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Author SHA1 Message Date
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
Efraim Flashner 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
Ricardo Wurmus 5ea5ea6066
gnu: Add python-pyliftover.
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
2021-04-28 10:52:12 +02:00
Efraim Flashner 562c3a4e12
gnu: keepassxc: Wrap binary with wrap-qt-program.
* gnu/packages/password-utils.scm (keepassxc)[arguments]: Import
qt-utils module. Replace custom 'wrap-bin phase with 'wrap-qt phase.
2021-04-28 11:43:34 +03:00
Ricardo Wurmus d027637026
gnu: slurm: Link plugins with libslurm.
* gnu/packages/parallel.scm (slurm)[arguments]: Add phase
patch-plugin-linker-flags to link plugins with libslurm; run autoconf phase
after this new phase.
2021-04-28 10:18:07 +02:00
Ricardo Wurmus ffd5bc9600
gnu: krona-tools: Install download scripts.
* gnu/packages/web.scm (krona-tools)[inputs]: Add curl and make.
[arguments]: Patch and install update scripts to /share.
2021-04-28 10:18:07 +02:00
Ricardo Wurmus fe28f395bc
gnu: krona-tools: Update to 2.8.
* gnu/packages/web.scm (krona-tools): Update to 2.8.
2021-04-28 10:18:07 +02:00
Timothy Sample e74250c3c5
Revert "download: Use Disarchive as a last resort."
This reverts commit 66b14dccdd, which broke
'guix pull'.
2021-04-28 00:24:28 -04:00
Leo Famulari 1f6854bd06
gnu: Add mmc-utils.
* gnu/packages/disk.scm (mmc-utils): New variable.
2021-04-28 00:01:17 -04:00
Timothy Sample 66b14dccdd
download: Use Disarchive as a last resort.
* guix/download.scm (%disarchive-mirrors): New variable.
(%disarchive-mirror-file): New variable.
(built-in-download): Add 'disarchive-mirrors' keyword argument and
pass its value along to the 'builtin:download' derivation.
(url-fetch): Pass '%disarchive-mirror-file' to 'built-in-download'.
* guix/scripts/perform-download.scm (perform-download): Read
Disarchive mirrors from the environment and pass them to
'url-fetch'.
* guix/build/download.scm (disarchive-fetch/any): New procedure.
(url-fetch): Add 'disarchive-mirrors' keyword argument, use it to
make a list of URIs, and use the new procedure to fetch the file if
all other methods fail.
2021-04-27 21:27:02 -04:00
Timothy Sample 4f59ef3edb
swh: Add a directory download procedure.
* guix/swh.scm (swh-directory-download): New procedure (with
implementation extracted from 'swh-download').
(swh-download): Use it to download the revision directory.
2021-04-27 21:26:50 -04:00
methuselah-0 3802bb0ba0
services: mysql: Add extra-environment as configuration option.
* gnu/services/databases.scm (mysql-configuration): Add extra-environment
(mysql-service): Use #:log-file and #:environment-variables
* doc/guix.texi: Document it.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>
2021-04-27 20:45:35 +02:00
Efraim Flashner 1f5543e7ff
gnu: Add gdc-11.
* gnu/packages/gcc.scm (gdc-11): New variable.
2021-04-27 17:10:22 +03:00
Efraim Flashner 007ec66206
gnu: Add gcc-toolchain-11.
* gnu/packages/gcc.scm (gcc-11): New variable.
* gnu/packages/commencement.scm (gcc-toolchain-11): New variable.
2021-04-27 17:10:22 +03:00
Tobias Geerinckx-Rice e97376c15f
gnu: lagrange: Update to 1.3.4.
* gnu/packages/web-browsers.scm (lagrange): Update to 1.3.4.
2021-04-27 15:59:05 +02:00
Tobias Geerinckx-Rice 19f67a9197
gnu: ugrep: Use GIT-FILE-NAME helper.
* gnu/packages/search.scm (ugrep)[source]: Use GIT-FILE-NAME.
2021-04-27 15:54:00 +02:00
Tobias Geerinckx-Rice 4206cf1fa8
gnu: ugrep: Update to 3.1.12.
* gnu/packages/search.scm (ugrep): Update to 3.1.12.
2021-04-27 15:54:00 +02:00
Efraim Flashner f664c4234e
gnu: gcide: Update to 0.53.
* gnu/packages/dictionaries.scm (gcide): Update to 0.53.
2021-04-27 16:32:32 +03:00
Tobias Geerinckx-Rice 5203ef4d4e
gnu: freecad: Update to 0.19.2.
* gnu/packages/engineering.scm (freecad): Update to 0.19.2.
2021-04-27 15:06:24 +02:00
Tobias Geerinckx-Rice e009b8d712
gnu: html2text: Add informative BSD-4 licence.
* gnu/packages/textutils.scm (html2text)[license]: Add bsd-4.
2021-04-27 14:03:16 +02:00
Tobias Geerinckx-Rice 5c81cbda5e
gnu: html2text: Fix cross-compilation.
* gnu/packages/textutils.scm (html2text)[arguments]: Set $CXX to
the correct (CC-FOR-TARGET).
2021-04-27 13:57:45 +02:00
Tobias Geerinckx-Rice b0020938e1
gnu: html2text: Run ./configure without errors.
* gnu/packages/textutils.scm (html2text)[arguments]: Add a custom
'configure phase.  Replace the custom 'fix-paths phase with the
customary #:make-flags equivalent.
2021-04-27 13:54:44 +02:00
Guillaume Le Vaillant b43e9c8ecd
gnu: Add html2text.
* gnu/packages/textutils.scm (html2text): New variable.
2021-04-27 13:36:16 +02:00
Tobias Geerinckx-Rice bb9e77b544
gnu: python-skyfield: Match up input and variable names.
* gnu/packages/astronomy.scm (python-skyfield)[inputs]: Add "python-"
prefix to alist keys.
2021-04-27 12:26:19 +02:00
Tobias Geerinckx-Rice 6cf85268af
gnu: python-skyfield: Update to 1.39.
* gnu/packages/astronomy.scm (python-skyfield): Update to 1.39.
2021-04-27 12:26:19 +02:00
Tobias Geerinckx-Rice f063e411c0
gnu: python-pyerfa: Update to 1.7.3.
* gnu/packages/astronomy.scm (python-pyerfa): Update to 1.7.3.
2021-04-27 12:26:19 +02:00
Tobias Geerinckx-Rice bea70c372c
gnu: debootstrap: Update to 1.0.124.
* gnu/packages/debian.scm (debootstrap): Update to 1.0.124.
2021-04-27 12:26:18 +02:00
Tobias Geerinckx-Rice de5da4db36
gnu: bpytop: Update to 1.0.64.
* gnu/packages/admin.scm (bpytop): Update to 1.0.64.
[description]: Follow upstream changes.
2021-04-27 12:26:18 +02:00