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Author SHA1 Message Date
Roel Janssen
558d11c3a8
gnu: Update samtools to 1.12.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
2021-04-29 12:14:02 +02:00
Roel Janssen
b904bb89a0
gnu: Update bcftools to 1.12.
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
2021-04-29 12:13:56 +02:00
Roel Janssen
241994230b
gnu: htslib: Update to 1.12.
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
2021-04-29 12:13:46 +02:00
Mathieu Othacehe
a6a36059d5
gnu: kmscon: Fix layout setup.
Kmscon may discover multiple inputs, corresponding to multiple devices. This
means that the uxkb_dev_keymap_update function may be called multiple times,
and the FIFO is registered on each input poll loop.

When a new layout is written on the FIFO by the installer, the first input
picking up the message, will apply the new layout. However, that input may not
be the input that the user is currently using.

To fix it, register the FIFO on the first input poll loop, but apply the new
layout on all the inputs in the uxkb_keymap_update_handler function.

* gnu/packages/patches/kmscon-runtime-keymap-switch.patch
(uxkb_keymap_update_handler): Apply the new layout to all the inputs.
(input_new_dev): Register the FIFO fd only on the first input poll loop.
2021-04-29 12:12:13 +02:00
Ricardo Wurmus
74b3f2cbb1
gnu: Add r-qpcr.
* gnu/packages/cran.scm (r-qpcr): New variable.
2021-04-29 09:55:57 +02:00
Kyle Meyer
04ef4c7880
gnu: git-annex: Update to 8.20210428.
* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210428.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-29 10:17:23 +03:00
Ryan Prior
eed2c4843f
gnu: oil: Update to 0.8.10.
* gnu/packages/shells.scm (oil): Update to 0.8.10.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-29 10:14:03 +03:00
BonfaceKilz
f2b2016bfd
gnu: Add python-hissp.
* gnu/packages/python-xyz.scm (python-hissp): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-29 10:01:16 +03:00
Kei Kebreau
685e4733ad
gnu: xaos: Update to 4.2.1.
* gnu/packages/maths.scm (xaos): Update to 4.2.1.
[arguments]: Patch call to "lrelease" in XaoS.pro.
2021-04-29 00:44:03 -04:00
Vagrant Cascadian
d018a11ee0
gnu: linux-libre-arm64-generic@5.10: Add eDP panel, audio and battery
support for Pinebook Pro.

* gnu/packages/linux.scm (linux-libre-5.10-source): Add pinebook pro lcd patch.
  (linux-libre-arm64-generic-5.10): Add audio and battery modules.
2021-04-28 16:56:58 -07:00
Vagrant Cascadian
e7fbf10066
gnu: linux-libre-arm64-generic: Add eDP panel, battery and audio
support for Pinebook Pro.

* gnu/packages/linux.scm (linux-libre-5.11-source): Add Pinebook Pro
  lcd patch.
  (linux-libre-arm64-generic): Enable audio and battery modules for
  Pinebook Pro.
* gnu/packages/patches/linux-libre-arm64-generic-pinebook-lcd.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patch.
2021-04-28 16:56:35 -07:00
Ludovic Courtès
9dc1c591a4
inferior: Make sure test refers to guile@3.0.
* tests/inferior.scm ("inferior-package-inputs"): Compare with
GUILE-3.0-LATEST since that's what 'lookup-inferior-packages' returns.
2021-04-29 01:22:04 +02:00
Ludovic Courtès
524c9800af
diagnostics, ui: Adjust to 'read-error' and 'syntax-error' in Guile 3.0.6.
* guix/diagnostics.scm (source-properties->location): Add clause for
vectors.
* guix/ui.scm (report-load-error): Tweak 'read-error' handling for 3.0.6.
* tests/guix-package.sh: Relax regexp for the "unbound variable"
diagnostic check.
* tests/guix-system.sh: Adjust "missing closing paren" check for 3.0.6.
* tests/records.scm (location-alist): New procedure.
("define-record-type* & wrong field specifier")
("define-record-type* & wrong field specifier, identifier")
("define-record-type* & duplicate initializers"): Use it.
2021-04-29 01:22:04 +02:00
Ludovic Courtès
0ce1b28151
packages: 'package-with-patches' preserves package location.
* guix/packages.scm (package-with-patches): Preserve the 'location'
field of ORIGINAL.
2021-04-29 01:22:04 +02:00
Xinglu Chen
0d570b6019
gnu: emacs-hyperbole: Install images and help files.
* gnu/packages/emacs-xyz.scm (emacs-hyperbole)[arguments]: Include help file
and install images for the manual.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-04-29 00:29:41 +02:00
Xinglu Chen
43684b19da
gnu: emacs-corfu: Update to 0.4.
* gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.4.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-04-29 00:25:29 +02:00
Leo Famulari
22b3dd559c
gnu: isc-dhcp: Update bundled BIND to 9.11.31 [security fixes].
Fixes CVE-2021-{25214,25215,25216].

* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.31.
2021-04-28 17:26:05 -04:00
Tobias Geerinckx-Rice
b95f422714
gnu: bind: Update to 9.16.15 [fixes CVE-2021-25214, CVE-2021-25215, CVE-2021-25216].
* gnu/packages/dns.scm (isc-bind): Update to 9.16.15.
2021-04-28 22:35:13 +02:00
Leo Famulari
958613f1af
gnu: linux-libre 4.4: Update to 4.4.268.
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.268.
(linux-libre-4.4-pristine-source): Update hash.
2021-04-28 16:32:54 -04:00
Leo Famulari
cdd22eacae
gnu: linux-libre 4.9: Update to 4.9.268.
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.268.
(linux-libre-4.9-pristine-source): Update hash.
2021-04-28 16:32:54 -04:00
Leo Famulari
a3535c4383
gnu: linux-libre 4.14: Update to 4.14.232.
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.232.
(linux-libre-4.14-pristine-source): Update hash.
2021-04-28 16:32:54 -04:00
Leo Famulari
75d8067779
gnu: linux-libre 4.19: Update to 4.19.189.
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.189.
(linux-libre-4.19-pristine-source): Update hash.
2021-04-28 16:32:54 -04:00
Leo Famulari
3d1c37122e
gnu: linux-libre 5.4: Update to 5.4.115.
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.115.
(linux-libre-5.4-pristine-source): Update hash.
2021-04-28 16:32:53 -04:00
Leo Famulari
4499655166
gnu: linux-libre 5.10: Update to 5.10.33.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.33.
(linux-libre-5.10-pristine-source): Update hash.
2021-04-28 16:32:53 -04:00
Leo Famulari
82eb714cb3
gnu: linux-libre: Update to 5.11.17.
* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.17.
(linux-libre-5.11-pristine-source): Update hash.
2021-04-28 16:32:47 -04:00
Marius Bakke
2b063d92d2
.guix-authorizations: Remove lle_bout.
* .guix-authorizations: Remove lle_bout from the committers.
2021-04-28 22:03:18 +02:00
Ricardo Wurmus
e7707d5262
gnu: pigx-bsseq: Update to 0.1.3.
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3.
[inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
2021-04-28 21:58:05 +02:00
Tobias Geerinckx-Rice
7f9888516f
gnu: ustr: Don't use vsnprintf.
This follows up on 1059d1570b,
which caused new tests failures on non-cross builds.

* gnu/packages/textutils.scm (ustr)[arguments]: Return "0" for
./autoconf_vsnprintf.
2021-04-28 21:41:20 +02:00
Nicolas Goaziou
bbdd43fd11
gnu: giac: Update to 1.7.0-3.
* gnu/packages/algebra.scm (giac): Update to 1.7.0-3.
2021-04-28 21:37:16 +02:00
Nicolas Goaziou
510fbf7f93
gnu: python-pikepdf: Update to 2.11.4.
* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.11.4.
2021-04-28 21:30:39 +02:00
Nicolas Goaziou
00c06f3aae
gnu: emacs-auctex: Update to 13.0.10.
* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.0.10.
2021-04-28 21:27:26 +02:00
Tobias Geerinckx-Rice
1059d1570b
gnu: ustr: Cross-compile.
Also fix <http://issues.guix.gnu.org/48084>.

