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2020-04-01gnu: r-cytoml: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytoml): Update to 1.12.1. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-gofuncr: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.6.1. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-genomicinteractions: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.20.2. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-biomart: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-genomeinfodb: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-forecast: Update to 8.12.Ricardo Wurmus
* gnu/packages/cran.scm (r-forecast): Update to 8.12.
2020-04-01gnu: r-rematch2: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rematch2): Update to 2.1.1.
2020-04-01gnu: r-afex: Update to 0.27-2.Ricardo Wurmus
* gnu/packages/cran.scm (r-afex): Update to 0.27-2. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-fs: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-fs): Update to 1.4.0. [propagated-inputs]: Remove r-rcpp. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-performance: Update to 0.4.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-performance): Update to 0.4.5.
2020-04-01gnu: r-heatmaply: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-heatmaply): Update to 1.1.0.
2020-04-01gnu: r-quantmod: Update to 0.4.17.Ricardo Wurmus
* gnu/packages/cran.scm (r-quantmod): Update to 0.4.17.
2020-04-01gnu: r-tinytex: Update to 0.21.Ricardo Wurmus
* gnu/packages/cran.scm (r-tinytex): Update to 0.21.
2020-04-01gnu: r-callr: Update to 3.4.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-callr): Update to 3.4.3.
2020-04-01gnu: r-sn: Update to 1.6-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sn): Update to 1.6-0. [propagated-inputs]: Add r-quantreq.
2020-04-01gnu: r-gtools: Update to 3.8.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.2.
2020-04-01gnu: r-foreach: Update to 1.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-foreach): Update to 1.5.0. [native-inputs]: Add r-knitr.
2020-04-01gnu: r-tibble: Update to 3.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.0. [propagated-inputs]: Add r-ellipsis, r-lifecycle, r-magrittr, and r-vctrs. [native-inputs]: Add r-knitr.
2020-04-01gnu: Add emacs-elf-mode.John Soo
* gnu/packages/emacs-xyz.scm (emacs-elf-mode): New variable.
2020-04-01gnu: Add emacs-imenu-list.John Soo
* gnu/packages/emacs-xyz.scm (emacs-imenu-list): New variable.
2020-04-01gnu: Add emacs-evil-tmux-navigator.John Soo
* gnu/packages/emacs-xyz.scm (emacs-evil-tmux-navigator): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-04-01gnu: toot: Adjust custom phases.Efraim Flashner
* gnu/packages/mastodon.scm (toot)[arguments]: 'check is already run after 'install so replace 'check rather than re-inserting it.
2020-04-01gnu: toot: Update to 0.25.2.Efraim Flashner
* gnu/packages/mastodon.scm (toot): Update to 0.25.2.
2020-04-01gnu: vim-asyncrun: Update to 2.7.1.Efraim Flashner
* gnu/packages/vim.scm (vim-asyncrun): Update to 2.7.1.
2020-04-01gnu: mpv-mpris: Switch to copy-build-system.Efraim Flashner
* gnu/packages/video.scm (mpv-mpris)[build-system]: Switch to copy-build-system. [arguments]: Add custom 'build phase before 'install phase.
2020-04-01gnu: mpv-mpris: Update to 0.4.Efraim Flashner
* gnu/packages/video.scm (mpv-mpris): Update to 0.4.
2020-04-01gnu: font-gnu-unifont: Update to 13.0.01.Efraim Flashner
* ngu/packages/fonts.scm (font-gnu-unifont): Update to 13.0.01. [home-page]: Follow redirect.
2020-04-01gnu: emacs-discover-my-major: Don't use unstable tarball.Efraim Flashner
* gnu/packages/emacs-xyz.scm (emacs-discover-my-major)[source]: Download using git-fetch. Use new upstream URI. [home-page]: Update to new home-page.
2020-04-01system: Move nanorc to XDG_CONFIG_HOME.Efraim Flashner
* gnu/system/shadow.scm (skeleton-directory): Move .nanorc to .config/nano/nanorc.
2020-04-01gnu: mumi: Update to 0.0.0-11.0e9af8d.Ricardo Wurmus
* gnu/packages/mail.scm (mumi): Update to 0.0.0-11.0e9af8d.
