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2020-06-22gnu: mate: Don't propagate glib:bin....* 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> Jonathan Brielmaier
2020-06-22gnu: mate-common: Update to 1.24.1....* gnu/packages/mate.scm (mate-common): Update to 1.24.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jonathan Brielmaier
2020-06-22gnu: Add python-pytest-lazy-fixture....* gnu/packages/check.scm (python-pytest-lazy-fixture): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Vinicius Monego
2020-06-22gnu: r-with-tests, r-minimal: Update to 4.0.2....* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.2. Ricardo Wurmus
2020-06-22system: image: Remove "image-root" when building raw disk-images....The "image-root" derivation output is used as a temporary directory that is passed to mke2fs and mkdosfs later on. By merging the creation of this directory and the production of partition images, we can get rid of the derivation. As mke2fs and mkdosfs are not able to override file permissions, call those commands with fakeroot. This way, all the image files will be owned by root, even if image generation is done in an unprivilegded context. * gnu/system/image.scm (system-disk-image): Merge "image-root" and "iso9660-image" derivations so that we spare an extra derivation. Also add "fakeroot" and its runtime dependencies to the inputs. * gnu/build/image.scm (make-ext-image, make-vfat-image): Make sure that mke2fs and mkdosfs are respectively called by fakeroot. Mathieu Othacehe
2020-06-22gnu: gn: Update to 0.0-1794.eb997b5....* gnu/packages/build-tools.scm (gn): Update to 0.0-1794.eb997b5. Marius Bakke
2020-06-22gnu: ungoogled-chromium: Update to 83.0.4103.106-0.f08ce8b [security fixes]....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. Marius Bakke
2020-06-22gnu: icu4c: Add 67.1....* gnu/packages/icu4c.scm (icu4c-67): New public variable. Marius Bakke
2020-06-22gnu: ungoogled-chromium: Specify CPE name....* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: Add CPE-NAME. Marius Bakke
2020-06-22gnu: ungoogled-chromium: Remove non-free file....* gnu/packages/chromium.scm (ungoogled-chromium-source): Remove (unused) SVG file that is licensed under a NoDerivatives license. Marius Bakke
2020-06-22gnu: ungoogled-chromium: Build with ffmpeg@4.2....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. Marius Bakke
2020-06-22gnu: ffmpeg: Enable rav1e on x86_64 only....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. Marius Bakke
2020-06-22system: image: Remove "image-root" derivation when building ISO....The "image-root" derivation output is used as a temporary directory that is passed to GNU Xorriso later on. By merging the creation of this directory and the production of an ISO image, we can get rid of the derivation. * gnu/system/image.scm (system-iso9660-image): Merge "image-root" and "iso9660-image" derivations so that we spare an extra derivation. Mathieu Othacehe
2020-06-22gnu: xl2tpd: Fix build....* gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path instead of trying to set CFLAGS variable. Mathieu Othacehe
2020-06-22gnu: python-plotly: Update to 4.8.1....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> Pierre Langlois
2020-06-22gnu: Add python-xarray....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> Pierre Langlois
2020-06-22gnu: Add python-retrying....* gnu/packages/python-xyz.scm (python-retrying): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pierre Langlois
2020-06-22gnu: python-pandas: Update to 1.0.5....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> Pierre Langlois
2020-06-22gnu: deeptools: Deprecate in favor of python-deeptools....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> Pierre Langlois
2020-06-22self: Build with Guile 3.0.3....* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3. Ludovic Courtès