* gnu/packages/text-utils.scm (ustr)[arguments]: Use CC-FOR-TARGET.
Add a new 'fix-cross-compilation phase.
2021-04-28 20:48:22 +02:00
Tobias Geerinckx-Rice
f3b2d6681c
gnu: less: Update to 581.2.
* gnu/packages/less.scm (less): Update to 581.2.
2021-04-28 19:11:14 +02:00
Tobias Geerinckx-Rice
a8dde2fd17
gnu: iproute2: Update to 5.12.0.
* gnu/packages/linux.scm (iproute2): Update to 5.12.0.
2021-04-28 19:11:13 +02:00
Tobias Geerinckx-Rice
9dbedb8bae
gnu: folly: Update to 2021.04.26.00.
* gnu/packages/cpp.scm (folly): Update to 2021.04.26.00.
2021-04-28 19:11:13 +02:00
Tobias Geerinckx-Rice
97d9814167
gnu: xsimd: Update to 7.5.0.
* gnu/packages/cpp.scm (xsimd): Update to 7.5.0.
2021-04-28 19:11:13 +02:00
Tobias Geerinckx-Rice
794bb59b19
gnu: fcitx-qt5: Update to 1.2.6.
* gnu/packages/fcitx.scm (fcitx-qt5): Update to 1.2.6.
2021-04-28 19:11:12 +02:00
Marius Bakke
8dcbd8a374
gnu: ungoogled-chromium: Update to 90.0.4430.93.
* gnu/packages/patches/ungoogled-chromium-system-nspr.patch,
gnu/packages/patches/ungoogled-chromium-system-opus.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for 90.
(debian-patch): Make REVISION optional, default to %DEBIAN-REVISION.
(%chromium-version): New variable.
(%ungoogled-revision): Set to 90.0.4430.85-1-11-g3184907.
(%debian-revision): Set to debian/90.0.4430.85-1.
(%debian-patches): Add more patches; update hashes.
(%ungoogled-origin): Update hash.
(%guix-patches): Remove obsolete patches.
(libvpx/chromium): Update to 1.9.0-147-g61edec1ef.
(ungoogled-chromium)[version]: Base on %CHROMIUM-REVISION and the last
component of %UNGOOGLED-REVISION, a 'git describe --long' style ID.
[arguments]: Add build_with_flite_lib in #:configure-flags.  Add openjpeg
substitution in #:phases.
2021-04-28 17:59:32 +02:00
Marius Bakke
cc03603514
gnu: uBlock Origin: Update to 1.35.0.
* gnu/packages/browser-extensions.scm (uassets): Update to edfb13aae.
(ublock-origin): Update to 1.35.0.
2021-04-28 17:59:32 +02:00
Marius Bakke
8fa86141b7
gnu: LLVM, Clang: Add 12.0.0.
* gnu/packages/patches/clang-12-tools-extra-directory.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/llvm.scm (llvm-12, clang-runtime-12, clang-12,
clang-toolchain-12): New variables.
(llvm-11): Inherit from LLVM-12.
2021-04-28 17:59:32 +02:00
Ricardo Wurmus
01e33a031e
gnu: Add lofreq.
* gnu/packages/bioinformatics.scm (lofreq): New variable.
2021-04-28 17:41:47 +02:00
Mathieu Othacehe
95b3fc12bc
tests: Add gui-uefi-installed-os test.
* gnu/installer/tests.scm (conclude-installation): Rename it into ...
(start-installation): ... this new procedure.
(complete-installation): New procedure.
(choose-partitioning): Add an uefi-support? argument.
* gnu/tests/install.scm (uefi-firmware): New procedure.
(run-install, qemu-command/writable-image, gui-test-program,
installation-target-os-for-gui-tests): Add an uefi-support? argument.
(%extra-packages): Add grub-efi, fatfsck/static and dosfstools.
(%test-gui-installed-os): New variable.
2021-04-28 15:51:12 +02:00
Mathieu Othacehe
af7a615c5b
installer: Add MSDOS disk label support on UEFI systems.
Fixes: <https://issues.guix.gnu.org/47889>.

* gnu/installer/parted.scm (esp-partition?): Remove the MSDOS check.
(auto-partition!): On MSDOS disks, check if an ESP partition is present. If
that's the case, do not remove it. Otherwise, if UEFI is supported, create
one.
2021-04-28 15:50:02 +02:00
Mathieu Othacehe
3f8ea83e2a
installer: Force GPT disk label when UEFI is supported.
* gnu/installer/newt/partition.scm (run-label-page): Force the GPT disk label
when UEFI is supported.
2021-04-28 15:49:53 +02:00
Ricardo Wurmus
f01b3cd063
gnu: kraken2: Replace references to rsync.
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
2021-04-28 14:50:50 +02:00
f7ff886213
gnu: global: Fix cross compiling.
Coreutils was removed during patch review erroneously.
Reported by Maxime Devos <maximedevos@telenet.be>.

* gnu/packages/code.scm (global)[inputs]: Add coreutils.
2021-04-28 14:41:31 +03:00
Mathieu Othacehe
f97e220b45
ci: Add custom subset.
* gnu/ci.scm (cuirass-jobs): Add 'custom susbset.
2021-04-28 11:53:33 +02:00
Mathieu Othacehe
3034f3d05b
ci: Add arguments->systems procedure.
* gnu/ci.scm (arguments->systems): New procedure.
(cuirass-jobs): Use it.
2021-04-28 11:53:32 +02:00
Mathieu Othacehe
996b5edf51
ci: Factorize image->job procedure.
* gnu/ci.scm (image-jobs): Extract ->job procedure into ...
(image->job): ... this new procedure.
2021-04-28 11:53:32 +02:00
luhui
93242b54e4
gnu: global: Fix globash.
* gnu/packages/code.scm (global)[arguments]: Add 'fix-globash phase.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-04-28 12:25:09 +03:00