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* gnu: Remove duplicated perl-extutils-depends.Christopher Baines2018-07-29
| | | | | | | | This was first added in 84e8b19fe150ae843d63ca7343aa7172f35153f3, and then again in 017b014ce4a5defed12836886c4dfe2c5ae89d2d. * gnu/packages/perl.scm (perl-extutils-depends): Remove duplicated package definition.
* gnu: Remove duplicated ghc-time-locale-compat.Christopher Baines2018-07-29
| | | | | | | | It was first added in 5e51bcf7b38511d943f4d24621be5817144061cd, then again in c56a30b3ba3e1e93ced3c6ba2cfb4c738b805074. * gnu/packages/haskell.scm (ghc-time-locale-compat): Remove duplicated package definition.
* gnu: Remove duplicated ghc-th-lift-instances.Christopher Baines2018-07-29
| | | | | | | | It was first added in a6d1c4e75a76399c8d82a9570db5cd14351f661b, then again in ff7dd11f0a4fd6ca947cfa40cec42628fde44667. * gnu/packages/haskell.scm (ghc-th-lift-instances): Remove duplicated package definition.
* gnu: Remove duplicated r-psych package.Christopher Baines2018-07-29
| | | | | | | It was first added in cdc129dc53b1c04e9a6577f7d2b9641a0a03c32f, then again in db80dd4a1d7e2371bc3c300f48b84a817adb3550. * gnu/packages/cran.scm (r-psych): Remove duplicated package definition.
* gnu: Remove duplicated emacs-load-relative.Christopher Baines2018-07-29
| | | | | | | | It was first added in fa1a17b78631681a23ae1fb7b1f902148bbebdbb, and then again in f8a88f223ea2ac36576cd92f457790df5a6f2408. * gnu/packages/emacs.scm (emacs-load-relative): Remove duplicated package definition.
* gnu: Remove duplicated emacs-csv-mode.Christopher Baines2018-07-29
| | | | | | | | It was first added in 9faa46ee48d12bf55355805a84a7c533f904a39d, and then again in 8bc8efc753605e404c1efcdc5b53a780feb0760c. * gnu/packages/emacs.scm (emacs-csv-mode): Remove duplicated package definition.
* linux-initrd: Report only missing modules, not all needed modules.Ludovic Courtès2018-07-29
| | | | | | | | Previously the warning would list all the required modules rather than just those that are missing. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Compute 'missing' and report it.
* linux-initrd: Try several file names when looking up modules.Ludovic Courtès2018-07-29
| | | | | | | | | | | Fixes <https://bugs.gnu.org/31714>. Reported by Tonton <tonton@riseup.net>. * gnu/build/linux-modules.scm (find-module-file): New procedure. * gnu/system/linux-initrd.scm (flat-linux-module-directory)[build-exp]: Remove 'lookup' procedure and use 'find-module-file' instead. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Add comment.
* linux-initrd: Improve check of initrd modules.Ludovic Courtès2018-07-29
| | | | | | | | Previously we would not strip the ".ko" suffix if present. * gnu/build/linux-modules.scm (file-name->module-name): Export. * gnu/system/mapped-devices.scm (check-device-initrd-modules): Use 'file-name->module-name' instead of 'normalize-module-name'.
* services: openssh: Add forwarding options.Eric Brown2018-07-29
| | | | | | | | | * gnu/services/ssh.scm (<openssh-configuration>)[allow-agent-forwarding?] [allow-tcp-forwarding?, gateway-ports?]: New fields. (openssh-config-file): Handle them. * doc/guix.texi (Networking Services): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: taxtastic: Add missing propagated-inputs.Ben Woodcroft2018-07-29
| | | | | | * gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2, python-dendropy.
* gnu: python-dendropy: Update to 4.4.0.Ben Woodcroft2018-07-29
| | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): Update to 4.4.0. [source]: Use GitHub URI. Remove patch. [properties]: Remove field. (python2-dendropy)[arguments]: Run tests with setup.py. [native-inputs]: Remove 'python2-nose. * gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Delete it.
* gnu: python2-psycopg2: Update to 2.7.5.Ben Woodcroft2018-07-29
| | | | * gnu/packages/bioinformatics.scm (python2-psycopg2): Update to 2.7.5.
* gnu: Add python-fastalite.Ben Woodcroft2018-07-29
| | | | | * gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite): New variables.
* gnu: Add chroma.Christopher Lemmer Webber2018-07-29
| | | | * gnu/packages/games.scm (chroma): New variable.
* gnu: linux-libre: Update to 4.17.11.Mark H Weaver2018-07-29
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.11. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.59.Mark H Weaver2018-07-29
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.59. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.116.Mark H Weaver2018-07-29
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.116.
* gnu: linux-libre@4.4: Update to 4.4.145.Mark H Weaver2018-07-29
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.145.
* gnu: clojure: Fix index generation.Gábor Boskovits2018-07-29
| | | | | * gnu/packages/java.scm (clojure)[arguments]: Add phase 'fix-manifest-classpath to remove offending directory entry making indexing fail.
* gnu: openlibm: Update to 0.6.0.Marius Bakke2018-07-28
| | | | * gnu/packages/maths.scm (openlibm): Update to 0.6.0.
* gnu: glm: Update home page.Marius Bakke2018-07-28
| | | | * gnu/packages/maths.scm (glm)[home-page]: Use HTTPS.
* gnu: glm: Update to 0.9.9.0.Marius Bakke2018-07-28
| | | | | * gnu/packages/maths.scm (glm): Update to 0.9.9.0. [source](uri): Change to new download location.
* gnu: libjpeg-turbo: Update license.Marius Bakke2018-07-28
| | | | * gnu/packages/image.scm (libjpeg-turbo)[license]: Add ZLIB.