2020-06-22gnu: emacs-helm: Update to 3.6.3....* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3. Pierre Neidhardt
2020-06-22gnu: emacs-helm-fish-completion: Update to 0.5....* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5. Pierre Neidhardt
2020-06-22gnu: js8call: Fix build....* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib. Guillaume Le Vaillant
2020-06-22gnu: wsjtx: Update to 2.2.1....* gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1. [arguments]: Add a 'fix-tests' phase. (wsjtx): Update to 2.2.1. Guillaume Le Vaillant
2020-06-22gnu: qgis: Disable some failing tests....* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests. Guillaume Le Vaillant
2020-06-22gnu: Add r-rgreat....* gnu/packages/bioconductor.scm (r-rgreat): New variable. Ricardo Wurmus
2020-06-22gnu: rust-libc-0.2: Don't skip build....* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip build. Efraim Flashner
2020-06-22gnu: rust-libc-0.2: Update to 0.2.71....* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71. Efraim Flashner
2020-06-22gnu: rust-rayon-1.3: Rename to rust-rayon-1....* gnu/packages/crates-io.scm (rust-rayon-1.3): Rename to rust-rayon-1. (rust-criterion-0.3, rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5, rust-indexmap-1.3, rust-jpeg-decoder-0.1, rust-nasm-rs-0.1, rust-scroll-0.9, rust-syn-1.0, rust-syn-0.15) [arguments]: Adjust accordingly. * gnu/packages/gnome.scm (librsvg-next)[arguments]: Same. * gnu/packages/rust-apps.scm (tokei)[arguments]: Same. * gnu/packages/video.scm (rav1e)[arguments]: Same. Efraim Flashner
2020-06-22gnu: Remove rust-rayon-1.1....* gnu/packages/crates-io.scm (rust-rayon-1.1): Remove variable. (rust-criterion-0.2, rust-gimli-0.18, rust-hashbrown-0.5, rust-jpeg-decoder-0.1, rust-scroll-0.9, rust-syn-0.15) [arguments]: Replace rust-rayon-1.1 with 1.3. Efraim Flashner
2020-06-22gnu: rust-rayon-core-1.7: Rename to rust-rayon-core-1....* gnu/packages/crates-io.scm (rust-rayon-core-1.7): Rename to rust-rayon-core-1. (rust-criterion-0.2, rust-rayon-1.3, rust-rayon-1.1, rust-rayon-0.8) [arguments]: Adjust accordingly. Efraim Flashner
2020-06-22gnu: Remove rust-rayon-core-1.5....* gnu/packages/crates-io.scm (rust-rayon-core-1.5): Remove variable. (rust-criterion-0.2, rust-rayon-1.1) [arguments]: Replace rust-rayon-core-1.5 with 1.7. Efraim Flashner
2020-06-22gnu: sequoia: Fix typos....* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to the expression it applies to. Efraim Flashner
2020-06-22gnu: rust-regex-1.3: Rename to rust-regex-1....* gnu/packages/crates-io.scm (rust-regex-1.3): Rename to rust-regex-1. (rust-ansi-term-0.12, rust-bindgen-0.52, rust-bindgen-0.51, rust-bindgen-0.50, rust-bindgen-0.37, rust-bindgen-0.49, rust-clap-2, rust-compiletest-rs-0.3, rust-console-0.9, rust-console-0.7, rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1, rust-ignore-0.4, rust-lalrpop-0.17, rust-lalrpop-util-0.17, rust-locale-config-0.3, rust-localeconfig-0.2, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1, rust-rusqlite-0.19, rust-scan-fmt-0.2, rust-syn-1.0, rust-syn-0.15, rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Adjust accordingly. * gnu/packages/gnome.scm (librsvg-next)[arguments]: Same. * gnu/packages/rust-apps.scm (fd, ripgrep, tokei, rust-cargo-c) [arguments]: Same. * gnu/packages/sequoia.scm (sequoia)[arguments]: Same. Efraim Flashner
2020-06-22gnu: Remove rust-regex-1.1....* gnu/packages/crates-io.scm (rust-regex-1.1): Remove variable. (rust-bindgen-0.50, rust-bindgen-0.49, rust-clap-2, rust-compiletest-rs-0.2, rust-console-0.7, rust-docopt-1.1, rust-env-logger-0.7, rust-env-logger-0.6, rust-env-logger-0.5, rust-gimli-0.18, rust-globset-0.4, rust-grep-cli-0.1, rust-grep-matcher-0.1, rust-grep-regex-0.1, rust-grep-searcher-0.1, rust-ignore-0.4, rust-nom-5, rust-nom-4.2, rust-once-cell-1.2, rust-proptest-0.9, rust-proptest-0.8, rust-pulldown-cmark-0.4, rust-regex-automata-0.1, rust-rusqlite-0.19, rust-syn-0.15, rust-ucd-parse-0.1, rust-version-sync-0.8) [arguments]: Replace rust-regex-1.1 with 1.3. * gnu/packages/rust-apps.scm (ripgrep)[arguments]: Same. Efraim Flashner
