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Author SHA1 Message Date
Marius Bakke 75527eb1cb
gnu: 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.
 2020-06-22 17:16:39 +02:00
Marius Bakke 8169cc736a
gnu: icu4c: Add 67.1. 
* gnu/packages/icu4c.scm (icu4c-67): New public variable.
 2020-06-22 17:16:39 +02:00
Marius Bakke acac3b94d7
gnu: ungoogled-chromium: Specify CPE name. 
* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: Add CPE-NAME.
 2020-06-22 17:16:39 +02:00
Marius Bakke cafc5f8927
gnu: ungoogled-chromium: Remove non-free file. 
* gnu/packages/chromium.scm (ungoogled-chromium-source): Remove (unused) SVG
file that is licensed under a NoDerivatives license.
 2020-06-22 17:16:39 +02:00
Marius Bakke 3d5a217d5e
gnu: 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.
 2020-06-22 17:16:38 +02:00
Marius Bakke 402d03751c
gnu: 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.
 2020-06-22 17:16:38 +02:00
Mathieu Othacehe 1cb9effc3e
system: 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.
 2020-06-22 17:07:22 +02:00
Mathieu Othacehe 0919d6148f
gnu: xl2tpd: Fix build. 
* gnu/packages/vpn.scm (xl2tpd)[arguments]: Substitute hardcoded pppd path
instead of trying to set CFLAGS variable.
 2020-06-22 16:48:58 +02:00
Pierre Langlois 6e31d6f3c4
gnu: 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>
 2020-06-22 15:44:16 +02:00
Pierre Langlois 3417a25156
gnu: 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>
 2020-06-22 15:44:14 +02:00
Pierre Langlois 7fd33283df
gnu: Add python-retrying. 
* gnu/packages/python-xyz.scm (python-retrying): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-06-22 15:44:12 +02:00
Pierre Langlois 20b545f768
gnu: 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>
 2020-06-22 15:44:08 +02:00
Pierre Langlois 3a79adab41
gnu: 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>
 2020-06-22 15:43:59 +02:00
Ludovic Courtès 955caaab26
self: Build with Guile 3.0.3. 
* gnu/packages/guile.scm (guile-3.0/libgc-7): Inherit from GUILE-3.0.3.
 2020-06-22 15:42:56 +02:00
Ludovic Courtès fe5de925aa
deduplicate: Avoid traversing directories twice. 
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.
 2020-06-22 15:42:55 +02:00
Ludovic Courtès a0d419e639
compile: Build gnu/{packages,tests}/* with '-O1'. 
* guix/build/compile.scm (optimization-options): Use '-O1' for the
simple case.
 2020-06-22 15:42:55 +02:00
Pierre Neidhardt a0dccc71a6
gnu: emacs-helm: Update to 3.6.3. 
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.6.3.
 2020-06-22 15:05:46 +02:00
Pierre Neidhardt 561aeefb0b
gnu: emacs-helm-fish-completion: Update to 0.5. 
* gnu/packages/emacs-xyz.scm (emacs-helm-fish-completion): Update to 0.5.
 2020-06-22 15:01:09 +02:00
Guillaume Le Vaillant 69b82c6078
gnu: js8call: Fix build. 
* gnu/packages/radio.scm (js8call)[inputs]: Use regular hamlib.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant 09e27115d6
gnu: 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.
 2020-06-22 14:50:50 +02:00
Guillaume Le Vaillant 0213f0940e
gnu: qgis: Disable some failing tests. 
* gnu/packages/geo.scm (qgis)[arguments]: Disable a few more failing tests.
 2020-06-22 14:50:50 +02:00
Ricardo Wurmus c89afe7516
gnu: Add r-rgreat. 
* gnu/packages/bioconductor.scm (r-rgreat): New variable.
 2020-06-22 14:39:03 +02:00
Efraim Flashner 277ac1f242
gnu: rust-libc-0.2: Don't skip build. 