* gnu: libjpeg-turbo: Update to 2.0.0.Marius Bakke2018-07-28
| | | | | | * gnu/packages/image.scm (libjpeg-turbo): Update to 2.0.0. [build-system]: Change to CMAKE-BUILD-SYSTEM. [arguments]: Adjust accordingly.
* gnu: accountsservice: Update to 0.6.50.Marius Bakke2018-07-28
| | | | | | * gnu/packages/freedesktop.scm (accountsservice): Update to 0.6.50. [arguments]: Add "--enable-elogind" and "--disable-systemd" to #:configure-flags. [inputs]: Add ELOGIND.
* gnu: dconf: Update to 0.28.0.Marius Bakke2018-07-28
| | | | | | | * gnu/packages/gnome.scm (dconf): Update to 0.28.0. [build-system]: Switch to MESON-BUILD-SYSTEM. [arguments]: Adjust accordingly. [native-inputs]: Add VALA and GLIB:BIN.
* gnu: dconf: Update license.Marius Bakke2018-07-28
| | | | * gnu/packages/gnome.scm (dconf)[license]: Change from LGPL2.1 to LGPL2.1+.
* gnu: dconf: Install GTK documentation.Marius Bakke2018-07-28
| | | | | * gnu/packages/gnome.scm (dconf)[native-inputs]: Add GTK-DOC. [arguments]: Adjust #:configure-flags accordingly.
* gnu: dconf: Adjust inputs and remove obsolete workaround.Marius Bakke2018-07-28
| | | | | | | * gnu/packages/gnome.scm (dconf)[inputs]: Remove GLIB and LIBXML2. [propagated-inputs]: Add GLIB. [native-inputs]: Add LIBXML2. Remove INTLTOOL. [arguments]: Remove #:phases.
* gnu: x265: Fix compilation on ARMv7.Ludovic Courtès2018-07-28
| | | | | | * gnu/packages/patches/x265-arm-asm-primitives.patch: New file. * gnu/packages/video.scm (x265)[sources](patches): Add it. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: mariadb: Work around GCC ICE on armhf-linux.Ludovic Courtès2018-07-28
| | | | | | | * gnu/packages/patches/mariadb-gcc-ice.patch: New file. * gnu/packages/databases.scm (mariadb)[arguments]: Conditionally add 'apply-patch' phase. [native-inputs]: Conditionally add "gcc-ice-patch" input.
* gnu: allegro: Update to 5.2.4.0.Kei Kebreau2018-07-27
| | | | | * gnu/packages/game-development.scm (allegro): Update to 5.2.4.0. [source]: Update URL.
* gnu: gcc@8: Update to 8.2.0.Ludovic Courtès2018-07-27
| | | | * gnu/packages/gcc.scm (gcc-8): Update to 8.2.0.
* gnu: Add font-blackfoundry-inria.Ludovic Courtès2018-07-27
| | | | * gnu/packages/fonts.scm (font-blackfoundry-inria): New file.
* gnu: emacs-flycheck: Don't rely on pkg-info.el for 'flycheck-version'.Ludovic Courtès2018-07-27
| | | | | * gnu/packages/emacs.scm (flycheck)[source]: Add 'modules' and 'snippet'.
* gnu: pigx-scrnaseq: Disable another expensive test.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc test.
* gnu: Add snakemake-4.Ricardo Wurmus2018-07-27
| | | | | | * gnu/packages/python.scm (snakemake-4): New variable. * gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq, pigx-chipseq)[inputs]: Use it.
* gnu: snakemake: Add missing dependencies.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-datrie, python-docutils, python-jinja2, python-jsonschema, and python-networkx.
* gnu: Add python-datrie.Ricardo Wurmus2018-07-27
| | | | * gnu/packages/python.scm (python-datrie): New variable.
* gnu: imagemagick: Update to 6.9.10-8.Marius Bakke2018-07-27
| | | | * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-8.
* gnu: mbedtls-apache: Update to 2.7.5.Marius Bakke2018-07-27
| | | | * gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.5.
* gnu: snakemake: Update to 5.2.0.Ricardo Wurmus2018-07-27
| | | | * gnu/packages/python.scm (snakemake): Update to 5.2.0.
* gnu: guile-sdl2: Update to 0.3.0.Ricardo Wurmus2018-07-27
| | | | | * gnu/packages/sdl.scm (guile-sdl2): Update to 0.3.0. [arguments]: Remove "patch-makefile" phase.
* gnu: tiled: Update to 1.1.6.Kei Kebreau2018-07-27
| | | | | * gnu/packages/game-development.scm (tiled): Update to 1.1.6. [arguments]: Substitute invoke for system*.
* gnu: python-xsge: Update to 2018.02.26.Kei Kebreau2018-07-26
| | | | | | * gnu/packages/game-development.scm (python-xsge, python2-xsge): Update to 2018.02.26. [arguments]: Substitute invoke for system*.
* gnu: freeciv: Update to 2.6.0.Kei Kebreau2018-07-26
| | | | * gnu/packages/games.scm (freeciv): Update to 2.6.0.
* gnu: ecryptfs-utils: Patch more hardcoded paths.Brendan Tildesley2018-07-26
| | | | | | | | | * gnu/packages/linux.scm (ecryptfs-utils): [arguments]: Add an additional file to be patched that was missing in the last fix. Ecryptfs will now find the umount binary path as well as mount and others. Re-sort the list of files to be substituted. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: cabextract: Delete bundled libmspack.Marius Bakke2018-07-26
| | | | * gnu/packages/compression.scm (cabextract)[source](modules, snippet): New field.
* gnu: cabextract: Update to 1.7.Marius Bakke2018-07-26
| | | | * gnu/packages/compression.scm (cabextract): Update to 1.7.
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