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2020-11-13maint: Add '.guix-authorizations' to the distribution.Ludovic Courtès
Reported by Vagrant Cascadian. * Makefile.am (EXTRA_DIST): Add .guix-authorizations.
2020-11-13gnu: julia: Update to 1.5.3.Tobias Geerinckx-Rice
* gnu/packages/julia.scm (julia): Update to 1.5.3. (libuv-julia): Update to 1fcc6d66f9df74189c74d3d390f02202bb7db953. (julia-patch): Update version. No change to patches.
2020-11-13gnu: libwhich: Compile natively, too.Tobias Geerinckx-Rice
This follows up on commit 12424b3ecfdf401c72804ddfa4b2fa2d8b1b68e5. * gnu/packages/julia.scm (libwhich)[arguments]: Fix non-cross compilation.
2020-11-13guix build: Expose log-url for third parties.John Soo
* guix/scripts/build.scm (log-url): Expose it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-11-13pack: Expose some bindings for third-party use.John Soo
* guix/scripts/pack.scm (compressor-name, compressor-extension, compressor-command, %compressors, %formats): Export. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-11-13Merge branch 'version-1.2.0' of ssh://git.sv.gnu.org/srv/git/guix into ↵Ludovic Courtès
version-1.2.0
2020-11-13gnu: python-pysam: Update to version 0.16.0.1.Maxim Cournoyer
The check phase was failing with: starting phase `check' make: Entering directory '...drv-0/python-pysam-0.15.1-checkout/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam [main] "samtools import" has been removed. Please use "samtools view" instead. make: *** [Makefile:56: ex1.bam] Error 1 * gnu/packages/bioinformatics.scm (python-pysam): Update to version 0.16.0.1. [phases]{check}: Delete a couple more failing test files. [native-inputs]: Add python-pytest.
2020-11-13gnu: Fix build for python-pysam.Roel Janssen
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9, samtools-1.9, and bcftools-1.9.
2020-11-13gnu: Add bcftools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
2020-11-13gnu: dino: Update to 0.2.0Ekaitz Zarraga
Update of the recently released Dino 0.2.0 version. Thanks! From 0b764d48996f3851ee2596a25f1fd42a8d3f4063 Mon Sep 17 00:00:00 2001 From: Ekaitz Zarraga <ekaitz@elenq.tech> Date: Fri, 13 Nov 2020 12:18:11 +0100 Subject: [PATCH] gnu: dino: Update to 0.2.0 * gnu/packages/messaging.scm (dino): Update to 0.2.0 Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2020-11-13gnu: libwhich: Cross-compile.Tobias Geerinckx-Rice
* gnu/packages/julia.scm (libwhich)[arguments]: Use CC-FOR-TARGET. Look for zlib in NATIVE-INPUTS.
2020-11-13gnu: guix: Update to 3ba6ffd.Ludovic Courtès
2020-11-13gnu: bedtools: Use samtools-1.9.Roel Janssen
The build for bedtools with samtools 1.11 triggers a testsuite failure which is reported here: https://github.com/arq5x/bedtools2/issues/814 * gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
2020-11-13gnu: Add samtools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
2020-11-13gnu: Add htslib-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
2020-11-13gnu: guix: Update to 1.2.0rc1.Ludovic Courtès
2020-11-13Update NEWS.Ludovic Courtès
2020-11-13gnu: glib: Graft patch to detect changes to the installed applications.Ludovic Courtès
Fixes <https://bugs.gnu.org/35594>. Reported by sirgazil <sirgazil@zoho.com> and others. * gnu/packages/patches/glib-appinfo-watch.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/glib.scm (glib)[replacement]: New field. (glib-with-gio-patch): New variable. (glib-with-documentation): Use 'package/inherit'.
2020-11-13maint: Use 'guix' instead of 'guile3.0-guix' for the binary tarball.Ludovic Courtès
* Makefile.am (GUIX_FOR_BINARY_TARBALL): Change to 'guix'.
2020-11-13gnu: vim: Update to 8.2.1980.Tobias Geerinckx-Rice
* gnu/packages/vim.scm (vim): Update to 8.2.1980.
2020-11-13gnu: criu: Support nftables.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (criu)[inputs]: Add nftables.
2020-11-13gnu: criu: Update to 3.15.Tobias Geerinckx-Rice
* gnu/packages/virtualization.scm (criu): Update to 3.15.
2020-11-13gnu: youtube-dl: Update to 2020.11.12.Tobias Geerinckx-Rice
* gnu/packages/video.scm (youtube-dl): Update to 2020.11.12.
2020-11-13gnu: knot: Update to 3.0.2.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (knot): Update to 3.0.2.
2020-11-13gnu: muchsync: Update to 6.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (muchsync): Update to 6.
2020-11-13gnu: gpxsee: Update to 7.36.Tobias Geerinckx-Rice
* gnu/packages/gps.scm (gpxsee): Update to 7.36.