* gnu/packages/crates-io.scm (rust-libc-0.2)[arguments]: Don't skip
build.
 2020-06-22 14:15:34 +03:00
Efraim Flashner a1b79c09ee
gnu: rust-libc-0.2: Update to 0.2.71. 
* gnu/packages/crates-io.scm (rust-libc-0.2): Update to 0.2.71.
 2020-06-22 14:15:34 +03:00
Efraim Flashner a56305539f
gnu: 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 6c2189c858
gnu: 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 8781c8edd2
gnu: 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.
 2020-06-22 14:15:34 +03:00
Efraim Flashner 4f76fbfcd9
gnu: 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner df4d2ddaee
gnu: sequoia: Fix typos. 
* gnu/packages/sequoia.scm (sequoia)[arguments]: Move unquote next to
the expression it applies to.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 6cd7b35544
gnu: 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 9c13497df4
gnu: 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.
 2020-06-22 14:15:33 +03:00
Efraim Flashner 80cfe5458c
gnu: Add rust-once-cell-0.1. 
* gnu/packages/crates-io.scm (rust-once-cell-0.1): New variable.
 2020-06-22 14:15:33 +03:00
Efraim Flashner f4022d8549
gnu: Add rust-gettext-rs-0.4. 
* gnu/packages/crates-io.scm (rust-gettext-rs-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner e1240cb249
gnu: Add rust-gettext-sys-0.19. 
* gnu/packages/crates-io.scm (rust-gettext-sys-0.19): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner b3987cd3d2
gnu: Add rust-locale-config-0.2. 
* gnu/packages/crates-io.scm (rust-locale-config-0.2): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner d77146e9fe
gnu: Add rust-proptest-0.7. 
* gnu/packages/crates-io.scm (rust-proptest-0.7): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner eba1524df2
gnu: Add rust-regex-syntax-0.4. 
* gnu/packages/crates-io.scm (rust-regex-syntax-0.4): New variable.
 2020-06-22 14:15:32 +03:00
Efraim Flashner 5247f79db6
gnu: Add rust-section-testing-0.0. 
* gnu/packages/crates-io.scm (rust-section-testing-0.0): New variable.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 7c6948c71e
gnu: 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.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 0c9bca4ffe
gnu: 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.
 2020-06-22 14:15:31 +03:00
Efraim Flashner 9f2bb42bee
gnu: 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.
 2020-06-22 14:15:28 +03:00
Ricardo Wurmus fae72ebb49
gnu: 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.
 2020-06-22 12:46:03 +02:00
Ricardo Wurmus d30ab75a7d
gnu: 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.
 2020-06-22 12:42:19 +02:00
Ricardo Wurmus 5c1aab1dc1
gnu: 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.
 2020-06-22 12:39:51 +02:00
Ricardo Wurmus 6c9834f59f
gnu: r-boruta: Fix indentation and description. 
* gnu/packages/statistics.scm (r-boruta)[description]: Fix indentation, add
line breaks, and complete the first sentence fragment.
 2020-06-22 12:38:41 +02:00
Ricardo Wurmus 62648f4ae3
gnu: r-fit-models: Update to 0.63. 
* gnu/packages/statistics.scm (r-fit-models): Update to 0.63.
 2020-06-22 12:15:51 +02:00
Ricardo Wurmus 913eaa619c
gnu: r-glmnet: Update to 4.0-2. 
* gnu/packages/statistics.scm (r-glmnet): Update to 4.0-2.
[propagated-inputs]: Add r-survival.
 2020-06-22 12:15:51 +02:00
Ricardo Wurmus 15bee10afe
gnu: r-rmarkdown: Update to 2.3. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.3.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 55e89c6aa6
gnu: r-backports: Update to 1.1.8. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.8.
 2020-06-22 12:15:50 +02:00
Ricardo Wurmus 3c37c67224
gnu: r-ggplot2: Update to 3.3.2. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.2.
 2020-06-22 12:15:50 +02:00