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26609 Commits

Author SHA1 Message Date
Ricardo Wurmus 28d25d037e
gnu: r-rtracklayer: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus d41f678420
gnu: r-limma: Update to 3.34.4. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus ab0dd8ac10
gnu: r-edger: Update to 3.20.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 7665fb39f5
gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 756ac7254c
gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 8d11ef4470
gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Ludovic Courtès 618f0582b4
upstream: Reject bogus archive type guesses. 
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.
 2017-12-19 18:16:47 +01:00
Danny Milosavljevic 68f1869cfc
gnu: xfce4-session: Disable (duplicate) Gtk+ icon cache generation. 
* gnu/packages/xfce.scm (xfce4-session)[arguments]: Add make-flags to disable
Gtk+ icon cache generation.
 2017-12-19 18:11:56 +01:00
Leo Famulari 9a56cf2b5b
services: urandom-seed: Try using a HWRNG to seed the Linux CRNG at boot. 
* 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.
 2017-12-19 11:31:24 -05:00
Kei Kebreau a8db968fa4
gnu: wxmaxima: Update to 17.10.1. 
* gnu/packages/maths.scm (wxmaxima): Update to 17.10.1.
 2017-12-19 11:26:16 -05:00
nee 7a070f020b
gnu: Add quakespasm. 
* gnu/packages/games.scm (quakespasm): New variable.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2017-12-19 10:21:14 -05:00
Ricardo Wurmus 0464dc1c1e
gnu: gajim: Update to 0.16.9. 
* gnu/packages/messaging.scm (gajim): Update to 0.16.9.
 2017-12-19 13:17:17 +01:00
Ricardo Wurmus f3b985fa61
gnu: python-nbxmpp: Update to 0.6.1. 
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.1.
 2017-12-19 13:17:16 +01:00
Ricardo Wurmus 21bc352664
gnu: dino: Update to 0.0-3.f25fadde2. 
* gnu/packages/messaging.scm (dino): Update to 0.0-3.f25fadde2.
 2017-12-19 13:16:53 +01:00
Ricardo Wurmus 79b43bc3a1
gnu: pcsc-lite: Update to 1.8.23. 
* gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.23.
[arguments]: Disable libsystemd check.
 2017-12-19 13:16:42 +01:00
Ricardo Wurmus b28e05d45e
gnu: antiword: Fix broken embedded directory name. 
* gnu/packages/textutils.scm (antiword)[arguments]: Replace "configure" phase
to substitute reference to "/usr/share/antiword" with the actual directory in
the store.
 2017-12-19 13:16:36 +01:00
Roel Janssen fb6ca493f1
gnu: Update gwl to 0.1.1. 
* gnu/packages/package-management.scm (gwl): Update to 0.1.1.
 2017-12-19 12:27:43 +01:00
Efraim Flashner ba1ba9fcbd
gnu: emulation-station: Add missing file-name field. 
* gnu/packages/games.scm (emulation-station)[source]: Add missing
file-name field.
 2017-12-19 12:19:04 +02:00
Roel Janssen 28fc96cb1e
gnu: Update r-cowplot to 0.9.2. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.9.2.
 2017-12-19 10:47:19 +01:00
Ludovic Courtès a1ac7bf361
tests: Adjust php-fpm test to new nginx API. 
Fixes <https://bugs.gnu.org/29769>.
Reported by Mark H Weaver <mhw@netris.org>.

This is a followup to 8b223ceac4.