2020-03-31gnu: Add libantlr3c.Raghav Gururajan
* gnu/packages/java.scm (libantlr3c): New variable. Co-authored by Maxim Cournoyer. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2020-04-01gnu: mumi: Update to 0.0.0-10.f7d6a54.Ricardo Wurmus
* gnu/packages/mail.scm (mumi): Update to 0.0.0-10.f7d6a54.
2020-04-01gnu: git-annex: Update to 8.20200330.Kyle Meyer
* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20200330. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2020-03-31gnu: gimp: Disable automatic update checkingJack Hill
* gnu/packages/gimp.scm (gimp)[arguments]: Disable update checking in #:configure-flags. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-04-01gnu: gnumach: Fix compilation.Ludovic Courtès
* gnu/packages/hurd.scm (gnumach)[arguments]: Inherit arguments from GNUMACH-HEADERS. [native-inputs]: Add AUTOCONF, AUTOMAKE, and TEXINFO-4.
2020-04-01Revert "gnu: coreutils: Fix cross-compilation to i586-pc-gnu."Ludovic Courtès
This reverts commit 67cbfeae30eb9b7c56145bf72582d71eea177370, which is not longer necessary now that the 'ld.so' linker script of the cross glibc contains "libhurduser.so libmachuser.so".
2020-04-01gnu: cross-libc: Build fix for the Hurd.Jan Nieuwenhuizen
This fixes cross building of coreutils, e.g. ./pre-inst-env guix build --target=i586-pc-gnu coreutils * gnu/packages/cross-base.scm (cross-libc): Add -lhurduser, -lmachuser for the Hurd.
2020-03-31gnu: Add spandsp.Raghav Gururajan
* gnu/packages/telephony.scm (spandsp): New variable. Co-authored by Maxim Cournoyer. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2020-03-31gnu: Add neverballVitaliy Shatrov
* gnu/packages/games.scm (neverball): New variable.
2020-03-31gnu: pam-krb5: Fix CVE-2020-10595.Leo Famulari
* gnu/packages/patches/pam-krb5-CVE-2020-10595.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (pam-krb5)[source]: Use it.
2020-03-31gnu: python-pyyaml: Update to 5.3.1 [fixes CVE-2020-1747]Leo Famulari
* gnu/packages/python-xyz.scm (python-pyyaml): Update to 5.3.1.
2020-03-31gnu: Add perl-class-mix.Paul Garlick
* gnu/packages/perl.scm (perl-class-mix): New variable.
2020-03-31gnu: Add perl-params-classify.Paul Garlick
* gnu/packages/perl.scm (perl-params-classify): New variable.
2020-03-31gnu: Add perl-devel-callchecker.Paul Garlick
* gnu/packages/perl.scm (perl-devel-callchecker): New variable.
2020-03-31gnu: Add perl-dynaloader-functions.Paul Garlick
* gnu/packages/perl.scm (perl-dynaloader-functions): New variable.
2020-03-31gnu: mumi: Update to 0.0.0-9.5fdbc3e.Ricardo Wurmus
* gnu/packages/mail.scm (mumi): Update to 0.0.0-9.5fdbc3e.
2020-03-31profiles: Compute manual database entries in parallel.Arne Babenhauserheide
This provides a 36% speedup on an SSD and 4 cores for the 1.5K man pages in the manual database derivation of: guix environment --ad-hoc jupyter python-ipython python-ipykernel * guix/profiles.scm (manual-database)[build]: Add 'print-string', 'print', and 'compute-entry'. Change 'compute-entries' to call 'compute-entry' in 'n-par-map'. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2020-03-31gnu: coreutils: Fix cross-compilation to i586-pc-gnu.Ludovic Courtès
Until now cross-compilation would fail with: i586-pc-gnu-ld: src/copy.o: undefined reference to symbol 'file_chauthor' i586-pc-gnu-ld: /gnu/store/…-glibc-cross-i586-pc-gnu-2.29/lib/libhurduser.so.0.3: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status * gnu/packages/base.scm (coreutils)[arguments]: When 'hurd-target?', add #:configure-flags.
2020-03-31ci: Fix 'evaluation-spec' binding.Ludovic Courtès
* guix/ci.scm (<evaluation>)[spec]: Add "specification", which is what the JSON field is actually called.
2020-03-31gnu: hwloc@2: Update to 2.2.0.Ludovic Courtès
* gnu/packages/mpi.scm (hwloc-2): Update to 2.2.0.
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