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Author SHA1 Message Date
Mathieu Othacehe
7f75a7ec08
system: 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.
 2020-06-22 17:49:19 +02:00
Marius Bakke
cf14e67963
gnu: gn: Update to 0.0-1794.eb997b5. 
* gnu/packages/build-tools.scm (gn): Update to 0.0-1794.eb997b5.
 2020-06-22 17:16:39 +02:00
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