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* gnu: Add go-github-com-danwakefield-fnmatch.Martin Becze2020-06-23
| | | | | | | * gnu/packages/golang.scm (go-github-com-danwakefield-fnmatch): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add r-kmer.Ricardo Wurmus2020-06-23
| | | | | | * gnu/packages/cran.scm (r-kmer): New variable. Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
* gnu: Add r-phylogram.Ricardo Wurmus2020-06-23
| | | | | | * gnu/packages/cran.scm (r-phylogram): New variable. Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
* gnu: Add r-fourcseq.Ricardo Wurmus2020-06-23
| | | | | | * gnu/packages/cran.scm (r-fourcseq): New variable. Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
* gnu: Add r-lsd.Ricardo Wurmus2020-06-23
| | | | | | * gnu/packages/cran.scm (r-lsd): New variable. Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
* gnu: cuirass: Update to 0.0.1-34.10b16e.Mathieu Othacehe2020-06-23
| | | | * gnu/packages/ci.scm (cuirass): Update to 0.0.1-34.10b16e.
* gnu: fakeroot: Do not assume "sed" and "cut" to be available.Mathieu Othacehe2020-06-23
| | | | | | * gnu/packages/linux.scm (fakeroot)[inputs]: Add "sed" and "coreutils", [arguments]: substitute "sed" and "cut" by their absolute path in fakeroot script. Rename the associated phase from patch-getopt to patch-script.
* gnu: linux-libre: Update to 5.4.48.Mark H Weaver2020-06-22
| | | | | * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.48. (linux-libre-5.4-pristine-source): Update hash.
* gnu: linux-libre@5.7: Update to 5.7.5.Mark H Weaver2020-06-22
| | | | | * gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.5. (linux-libre-5.7-pristine-source): Update hash.
* gnu: linux-libre@4.19: Update to 4.19.129.Mark H Weaver2020-06-22
| | | | | * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.129. (linux-libre-4.19-pristine-source): Update hash.
* gnu: sequoia: Update to 0.17.0.Jakub Kądziołka2020-06-23
| | | | | | * gnu/packages/sequoia.scm (sequoia): Update to 0.17.0. [cargo-inputs]: Add rust-structopt-0.3. [phases](unpin-deps): New phase.
* gnu: liferea: Update to 1.12.8.Vinicius Monego2020-06-22
| | | | | | * gnu/packages/syndication.scm (liferea): Update to 1.12.8. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: mlt: Build with the latest ffmpeg.Marius Bakke2020-06-22
| | | | * gnu/packages/video.scm (mlt)[inputs]: Change from FFMPEG-3.4 to FFMPEG.
* gnu: mlt: Update to 6.20.0.Vinicius Monego2020-06-22
| | | | | | * gnu/packages/video.scm (mlt): Update to 6.20.0. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: darktable: Update to 3.0.2.Vinicius Monego2020-06-22
| | | | | | | | | | | | * gnu/packages/photo.scm (darktable): Update to 3.0.2. [arguments]: Compile with clang. Wrap GSETTINGS_SCHEMAS_DIR. [license]: Add license information for Rawspeed. [native-inputs]: Add clang, desktop-file-utils, glib, gobject-instrospection, llvm, and po4a. Reorder alphabetically. [inputs]: Add colord-gtk, cups, graphicsmagick, gsettings-desktop-schemas, iso-codes, libsecret, lua, openjpeg, and osm-gps-map. Reorder alphabetically. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: jamvm: Fix to work with current gcc and glibc.Simon South2020-06-22
| | | | | | | | | * gnu/packages/java.scm (jamvm)[source]: Add patch. (jamvm-1-bootstrap)[native-inputs]: Remove. * gnu/packages/patches/jamvm-2.0.0-disable-branch-patching.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: template-glib: Update to 3.34.0.Giacomo Leidi2020-06-22
| | | | | | * gnu/packages/glib.scm (template-glib): Update to 3.34.0. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-daemux.Edouard Klein2020-06-22
| | | | | | * gnu/packages/tmux.scm (python-daemux): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-libtmux.Edouard Klein2020-06-22
| | | | | | * gnu/packages/tmux.scm (python-libtmux): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-pyfiglet.Edouard Klein2020-06-22
| | | | | | * gnu/packages/python-xyz.scm (python-pyfiglet): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-flask-restx.Edouard Klein2020-06-22
| | | | | | * gnu/packages/python-web.scm (python-flask-restx): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-pytest-flask.Edouard Klein2020-06-22
| | | | | | * gnu/packages/python-check.scm (python-pytest-flask): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-pytest-benchmark.Edouard Klein2020-06-22
| | | | | | * gnu/packages/python-check.scm (python-pytest-benchmark): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add python-py-cpuinfo.Edouard Klein2020-06-22
| | | | | | * gnu/packages/python-xyz.scm (python-py-cpuinfo): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
* gnu: Add abe.Nicolas Goaziou2020-06-22
| | | | * gnu/packages/games.scm (abe): New variable.
