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2017-12-19gnu: r-gqtlstats: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
2017-12-19gnu: r-rtracklayer: Update to 1.38.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
2017-12-19gnu: r-limma: Update to 3.34.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
2017-12-19gnu: r-edger: Update to 3.20.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
2017-12-19gnu: r-biocstyle: Update to 2.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
2017-12-19gnu: r-dexseq: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
2017-12-19gnu: r-vegan: Update to 2.4-5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
2017-12-19upstream: Reject bogus archive type guesses.Ludovic Courtès
This would crash 'guix refresh -u' with source URLs ending in "…/v1.2.3". * guix/upstream.scm (package-update): Be stricter when determining ARCHIVE-TYPE.
2017-12-19gnu: xfce4-session: Disable (duplicate) Gtk+ icon cache generation.Danny Milosavljevic
* gnu/packages/xfce.scm (xfce4-session)[arguments]: Add make-flags to disable Gtk+ icon cache generation.
2017-12-19services: urandom-seed: Try using a HWRNG to seed the Linux CRNG at boot.Leo Famulari
* gnu/services/base.scm (urandom-seed-shepherd-service): Try to read from '/dev/hwrng' at boot, as a supplement to any saved random seed. * doc/guix.texi (Base Services): Document the new feature.
2017-12-19gnu: wxmaxima: Update to 17.10.1.Kei Kebreau
* gnu/packages/maths.scm (wxmaxima): Update to 17.10.1.
2017-12-19gnu: Add quakespasm.nee
* gnu/packages/games.scm (quakespasm): New variable. Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
2017-12-19gnu: gajim: Update to 0.16.9.Ricardo Wurmus
* gnu/packages/messaging.scm (gajim): Update to 0.16.9.
2017-12-19gnu: python-nbxmpp: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.1.
2017-12-19gnu: dino: Update to 0.0-3.f25fadde2.Ricardo Wurmus
* gnu/packages/messaging.scm (dino): Update to 0.0-3.f25fadde2.
2017-12-19gnu: pcsc-lite: Update to 1.8.23.Ricardo Wurmus
* gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.23. [arguments]: Disable libsystemd check.
2017-12-19gnu: antiword: Fix broken embedded directory name.Ricardo Wurmus
* gnu/packages/textutils.scm (antiword)[arguments]: Replace "configure" phase to substitute reference to "/usr/share/antiword" with the actual directory in the store.
2017-12-19gnu: Update gwl to 0.1.1.Roel Janssen
* gnu/packages/package-management.scm (gwl): Update to 0.1.1.
2017-12-19gnu: emulation-station: Add missing file-name field.Efraim Flashner
* gnu/packages/games.scm (emulation-station)[source]: Add missing file-name field.
2017-12-19gnu: Update r-cowplot to 0.9.2.Roel Janssen
* gnu/packages/statistics.scm (r-cowplot): Update to 0.9.2.
2017-12-19tests: Adjust php-fpm test to new nginx API.Ludovic Courtès
Fixes <https://bugs.gnu.org/29769>. Reported by Mark H Weaver <mhw@netris.org>. This is a followup to 8b223ceac4ff0781e95d69362875f87cff03f4d6. * gnu/tests/web.scm (%php-fpm-nginx-server-blocks): Turn 'listen' into a list.
2017-12-19gnu: mpd: Update to 0.20.13.Leo Famulari
* gnu/packages/mpd.scm (mpd): Update to 0.20.13.
2017-12-19gnu: keepassxc: Update to 2.2.4.Leo Famulari
* gnu/packages/password-utils.scm (keepassxc): Update to 2.2.4.
2017-12-18gnu: GnuPG pinentry: Update to 1.1.0.Leo Famulari
* gnu/packages/gnupg.scm (pinentry-tty, pinentry-gtk2, pinentry-gnome3, pinentry-qt): Update to 1.1.0.
2017-12-18gnu: linux-libre: Update to 4.14.7.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.7. (%linux-libre-hash): Update hash.
2017-12-18gnu: linux-libre@4.9: Update to 4.9.70.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.70.
2017-12-18gnu: linux-libre@4.4: Update to 4.4.106.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.106.
2017-12-19gnu: termite: Update to 13.Marius Bakke
* gnu/packages/terminals.scm (termite): Update to 13.
2017-12-19gnu: pcsc-lite: Update to 1.8.23.Marius Bakke
* gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.23. [arguments]<#:configure-flags>: Add "--disable-libsystemd". [license]: Adjust to removed sd-daemon files.
2017-12-19gnu: qemu: Update to 2.10.2.Marius Bakke
* gnu/packages/patches/qemu-CVE-2017-15118.patch, gnu/packages/patches/qemu-CVE-2017-15119.patch, gnu/packages/patches/qemu-CVE-2017-15268.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. * gnu/packages/virtualization.scm (qemu): Update to 2.10.2. [source](patches): Remove obsolete.
