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2021-01-19gnu: freebayes: Don't include vcflib sources.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove vcflib-source, intervaltree-source. Move vcflib ... [inputs]: ... to here. [arguments]: Adjust 'patch-source and 'unpack-submodule-sources for changes in vendored code. * gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
2021-01-19gnu: vcflib: Add pkg-config file.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to create pkg-config file.
2021-01-19gnu: vcflib: Build a shared library.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to build a shared library instead of a static one.
2021-01-19gnu: freebayes: Extend test timeout on slower architectures.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom 'check phase on aarch64-linux and armhf-linux to extend the test timeout.
2021-01-19gnu: xpra: Add more encoding options.Michael Rohleder
* gnu/packages/xorg.scm (xpra)[inputs]: Add libx264, x265, libvpx. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-19gnu: xpra: Update to 4.0.6.Michael Rohleder
* gnu/packages/xorg.scm (xpra): Update to 4.0.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18gnu: libid3tag: Add comment justifying the 'install-pkg-config phase.Kei Kebreau
* gnu/packages/mp3.scm (libid3tag)[arguments]: Add a comment about Audacity requiring a pkg-config file for libid3tag.
2021-01-18gnu: libmad: Add comment justifying the 'install-pkg-config phase.Kei Kebreau
* gnu/packages/mp3.scm (libmad)[arguments]: Add a comment about Audacity requiring a pkg-config file for libmad.
2021-01-18gnu: Add guile-libyaml.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (guile-libyaml): New variable.
2021-01-18gnu: Add r-snapatac.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18gnu: mafft: Update to 7.475.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18gnu: musl: Update to 1.2.2.Vincent Legoll
* gnu/packages/musl.scm (musl): Update to 1.2.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18gnu: ruby-bio-vcf: Rename to bio-vcf.Efraim Flashner
This package is widely known in select circles specifically as 'bio-vcf'. * gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
2021-01-18gnu: Add ruby-bio-vcf.Efraim Flashner
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-18gnu: linux-libre 4.4: Update to 4.4.252.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.252. (linux-libre-4.4-pristine-source): Update hash.
2021-01-18gnu: linux-libre 4.9: Update to 4.9.252.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.252. (linux-libre-4.9-pristine-source): Update hash.
2021-01-18gnu: linux-libre 4.14: Update to 4.14.216.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.216. (linux-libre-4.14-pristine-source): Update hash.
2021-01-18gnu: linux-libre 4.19: Update to 4.19.168.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.168. (linux-libre-4.19-pristine-source): Update hash.
2021-01-18gnu: linux-libre 5.4: Update to 5.4.90.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.90. (linux-libre-5.4-pristine-source): Update hash.
2021-01-18gnu: linux-libre: Update to 5.10.8.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.8. (linux-libre-5.10-pristine-source): Update hash.
2021-01-18gnu: xapian, python-xapian-bindings: Update to 1.4.18.Tobias Geerinckx-Rice
* gnu/packages/search.scm (xapian, python-xapian-bindings): Update to 1.4.18.
2021-01-18gnu: iptables: Update to 1.8.7.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (iptables): Update to 1.8.7.
2021-01-18gnu: nftables: Update to 0.9.8.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (nftables): Update to 0.9.8.
2021-01-18gnu: libnftnl: Update to 1.1.9.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (libnftnl): Update to 1.1.9.
2021-01-18gnu: ktouch: Update to 20.12.1.Tobias Geerinckx-Rice
* gnu/packages/education.scm (ktouch): Update to 20.12.1.
2021-01-17gnu: wxmaxima: Update to 20.12.2.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 20.12.2. [arguments]: Remove #:test-target and disable tests. Remove 'pre-check phase. [native-inputs]: Remove xorg-server-for-tests. [inputs]: Add libomp.
2021-01-17gnu: gnuplot: Update to 5.4.1.Kei Kebreau
* gnu/packages/maths.scm (gnuplot): Update to 5.4.1. [arguments]: Set GNUTERM in #:make-flags.
2021-01-17gnu: Add emacs-org-mimeRyan Desfosses
* gnu/packages/emacs-xyz.scm (emacs-org-mime): New variable. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-01-17gnu: nbd: Update to 3.21.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (nbd): Update to 3.21.
2021-01-17gnu: mblaze: Update to 1.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (mblaze): Update to 1.1.
2021-01-17gnu: keepassxc: Update to 2.6.3.Tobias Geerinckx-Rice
* gnu/packages/password-utils.scm (keepassxc): Update to 2.6.3.
2021-01-17gnu: facter: Update to 4.0.49.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (facter): Update to 4.0.49.
2021-01-17gnu: inxi-minimal: Update to 3.2.02-2.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (inxi-minimal): Update to 3.2.02-2.
2021-01-17gnu: oil: Update to 0.8.6.Tobias Geerinckx-Rice
* gnu/packages/shells.scm (oil): Update to 0.8.6.
2021-01-17gnu: pd: Update to 0.51-4.Tobias Geerinckx-Rice
* gnu/packages/music.scm (pd): Update to 0.51-4.
2021-01-17gnu: libhandy: Update to 1.0.3.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (libhandy): Update to 1.0.3.
2021-01-17gnu: sbcl-cffi: Update to 0.23.0.Aurora
* gnu/packages/lisp-xyz.scm (sbcl-cffi): Update to 0.23.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-01-17gnu: freebayes: Update to 1.3.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3. [source]: Add patch. Add snippet to remove vendored library. [build-system]: Switch to meson-build-system. [inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp. [native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman source, multichoose source, fsom source, filevercmp source, fastahack source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib. [arguments]: Drop make-flags. Don't delete 'configure phase. Delete custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install phases. Adjust 'unpack-submodule-sources phase to changed native-inputs. Add new 'patch-source phase.
2021-01-17gnu: multichoose: Install header files.Efraim Flashner
* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust 'install phase to also install header files.
2021-01-17gnu: filevercmp: Install header files.Efraim Flashner
* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust 'install phase to install header files.
2021-01-17gnu: Add simde.Efraim Flashner
* gnu/packages/assembly.scm (simde): New variable.
2021-01-17gnu: rtl-433: Update to 20.11.Guillaume Le Vaillant
* gnu/packages/radio.scm (rtl-433): Update to 20.11.
2021-01-17gnu: gqrx: Update to 2.14.4.Guillaume Le Vaillant
* gnu/packages/radio.scm (gqrx): Update to 2.14.4.
2021-01-17gnu: abcl: Update to 1.8.0.Vincent Legoll
* gnu/packages/java.scm (abcl): Update to 1.8.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-01-17gnu: Add buildapp.Sharlatan Hellseher
* gnu/packages/lisp.scm (buildapp): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-01-17gnu: gama: Update to 2.13.Efraim Flashner
* gnu/packages/gps.scm (gama): Update to 2.13.
2021-01-17gnu: youtube-dl: Update to 2021.01.16.Oleg Pykhalov
* gnu/packages/video.scm (youtube-dl): Update to 2021.01.16.
2021-01-16gnu: Add markets.Alexandros Theodotou
* gnu/packages/gnome-xyz.scm (markets): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-01-16gnu: python-pep517: Update to 0.9.1.Tanguy Le Carrour
* gnu/packages/python-xyz.scm (python-pep517): Update to 0.9.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-01-16gnu: xfce4-whiskermenu-plugin: Update to 2.5.2.Michael Rohleder
* gnu/packages/xfce.scm (xfce4-whiskermenu-plugin): Update to 2.5.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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