* gnu: mate: Don't propagate glib:bin.Jonathan Brielmaier2020-06-22
| | | | | | | * gnu/packages/mate.scm (mate)[propagated-inputs]: Remove as the proper fix arrived from core-updates. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: mate-common: Update to 1.24.1.Jonathan Brielmaier2020-06-22
| | | | | | * gnu/packages/mate.scm (mate-common): Update to 1.24.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add python-pytest-lazy-fixture.Vinicius Monego2020-06-22
| | | | | | * gnu/packages/check.scm (python-pytest-lazy-fixture): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: r-with-tests, r-minimal: Update to 4.0.2.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.2.
* gnu: gn: Update to 0.0-1794.eb997b5.Marius Bakke2020-06-22
| | | | * gnu/packages/build-tools.scm (gn): Update to 0.0-1794.eb997b5.
* gnu: ungoogled-chromium: Update to 83.0.4103.106-0.f08ce8b [security fixes].Marius Bakke2020-06-22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This fixes CVE-2020-6465, CVE-2020-6466, CVE-2020-6467, CVE-2020-6468, CVE-2020-6469, CVE-2020-6470, CVE-2020-6471, CVE-2020-6472, CVE-2020-6473, CVE-2020-6474, CVE-2020-6475, CVE-2020-6476, CVE-2020-6477, CVE-2020-6478, CVE-2020-6479, CVE-2020-6480, CVE-2020-6481, CVE-2020-6482, CVE-2020-6483, CVE-2020-6484, CVE-2020-6485, CVE-2020-6486, CVE-2020-6487, CVE-2020-6488, CVE-2020-6489, CVE-2020-6490, CVE-2020-6491, CVE-2020-6493, CVE-2020-6494, CVE-2020-6495, CVE-2020-6496, CVE-2020-6497, and CVE-2020-6498. * gnu/packages/patches/ungoogled-chromium-system-jsoncpp.patch, gnu/packages/patches/ungoogled-chromium-system-zlib.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 83. (%chromium-version): Set to 83.0.4103.106. (%ungoogled-revision): Set to f08ce8b3f1300ef0750b5d6bf967b9cbbfd9a56d. (%gentoo-revision, %gentoo-patches, %debian-patches): New variables. (gentoo-patch, debian-patch): New procedures. (%chromium-origin, %ungoogled-origin): Update hashes. (ungoogled-chromium-source): Don't apply patches from %DEBIAN-ORIGIN, but take %GENTOO-PATCHES, %DEBIAN-PATCHES, and the local patch files. (ungoogled-chromium)[arguments]: Remove "enable_swiftshader=false" from #:configure-flags. Add "icu_use_data_file=false". Set CFLAGS in phase. Remove obsolete substitution. Adjust install phase to install .so files for ANGLE and Swiftshader. [native-inputs]: Change from CLANG-9 to CLANG-10. [inputs]: Replace ICU4C with ICU4C-67. (ungoogled-chromium/wayland): Remove obsolete substitution. Add "ozone_platform_x11=true" in #:configure-flags.