2020-06-22gnu: Add rust-once-cell-0.1....* gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable. Efraim Flashner
2020-06-22gnu: Add rust-gettext-rs-0.4....* gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable. Efraim Flashner
2020-06-22gnu: Add rust-gettext-sys-0.19....* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable. Efraim Flashner
2020-06-22gnu: Add rust-locale-config-0.2....* gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable. Efraim Flashner
2020-06-22gnu: Add rust-proptest-0.7....* gnu/packages/crates-io.scm (rust-proptest-0.7): New variable. Efraim Flashner
2020-06-22gnu: Add rust-regex-syntax-0.4....* gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable. Efraim Flashner
2020-06-22gnu: Add rust-section-testing-0.0....* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable. Efraim Flashner
2020-06-22gnu: rust-tempfile-3.1: Rename to rust-tempfile-3....* gnu/packages/crates-io.scm (rust-tempfile-3.1): Rename to ... (rust-tempfile-3): .. this. (rust-cairo-rs-0.8, rust-cairo-rs-0.7, rust-cc-1.0, rust-compiletest-rs-0.3, rust-filetime-0.2, rust-gdk-pixbuf-sys-0.9, rust-gio-sys-0.9, rust-git2-0.11, rust-glib-0.9, rust-glib-0.8, rust-glib-sys-0.9, rust-gobject-sys-0.9, rust-handlebars-2.0, rust-lscolors-0.6, rust-native-tls-0.2, rust-nix-0.15, rust-nix-0.14, rust-no-panic-0.1, rust-pango-sys-0.9, rust-pangocairo-0.10, rust-proptest-0.9, rust-proptest-0.8, rust-rustdoc-stripper-0.1, rust-rustls-0.16, rust-rusty-fork-0.2, rust-sourcefile-0.1, rust-tiff-0.2, rust-tokio-0.2, rust-tokio-fs-0.1, rust-tokio-uds-0.2, rust-wayland-client-0.23, rust-wayland-client-0.21, rust-xattr-0.2) [arguments]: Adjust accordingly. * gnu/packages/rust-apps.scm (rust-cbindgen, tokei)[arguments]: Same. * gnu/packages/sequoia.scm (sequoia)[arguments]: Same. * gnu/packages/terminals.scm (alacritty)[arguments]: Same. Efraim Flashner
2020-06-22gnu: Remove rust-tempfile-3.0....* gnu/packages/crates-io.scm (rust-tempfile-3.0): Remove variable. (rust-compiletest-rs-0.3, rust-filetime-0.2, rust-handlebars-2.0, rust-nix-0.15, rust-nix-0.14, rust-proptest-0.9, rust-proptest-0.8, rust-rustls-0.16, rust-rusty-fork-0.2, rust-tiff-0.2, rust-tokei-fs-0.1, rust-tokio-uds-0.2, rust-xattr-0.2) [arguments]: Replace rust-tempfile-3.0 with 3.1. * gnu/packages/rust-apps.scm (tokei)[arguments]: Same. Efraim Flashner
2020-06-22gnu: rust-proptest-0.9: Update to 0.9.6....* gnu/packages/crates-io.scm (rust-proptest-0.9): Update to 0.9. [arguments]: Don't skip build. In cargo-inputs replace rust-rand-0.4 with 0.6, rust-rand-chacha-0.2 with 0.1, rust-rand-xorshift-0.2 with 0.1. Efraim Flashner
2020-06-22gnu: r-zoo: Move to (gnu packages cran)....* gnu/packages/statistics.scm (r-zoo): Move this variable from here... * gnu/packages/cran.scm (r-zoo): ...to here. Ricardo Wurmus
2020-06-22gnu: r-directlabels: Move to (gnu packages cran)....* gnu/packages/statistics.scm (r-directlabels): Move this variable from here... * gnu/packages/cran.scm (r-directlabels): ...to here. Ricardo Wurmus
2020-06-22gnu: r-boruta: Move to (gnu packages cran)....* gnu/packages/statistics.scm (r-boruta): Move this variable from here... * gnu/packages/cran.scm (r-boruta): ...to here. Ricardo Wurmus
2020-06-22gnu: r-boruta: Fix indentation and description....* gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add line breaks, and complete the first sentence fragment. Ricardo Wurmus
2020-06-22gnu: r-fit-models: Update to 0.63....* gnu/packages/statistics.scm (r-fit-models): Update to 0.63. Ricardo Wurmus
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