
2021-04-29gnu: Add r-qpcr....* gnu/packages/cran.scm (r-qpcr): New variable. Ricardo Wurmus
2021-04-29gnu: git-annex: Update to 8.20210428....* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210428. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Kyle Meyer
2021-04-29gnu: oil: Update to 0.8.10....* gnu/packages/shells.scm (oil): Update to 0.8.10. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Ryan Prior
2021-04-29gnu: Add python-hissp....* gnu/packages/python-xyz.scm (python-hissp): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> BonfaceKilz
2021-04-29gnu: xaos: Update to 4.2.1....* gnu/packages/maths.scm (xaos): Update to 4.2.1. [arguments]: Patch call to "lrelease" in XaoS.pro. Kei Kebreau
2021-04-28gnu: linux-libre-arm64-generic@5.10: Add eDP panel, audio and battery...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. Vagrant Cascadian
2021-04-28gnu: linux-libre-arm64-generic: Add eDP panel, battery and audio...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. Vagrant Cascadian
2021-04-29gnu: emacs-hyperbole: Install images and help files....* 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> Xinglu Chen
2021-04-29gnu: emacs-corfu: Update to 0.4....* gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.4. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr> Xinglu Chen
2021-04-28gnu: isc-dhcp: Update bundled BIND to 9.11.31 [security fixes]....Fixes CVE-2021-{25214,25215,25216]. * gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.31. Leo Famulari
2021-04-28gnu: bind: Update to 9.16.15 [fixes CVE-2021-25214, CVE-2021-25215, CVE-2021-......* gnu/packages/dns.scm (isc-bind): Update to 9.16.15. Tobias Geerinckx-Rice
2021-04-28gnu: linux-libre 4.4: Update to 4.4.268....* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.268. (linux-libre-4.4-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre 4.9: Update to 4.9.268....* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.268. (linux-libre-4.9-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre 4.14: Update to 4.14.232....* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.232. (linux-libre-4.14-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre 4.19: Update to 4.19.189....* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.189. (linux-libre-4.19-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre 5.4: Update to 5.4.115....* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.115. (linux-libre-5.4-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre 5.10: Update to 5.10.33....* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.33. (linux-libre-5.10-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: linux-libre: Update to 5.11.17....* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.17. (linux-libre-5.11-pristine-source): Update hash. Leo Famulari
2021-04-28gnu: pigx-bsseq: Update to 0.1.3....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3. [inputs]: Add r-ggbio, r-matrixstats, and r-reshape2. Ricardo Wurmus
2021-04-28gnu: ustr: Don't use vsnprintf....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. Tobias Geerinckx-Rice
2021-04-28gnu: giac: Update to 1.7.0-3....* gnu/packages/algebra.scm (giac): Update to 1.7.0-3. Nicolas Goaziou
2021-04-28gnu: python-pikepdf: Update to 2.11.4....* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.11.4. Nicolas Goaziou
2021-04-28gnu: emacs-auctex: Update to 13.0.10....* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.0.10. Nicolas Goaziou
2021-04-28gnu: ustr: Cross-compile....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. Tobias Geerinckx-Rice
2021-04-28gnu: less: Update to 581.2....* gnu/packages/less.scm (less): Update to 581.2. Tobias Geerinckx-Rice
2021-04-28gnu: iproute2: Update to 5.12.0....* gnu/packages/linux.scm (iproute2): Update to 5.12.0. Tobias Geerinckx-Rice
