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2020-06-22gnu: Add python-pytest-lazy-fixture.Vinicius Monego
* gnu/packages/check.scm (python-pytest-lazy-fixture): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2020-06-22gnu: r-with-tests, r-minimal: Update to 4.0.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.2.
2020-06-22system: image: Remove "image-root" when building raw disk-images.Mathieu Othacehe
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.
2020-06-22gnu: gn: Update to 0.0-1794.eb997b5.Marius Bakke
* gnu/packages/build-tools.scm (gn): Update to 0.0-1794.eb997b5.
2020-06-22gnu: ungoogled-chromium: Update to 83.0.4103.106-0.f08ce8b [security fixes].Marius Bakke
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.
2020-06-22gnu: icu4c: Add 67.1.Marius Bakke
* gnu/packages/icu4c.scm (icu4c-67): New public variable.
2020-06-22gnu: ungoogled-chromium: Specify CPE name.Marius Bakke
* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: Add CPE-NAME.
2020-06-22gnu: ungoogled-chromium: Remove non-free file.Marius Bakke
* gnu/packages/chromium.scm (ungoogled-chromium-source): Remove (unused) SVG file that is licensed under a NoDerivatives license.
2020-06-22gnu: ungoogled-chromium: Build with ffmpeg@4.2.Marius Bakke
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.
2020-06-22gnu: ffmpeg: Enable rav1e on x86_64 only.Marius Bakke
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.
2020-06-22system: image: Remove "image-root" derivation when building ISO.Mathieu Othacehe
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.
2020-06-22gnu: xl2tpd: Fix build.Mathieu Othacehe
* gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path instead of trying to set CFLAGS variable.
2020-06-22gnu: python-plotly: Update to 4.8.1.Pierre Langlois
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>
2020-06-22gnu: Add python-xarray.Pierre Langlois
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>
2020-06-22gnu: Add python-retrying.Pierre Langlois
* gnu/packages/python-xyz.scm (python-retrying): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22gnu: python-pandas: Update to 1.0.5.Pierre Langlois
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>
2020-06-22gnu: deeptools: Deprecate in favor of python-deeptools.Pierre Langlois
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>
2020-06-22self: Build with Guile 3.0.3.Ludovic Courtès
* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
2020-06-22deduplicate: Avoid traversing directories twice.Ludovic Courtès
Until now, we'd call (nar-sha256 file) unconditionally. Thus, if FILE was a directory, we would traverse it for no reason, and then call 'deduplicate' on FILE, which would again traverse it. This change also removes redundant (mkdir-p store) calls from the loop, and avoids 'lstat' calls by using 'scandir*'. * guix/store/deduplication.scm (deduplicate): Add named loop. Move 'mkdir-p' outside the loop. Use 'scandir*' instead of 'scandir'. Do not call 'nar-sha256' when FILE has type 'directory.
2020-06-22compile: Build gnu/{packages,tests}/* with '-O1'.Ludovic Courtès
* guix/build/compile.scm (optimization-options): Use '-O1' for the simple case.
2020-06-22gnu: emacs-helm: Update to 3.6.3.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
2020-06-22gnu: emacs-helm-fish-completion: Update to 0.5.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
2020-06-22gnu: js8call: Fix build.Guillaume Le Vaillant
* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
2020-06-22gnu: wsjtx: Update to 2.2.1.Guillaume Le Vaillant
* gnu/packages/radio.scm (wsjtx-hamlib): Update to 2.2.1. [arguments]: Add a 'fix-tests' phase. (wsjtx): Update to 2.2.1.
2020-06-22gnu: qgis: Disable some failing tests.Guillaume Le Vaillant
* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
2020-06-22gnu: Add r-rgreat.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rgreat): New variable.
2020-06-22gnu: rust-libc-0.2: Don't skip build.Efraim Flashner
* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip build.
2020-06-22gnu: rust-libc-0.2: Update to 0.2.71.Efraim Flashner
* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.
2020-06-22gnu: rust-rayon-1.3: Rename to rust-rayon-1.Efraim Flashner
* 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.
2020-06-22gnu: Remove rust-rayon-1.1.Efraim Flashner
* 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.
2020-06-22gnu: rust-rayon-core-1.7: Rename to rust-rayon-core-1.Efraim Flashner
* 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.
2020-06-22gnu: Remove rust-rayon-core-1.5.Efraim Flashner
* 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.
2020-06-22gnu: sequoia: Fix typos.Efraim Flashner
* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to the expression it applies to.
2020-06-22gnu: rust-regex-1.3: Rename to rust-regex-1.Efraim Flashner
* 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.
2020-06-22gnu: Remove rust-regex-1.1.Efraim Flashner
* 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.
2020-06-22gnu: Add rust-once-cell-0.1.Efraim Flashner
* gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable.
2020-06-22gnu: Add rust-gettext-rs-0.4.Efraim Flashner
* gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable.
2020-06-22gnu: Add rust-gettext-sys-0.19.Efraim Flashner
* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.
2020-06-22gnu: Add rust-locale-config-0.2.Efraim Flashner
* gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable.
2020-06-22gnu: Add rust-proptest-0.7.Efraim Flashner
* gnu/packages/crates-io.scm (rust-proptest-0.7): New variable.
2020-06-22gnu: Add rust-regex-syntax-0.4.Efraim Flashner
* gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable.
2020-06-22gnu: Add rust-section-testing-0.0.Efraim Flashner
* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.
2020-06-22gnu: rust-tempfile-3.1: Rename to rust-tempfile-3.Efraim Flashner
* 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.
2020-06-22gnu: Remove rust-tempfile-3.0.Efraim Flashner
* 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.
2020-06-22gnu: rust-proptest-0.9: Update to 0.9.6.Efraim Flashner
* 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.
2020-06-22gnu: r-zoo: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Move this variable from here... * gnu/packages/cran.scm (r-zoo): ...to here.
2020-06-22gnu: r-directlabels: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/statistics.scm (r-directlabels): Move this variable from here... * gnu/packages/cran.scm (r-directlabels): ...to here.
2020-06-22gnu: r-boruta: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/statistics.scm (r-boruta): Move this variable from here... * gnu/packages/cran.scm (r-boruta): ...to here.
2020-06-22gnu: r-boruta: Fix indentation and description.Ricardo Wurmus
* gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add line breaks, and complete the first sentence fragment.
2020-06-22gnu: r-fit-models: Update to 0.63.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fit-models): Update to 0.63.
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