2017-12-18gnu: libjpeg-turbo: Update to 1.5.3.Marius Bakke
* gnu/packages/image.scm (libjpeg-turbo): Update to 1.5.3.
2017-12-18gnu: libsodium: Update to 1.0.16.Marius Bakke
* gnu/packages/crypto.scm (libsodium): Update to 1.0.16.
2017-12-18gnu: expect: Update to 5.45.3.Marius Bakke
* gnu/packages/tcl.scm (expect): Update to 5.45.3.
2017-12-18gnu: deutex: Update to 5.1.0.Kei Kebreau
* gnu/packages/games.scm (deutex): Update to 5.1.0.
2017-12-18doc: Clarify treatment of the root account.Ludovic Courtès
* doc/guix.texi (operating-system Reference): Clarify the situation of UID 0.
2017-12-18guix gc: '--verify=foo' is reported as an error.Ludovic Courtès
Fixes <https://bugs.gnu.org/29761>. Reported by Martin Castillo <castilma@uni-bremen.de>. * guix/scripts/gc.scm (argument->verify-options): New procedure. (%options) ["verify"]: Adjust to use it. * tests/guix-gc.sh: Add test.
2017-12-18gnu: emacspeak: Update to 47.0.Kei Kebreau
* gnu/packages/emacs.scm (emacspeak): Update to 47.0. [source]: Remove snippet. [arguments]: Set SHELL environment variable.
2017-12-18gnu: rsync: Patch CVE-2017-{16548,17433,17434}.Efraim Flashner
* gnu/packages/rsync.scm (rsync)[source]: Add patches. [properties]: Mark CVE-2017-15994 as not relevant. * gnu/packages/patches/rsync-CVE-2017-16548.patch, gnu/packages/patches/rsync-CVE-2017-17433.patch, gnu/packages/patches/rsync-CVE-2017-17433-fix-tests.patch, gnu/packages/patches/rsync-CVE-2017-17434-pt1.patch, gnu/packages/patches/rsync-CVE-2017-17434-pt2.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them.
2017-12-18gnu: psm: Update home page URL.Ludovic Courtès
* gnu/packages/linux.scm (psm)[home-page]: Update. [source](uri): Use it.
2017-12-18gexp: 'computed-file' has a new #:guile parameter.Ludovic Courtès
* guix/gexp.scm (<computed-file>)[guile]: New field. (computed-file): Add #:guile. (computed-file-compiler): Honor 'guile'.
2017-12-18gnu: Fix ambiguous 'zip' reference.Ludovic Courtès
* gnu/packages/photo.scm: Hide 'zip' from (srfi srfi-1).
2017-12-18ui: Non-zero exit for compound '&message' and '&error-location' conditions.Ludovic Courtès
* guix/ui.scm (call-with-error-handling): When both 'message?' and 'error-location?' are true, add call to 'exit'.
2017-12-18system: examples: Add a template for BeagleBone Black.Mathieu Othacehe
* gnu/system/examples/beaglebone-black.tmpl: New file. * Makefile.am (EXAMPLES): Add it. * gnu/system/install.scm (/etc/configuration-files): Add it.
2017-12-18gnu: claws-mail: Update to 3.16.0.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (claws-mail): Update to 3.16.0.
2017-12-18services: nginx: Allow to add raw content to the server blocks.Clément Lassieur
* doc/guix.texi (Web Services): Document 'raw-content'. * gnu/services/web.scm (<nginx-server-configuration>)[raw-content]: New field. (emit-nginx-server-config): Add it.
2017-12-18services: nginx: Replace 'http-port' and 'https-port' with 'listen'.Clément Lassieur
* doc/guix.texi (Web Services, Version Control Services): Update accordingly. * gnu/services/certbot.scm (certbot-nginx-server-configurations): Likewise. * gnu/services/version-control.scm (%cgit-configuration-nginx): Likewise. * gnu/services/web.scm (<nginx-server-configuration>, emit-nginx-server-config): Likewise. * gnu/tests/version-control.scm (%cgit-configuration-nginx, %git-nginx-configuration): Likewise. * gnu/tests/web.scm (%nginx-servers, %php-fpm-nginx-server-blocks): Likewise.
2017-12-18gnu: r-seurat: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0. [propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica, r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr, r-rcppeigen, r-fastica.
2017-12-18gnu: Add r-diffusionmap.Ricardo Wurmus
* gnu/packages/graph.scm (r-diffusionmap): New variable.
2017-12-18gnu: Add r-ggjoy.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggjoy): New variable.
2017-12-18gnu: Add r-ggridges.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggridges): New variable.
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