2020-11-12gnu: alot: Update to 0.9.1.Tanguy Le Carrour
* gnu/packages/mail.scm (alot): Update to 0.9.1. [arguments]: Fix some tests and disable some others. [native-inputs]: Add procps. [inputs]: Remove python2-magic, python2-configobj, python2-twisted, python2-urwid, python2-urwidtrees, python2-pygpgme and python2-notmuch. Add gnupg, python-magic, python-configobj, python-twisted, python-service-identity, python-urwid, python-urwidtrees, python-gpg and python-notmuch. [synopsis]: Update synopsis. [description]: Update description. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2020-11-12gnu: afew: Update to 3.0.1.Tanguy Le Carrour
* gnu/packages/mail.scm (afew): Update to 3.0.1. [inputs]: Add notmuch and python-dkimpy. [native-inputs]: Add python-freezegun. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2020-11-12gnu: ungoogled-chromium: Update to 86.0.4240.198-0.b68e17f [security fixes].Marius Bakke
This fixes CVE-2020-16013 and CVE-2020-16017. * gnu/packages/chromium.scm (%chromium-version): Set to 86.0.4240.198. (ungoogled-chromium): Update hash.
2020-11-12gnu: python-flask-basicauth: Fix indentation.Maxim Cournoyer
* gnu/packages/python-web.scm (python-flask-basicauth): Fix indentation.
2020-11-12gnu: python-flask-basicauth: Fix build.Maxim Cournoyer
* gnu/packages/python-web.scm (python-flask-basicauth)[phases]: Add a 'fix-imports phase.
2020-11-12gnu: tor: Update to 0.4.4.6 [fixes TROVE-2020-005].Tobias Geerinckx-Rice
* gnu/packages/tor.scm (tor): Update to 0.4.4.6.
2020-11-12maint: update-guix-package: Optionally add sources to store.Maxim Cournoyer
Following discussions in <https://issues.guix.gnu.org/43893>, keeping a copy of the updated package source is desirable when generating a release. * build-aux/update-guix-package.scm (version-controlled?): Remove variable. (call-with-temporary-git-worktree): Renamed from 'with-temporary-git-worktree'. Update doc. Do not change directory implicitly. Define as a procedure, not a syntax. (keep-source-in-store): New procedure. (main): Adjust to use with call-with-temporary-git-worktree. Add the sources to the store when GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT is set. Exit gracefully when FIND-ORIGIN-REMOTE returns #f. (%savannah-guix-git-repo-push-url-regexp): Adjust match for a potential colon separator. * Makefile.am (GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT): Adjust. * .dir-locals.el (scheme-mode): Remove entry for with-temporary-git-worktree. * doc/contributing.texi (Updating the Guix Package): Update doc. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2020-11-12gnu: emacs-lispy: Update to 20201109.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-lispy): Update to 20201109. [native-inputs]: Add which. [arguments]: Fix test command to not use straight.el and disable failing test related to Clojure.
2020-11-12Merge branch 'version-1.2.0'Ludovic Courtès
2020-11-12nls: Update string translations.Ludovic Courtès
2020-11-12nls: Update translations of the manual.Ludovic Courtès
2020-11-12nls: Update translations of the manual.Julien Lepiller
2020-11-12nls: Update 'ta' translation.Julien Lepiller
2020-11-12lint: patch-file-names: Simplify 'search-patch' error handling.Ludovic Courtès
* guix/lint.scm (check-patch-file-names): Remove 'message-condition?' guard, which is useless since d51bfe242fbe6f3f8f71d723e8fe0c7bbe711ba1. Remove call to 'format' in the 'formatted-message?' case.
2020-11-11gnu: sbcl-cffi-libffi: Fix building on ARM hardware.Efraim Flashner
* gnu/packages/lisp-xyz.scm (sbcl-cffi-libffi-bootstrap)[arguments]: Add phase to adapt code to changes in libffi.
2020-11-11gnu: sbcl-cffi-grovel: End all phases with #t.Efraim Flashner
* gnu/packages/lisp-xyz.scm (sbcl-cffi-grovel)[arguments]: End custom 'install-headers phase with #t.
2020-11-11gnu: python-matplotlib: Remove unused input.Marius Bakke
* gnu/packages/python-xyz.scm (python-matplotlib)[inputs]: Remove IMAGEMAGICK.
2020-11-11gnu: i3lock-fancy: Fix defunct substitution.Marius Bakke
* gnu/packages/wm.scm (i3lock-fancy)[arguments]: Fix faulty regular expression.
2020-11-11gnu: i3lock-fancy: Inputs are not native.Marius Bakke
* gnu/packages/wm.scm (i3lock-fancy)[native-inputs]: Move everything ... [inputs]: ... here.
2020-11-11gnu: a2ps: Remove unused input.Marius Bakke
* gnu/packages/pretty-print.scm (a2ps)[inputs]: Remove IMAGEMAGICK.
2020-11-11gnu: fbida: Remove unused input.Marius Bakke
* gnu/packages/pdf.scm (fbida)[inputs]: Remove IMAGEMAGICK.
2020-11-11gnu: caja-extensions: Remove unused input.Marius Bakke
* gnu/packages/mate.scm (caja-extensions)[inputs]: Remove IMAGEMAGICK.
2020-11-11gnu: mgba: Remove unused input.Marius Bakke
* gnu/packages/emulators.scm (mgba)[inputs]: Remove IMAGEMAGICK.
2020-11-11gnu: networking.scm: Remove unused module import.Marius Bakke
* gnu/packages/networking.scm: Don't import (gnu packages version-control).
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