2021-04-28gnu: folly: Update to 2021.04.26.00....* gnu/packages/cpp.scm (folly): Update to 2021.04.26.00. Tobias Geerinckx-Rice
2021-04-28gnu: xsimd: Update to 7.5.0....* gnu/packages/cpp.scm (xsimd): Update to 7.5.0. Tobias Geerinckx-Rice
2021-04-28gnu: fcitx-qt5: Update to 1.2.6....* gnu/packages/fcitx.scm (fcitx-qt5): Update to 1.2.6. Tobias Geerinckx-Rice
2021-04-28gnu: ungoogled-chromium: Update to 90.0.4430.93....* 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. Marius Bakke
2021-04-28gnu: uBlock Origin: Update to 1.35.0....* gnu/packages/browser-extensions.scm (uassets): Update to edfb13aae. (ublock-origin): Update to 1.35.0. Marius Bakke
2021-04-28gnu: LLVM, Clang: Add 12.0.0....* 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. Marius Bakke
2021-04-28gnu: Add lofreq....* gnu/packages/bioinformatics.scm (lofreq): New variable. Ricardo Wurmus
2021-04-28tests: Add gui-uefi-installed-os test....* gnu/installer/tests.scm (conclude-installation): Rename it into ... (start-installation): ... this new procedure. (complete-installation): New procedure. (choose-partitioning): Add an uefi-support? argument. * gnu/tests/install.scm (uefi-firmware): New procedure. (run-install, qemu-command/writable-image, gui-test-program, installation-target-os-for-gui-tests): Add an uefi-support? argument. (%extra-packages): Add grub-efi, fatfsck/static and dosfstools. (%test-gui-installed-os): New variable. Mathieu Othacehe
2021-04-28installer: Add MSDOS disk label support on UEFI systems....Fixes: <https://issues.guix.gnu.org/47889>. * gnu/installer/parted.scm (esp-partition?): Remove the MSDOS check. (auto-partition!): On MSDOS disks, check if an ESP partition is present. If that's the case, do not remove it. Otherwise, if UEFI is supported, create one. Mathieu Othacehe
2021-04-28installer: Force GPT disk label when UEFI is supported....* gnu/installer/newt/partition.scm (run-label-page): Force the GPT disk label when UEFI is supported. Mathieu Othacehe
2021-04-28gnu: kraken2: Replace references to rsync....* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync. [arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to avoid repeating "scripts". Ricardo Wurmus
2021-04-28gnu: global: Fix cross compiling....Coreutils was removed during patch review erroneously. Reported by Maxime Devos <maximedevos@telenet.be>. * gnu/packages/code.scm (global)[inputs]: Add coreutils. Efraim Flashner
2021-04-28ci: Add custom subset....* gnu/ci.scm (cuirass-jobs): Add 'custom susbset. Mathieu Othacehe
2021-04-28ci: Add arguments->systems procedure....* gnu/ci.scm (arguments->systems): New procedure. (cuirass-jobs): Use it. Mathieu Othacehe
2021-04-28ci: Factorize image->job procedure....* gnu/ci.scm (image-jobs): Extract ->job procedure into ... (image->job): ... this new procedure. Mathieu Othacehe
2021-04-28gnu: global: Fix globash....* gnu/packages/code.scm (global)[arguments]: Add 'fix-globash phase. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> luhui
2021-04-28gnu: Add python-pyliftover....* gnu/packages/bioinformatics.scm (python-pyliftover): New variable. Ricardo Wurmus
2021-04-28gnu: keepassxc: Wrap binary with wrap-qt-program....* gnu/packages/password-utils.scm (keepassxc)[arguments]: Import qt-utils module. Replace custom 'wrap-bin phase with 'wrap-qt phase. Efraim Flashner
2021-04-28gnu: slurm: Link plugins with libslurm....* gnu/packages/parallel.scm (slurm)[arguments]: Add phase patch-plugin-linker-flags to link plugins with libslurm; run autoconf phase after this new phase. Ricardo Wurmus
2021-04-28gnu: krona-tools: Install download scripts....* gnu/packages/web.scm (krona-tools)[inputs]: Add curl and make. [arguments]: Patch and install update scripts to /share. Ricardo Wurmus
2021-04-28gnu: krona-tools: Update to 2.8....* gnu/packages/web.scm (krona-tools): Update to 2.8. Ricardo Wurmus
2021-04-28gnu: Add mmc-utils....* gnu/packages/disk.scm (mmc-utils): New variable. Leo Famulari