* gnu: icu4c: Add 67.1.Marius Bakke2020-06-22
| | | | * gnu/packages/icu4c.scm (icu4c-67): New public variable.
* gnu: ungoogled-chromium: Specify CPE name.Marius Bakke2020-06-22
| | | | * gnu/packages/chromium.scm (ungoogled-chromium)[properties]: Add CPE-NAME.
* gnu: ungoogled-chromium: Remove non-free file.Marius Bakke2020-06-22
| | | | | * gnu/packages/chromium.scm (ungoogled-chromium-source): Remove (unused) SVG file that is licensed under a NoDerivatives license.
* gnu: ungoogled-chromium: Build with ffmpeg@4.2.Marius Bakke2020-06-22
| | | | | | | | | Fixes <https://bugs.gnu.org/41987>. Reported by Jonathan Brielmaier <jonathan.brielmaier@web.de>. * gnu/packages/video.scm (ffmpeg-4.2): New public variable. * gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG to FFMPEG-4.2.
* gnu: ffmpeg: Enable rav1e on x86_64 only.Marius Bakke2020-06-22
| | | | | | | | Fixes <https://bugs.gnu.org/41993>. Reported by Kurt I <gitlabcanada@runbox.com>. * gnu/packages/video.scm (ffmpeg)[inputs]: Conditionally add RAV1E. [arguments]: Adjust #:configure-flags accordingly.
* gnu: xl2tpd: Fix build.Mathieu Othacehe2020-06-22
| | | | | * gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path instead of trying to set CFLAGS variable.
* gnu: python-plotly: Update to 4.8.1.Pierre Langlois2020-06-22
| | | | | | | | | | | | | | | | But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-xarray.Pierre Langlois2020-06-22
| | | | | | | | | | | From 27ec21904f769c1e8114f767972d9037e1e9f68a Mon Sep 17 00:00:00 2001 From: Pierre Langlois <pierre.langlois@gmx.com> Date: Thu, 18 Jun 2020 00:58:02 +0200 Subject: [PATCH 4/5] gnu: Add python-xarray. * gnu/package/python-science.scm (python-xarray): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-retrying.Pierre Langlois2020-06-22
| | | | | | * gnu/packages/python-xyz.scm (python-retrying): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: python-pandas: Update to 1.0.5.Pierre Langlois2020-06-22
| | | | | | | | | | | | | | | | | | But also keep version 0.25.3 around for packages requiring an earlier versions, as well as version 0.24.2 for a version with python2. * gnu/packages/python-science.scm (python-pandas): Update to 1.0.5. [arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not delete tests that depend on "moto", they are skipped automatically. [propagated-inputs]: Add python-jinja2. [inputs]: Add xsel and xclip. [native-inputs]: Add xorg-server-for-tests so we can test clipboard support. (python-pandas-0.24): New variable. (python2-pandas): Inherit from python-pandas-0.25. * gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]: Switch to python-pandas-0.25. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: deeptools: Deprecate in favor of python-deeptools.Pierre Langlois2020-06-22
| | | | | | | | | | And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* self: Build with Guile 3.0.3.Ludovic Courtès2020-06-22
| | | | * gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
* gnu: emacs-helm: Update to 3.6.3.Pierre Neidhardt2020-06-22
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
* gnu: emacs-helm-fish-completion: Update to 0.5.Pierre Neidhardt2020-06-22
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
* gnu: js8call: Fix build.Guillaume Le Vaillant2020-06-22
| | | | * gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
* gnu: wsjtx: Update to 2.2.1.Guillaume Le Vaillant2020-06-22
| | | | | | * gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1. [arguments]: Add a 'fix-tests' phase. (wsjtx): Update to 2.2.1.
* gnu: qgis: Disable some failing tests.Guillaume Le Vaillant2020-06-22
| | | | * gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
* gnu: Add r-rgreat.Ricardo Wurmus2020-06-22
| | | | * gnu/packages/bioconductor.scm (r-rgreat): New variable.
* gnu: rust-libc-0.2: Don't skip build.Efraim Flashner2020-06-22
| | | | | * gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip build.
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