* gnu/tests/web.scm (%php-fpm-nginx-server-blocks): Turn 'listen' into a
list.
 2017-12-19 09:53:56 +01:00
Leo Famulari 4a408d847e
gnu: mpd: Update to 0.20.13. 
* gnu/packages/mpd.scm (mpd): Update to 0.20.13.
 2017-12-19 02:28:06 -05:00
Leo Famulari 4fad6598c6
gnu: keepassxc: Update to 2.2.4. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.2.4.
 2017-12-19 01:18:24 -05:00
Leo Famulari 4498cbd7ad
gnu: GnuPG pinentry: Update to 1.1.0. 
* gnu/packages/gnupg.scm (pinentry-tty, pinentry-gtk2, pinentry-gnome3,
pinentry-qt): Update to 1.1.0.
 2017-12-18 23:25:20 -05:00
Mark H Weaver 7a6a08c945
gnu: linux-libre: Update to 4.14.7. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.7.
(%linux-libre-hash): Update hash.
 2017-12-18 19:52:02 -05:00
Mark H Weaver 48e1f44415
gnu: linux-libre@4.9: Update to 4.9.70. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.70.
 2017-12-18 19:51:22 -05:00
Mark H Weaver 86300e61b9
gnu: linux-libre@4.4: Update to 4.4.106. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.106.
 2017-12-18 19:50:39 -05:00
Marius Bakke 98bd11cfe7
gnu: termite: Update to 13. 
* gnu/packages/terminals.scm (termite): Update to 13.
 2017-12-19 01:37:22 +01:00
Marius Bakke 972fa87039
gnu: pcsc-lite: Update to 1.8.23. 
* 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.
 2017-12-19 01:30:14 +01:00
Marius Bakke 937790df9d
gnu: qemu: Update to 2.10.2. 
* 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.
 2017-12-19 01:15:09 +01:00
Marius Bakke 2ea3333504
gnu: libjpeg-turbo: Update to 1.5.3. 
* gnu/packages/image.scm (libjpeg-turbo): Update to 1.5.3.
 2017-12-18 23:25:20 +01:00
Marius Bakke 7bd9af7376
gnu: libsodium: Update to 1.0.16. 
* gnu/packages/crypto.scm (libsodium): Update to 1.0.16.
 2017-12-18 23:25:20 +01:00
Marius Bakke 8e9b3c6647
gnu: expect: Update to 5.45.3. 
* gnu/packages/tcl.scm (expect): Update to 5.45.3.
 2017-12-18 23:25:20 +01:00
Kei Kebreau 63dc763816
gnu: deutex: Update to 5.1.0. 
* gnu/packages/games.scm (deutex): Update to 5.1.0.
 2017-12-18 17:19:58 -05:00
Ludovic Courtès 45f6211730
doc: Clarify treatment of the root account. 
* doc/guix.texi (operating-system Reference): Clarify the situation of
UID 0.
 2017-12-18 23:17:30 +01:00
Ludovic Courtès 3caab236c4
guix gc: '--verify=foo' is reported as an error. 
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.
 2017-12-18 23:17:30 +01:00
Kei Kebreau 147d42fc03
gnu: emacspeak: Update to 47.0. 
* gnu/packages/emacs.scm (emacspeak): Update to 47.0.
[source]: Remove snippet.
[arguments]: Set SHELL environment variable.
 2017-12-18 16:50:45 -05:00
Efraim Flashner 91675d5082
gnu: rsync: Patch CVE-2017-{16548,17433,17434}. 
* 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.
 2017-12-18 22:53:46 +02:00
Ludovic Courtès b50a9cc008
gnu: psm: Update home page URL. 
* gnu/packages/linux.scm (psm)[home-page]: Update.
[source](uri): Use it.
 2017-12-18 17:52:58 +01:00
Ludovic Courtès ab25eb7caa
gexp: 'computed-file' has a new #:guile parameter. 
* guix/gexp.scm (<computed-file>)[guile]: New field.
(computed-file): Add #:guile.
(computed-file-compiler): Honor 'guile'.
 2017-12-18 17:52:58 +01:00
Ludovic Courtès 4e9dfe399b
gnu: Fix ambiguous 'zip' reference. 
* gnu/packages/photo.scm: Hide 'zip' from (srfi srfi-1).
 2017-12-18 17:52:58 +01:00
Ludovic Courtès 399993f804
ui: Non-zero exit for compound '&message' and '&error-location' conditions. 
* guix/ui.scm (call-with-error-handling): When both 'message?' and
'error-location?' are true, add call to 'exit'.
 2017-12-18 17:52:58 +01:00
Mathieu Othacehe 9f1e39d1fc
system: examples: Add a template for BeagleBone Black. 
* gnu/system/examples/beaglebone-black.tmpl: New file.
* Makefile.am (EXAMPLES): Add it.
* gnu/system/install.scm (/etc/configuration-files): Add it.
 2017-12-18 15:28:14 +01:00
Tobias Geerinckx-Rice af8c547d33
gnu: claws-mail: Update to 3.16.0. 
* gnu/packages/mail.scm (claws-mail): Update to 3.16.0.
 2017-12-18 15:22:08 +01:00
Clément Lassieur b05e8ee120
services: nginx: Allow to add raw content to the server blocks. 
* 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.
 2017-12-18 12:03:14 +01:00
Clément Lassieur 8b223ceac4
services: nginx: Replace 'http-port' and 'https-port' with 'listen'. 
* 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.
 2017-12-18 12:03:14 +01:00
Ricardo Wurmus f1a2b1cb20
gnu: r-seurat: Update to 2.1.0. 
* 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.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus fff9b88439
gnu: Add r-diffusionmap. 
* gnu/packages/graph.scm (r-diffusionmap): New variable.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus 007f6d9885
gnu: Add r-ggjoy. 
* gnu/packages/cran.scm (r-ggjoy): New variable.
 2017-12-18 12:01:34 +01:00
Ricardo Wurmus f90018e568
gnu: Add r-ggridges. 
* gnu/packages/cran.scm (r-ggridges): New variable.
 2017-12-18 12:01:34 +01:00
Ricardo Wurmus ae3f207951
gnu: Add r-scatterplot3d. 
* gnu/packages/cran.scm (r-scatterplot3d): New variable.
 2017-12-18 12:01:34 +01:00