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25303 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice 5713bbf157
Use HTTPS for bioconductor.org. 
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
 2017-10-21 17:43:40 +02:00
Kei Kebreau 82bdcfe821
gnu: schismtracker: Update to 20170910. 
* gnu/packages/music.scm (schismtracker): Update to 20170910.
 2017-10-21 09:44:28 -04:00
Maxim Cournoyer fd75eb6cd4
gnu: Fix the hashes of mutated GitHub archives. 
Fixes <https://bugs.gnu.org/28745>.

* gnu/packages/audio.scm (csound): Fix hash.
* gnu/packages/engineering.scm (fritzing): Likewise.
* gnu/packages/erlang.scm (erlang): Likewise.
* gnu/packages/fonts.scm (font-google-material-design-icons): Likewise.
* gnu/packages/graphics.scm (ogre): Likewise.
* gnu/packages/java.scm (java-plexus-interpolation, antlr3): Likewise.
* gnu/packages/serialization.scm (yaml-cpp): Likewise.
* gnu/packages/version-control.scm (libgit2): Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-20 22:55:51 +02:00
Leo Famulari 7827032a7c
gnu: libvirt: Fix CVE-2017-1000256. 
* gnu/packages/patches/libvirt-CVE-2017-1000256.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/virtualization.scm (libvirt)[source]: Use it.
 2017-10-20 15:36:43 -04:00
Leo Famulari 48f8b07082
gnu: mysql: Update to 5.7.20. 
* gnu/packages/databases.scm (mysql): Update to 5.7.20.
 2017-10-20 15:36:42 -04:00
Leo Famulari 3890df5800
gnu: webkitgtk: Update to 2.18.1. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.18.1.
 2017-10-20 15:36:39 -04:00
Tobias Geerinckx-Rice a6e70e1169
gnu: youtube-dl: Update to 2017.10.20. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.10.20.
 2017-10-20 19:48:34 +02:00
Tobias Geerinckx-Rice 5a740d06b6
gnu: dovecot: Update to 2.2.33.2. 
* gnu/packages/mail.scm (dovecot): Update to 2.2.33.2.
 2017-10-20 19:48:34 +02:00
Tobias Geerinckx-Rice fa9ac83ec4
gnu: ola: Build with protobuf@2. 
This follows up commit dd12d4aad0.

* gnu/packages/protobuf.scm (protobuf-2): New variable.
* gnu/packages/lighting.scm (ola)[propagated-inputs]: Use it.
 2017-10-20 19:48:33 +02:00
Tobias Geerinckx-Rice 77aa706ab6
gnu: font-hack: Update to 3.000. 
* gnu/packages/fonts.scm (font-hack): Update to 3.000.
[source]: Download from new account.
[license]: Explicitly list all licences.
 2017-10-20 19:48:33 +02:00
Julien Lepiller c812f46058
gnu: Add aegisub. 
* gnu/packages/video.scm (aegisub): New variable.
 2017-10-20 19:41:57 +02:00
Julien Lepiller 6779ae27e6
gnu: Add ffms2. 
* gnu/packages/video.scm (aegisub): New variable.
 2017-10-20 19:41:34 +02:00
Efraim Flashner f71ce2824d
gnu: speexdsp: Fix building on aarch64-linux. 
* gnu/packages/xiph.scm (speexdsp)[arguments]: On aarch64-linux, disable
neon optimisations.
 2017-10-20 16:23:48 +03:00
Oleg Pykhalov 6df274073a
gnu: Add emacs-json-snatcher. 
* gnu/packages/emacs.scm (emacs-json-snatcher): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-20 14:41:41 +02:00
ng0 49d3d1d937
gnu: shellcheck: Update to 0.4.6. 
* gnu/packages/haskell.scm (shellcheck): Update to 0.4.6.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-20 14:41:41 +02:00
Tobias Geerinckx-Rice 3b2fa47879
gnu: dos2unix: Update to 7.4.0. 
* gnu/packages/textutils.scm (dos2unix): Update to 7.4.0.
 2017-10-20 02:16:56 +02:00
Tobias Geerinckx-Rice 6c0c175271
gnu: cowsay: Swap ‘build’ and ‘install’ phases. 
* gnu/packages/games.scm (cowsay)[arguments]: Invoke ‘install.sh’ during the
‘install’ phase.  Delete the ‘build’ phase, as there's nothing to be built.
 2017-10-20 02:16:55 +02:00
Tobias Geerinckx-Rice 46ba5337c0
gnu: cowsay: Update to 3.04. 
* gnu/packages/games.scm (cowsay): Update to 3.04.
[source]: Download from new location.
[home-page]: Point directly to the relevant page.
[description]: Correct mark-up and expand slightly.
 2017-10-20 02:16:54 +02:00
Tobias Geerinckx-Rice 8cccd09d3e
gnu: colordiff: Use HTTPS home page. 
* gnu/packages/patchutils.scm (colordiff)[home-page]: Use HTTPS.
 2017-10-20 02:16:54 +02:00
Tobias Geerinckx-Rice fc622383a7
gnu: unbound: Update to 1.6.7. 
* gnu/packages/dns.scm (unbound): Update to 1.6.7.
 2017-10-20 02:16:53 +02:00
Tobias Geerinckx-Rice 378140e591
gnu: neofetch: Update to 3.3.0. 
* gnu/packages/admin.scm (neofetch): Update to 3.3.0.
[arguments]: Add ‘install’ phase replacement that manually invokes make.
 2017-10-20 02:16:52 +02:00
Tobias Geerinckx-Rice 1e9433cf4d
gnu: qtox: Update to 1.12.1. 
* gnu/packages/messaging.scm (qtox): Update to 1.12.1.
 2017-10-20 02:16:52 +02:00
Tobias Geerinckx-Rice 57473bfc51
gnu: speedtest-cli: Update to 1.0.7. 
* gnu/packages/networking.scm (speedtest-cli): Update to 1.0.7.
 2017-10-20 02:16:51 +02:00
Tobias Geerinckx-Rice 47b85a69c0
gnu: cppcheck: Update to 1.81. 
* gnu/packages/check.scm (cppcheck): Update to 1.81.
 2017-10-20 02:16:51 +02:00
Kei Kebreau 7f65202990
gnu: python-sge-pygame: Update source URL. 
* gnu/packages/game-development.scm (python-sge-pygame)[source]: Update URL.
 2017-10-19 18:01:37 -04:00
Leo Famulari 9ccce79910
gnu: musl: Update to 1.1.17. 
* gnu/packages/musl.scm (musl): Update to 1.1.17.
[source]: Remove patch.
* gnu/packages/patches/musl-CVE-2016-8859.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-10-19 17:37:25 -04:00
Ludovic Courtès 37ce440dcf
download: Download a nar when a VCS checkout fails. 
Fixes <https://bugs.gnu.org/28709>.

* guix/build/download-nar.scm: New file.
* Makefile.am (MODULES): Add it.
* guix/cvs-download.scm (cvs-fetch)[zlib, config.scm, modules]: New
variables.
[build]: Use MODULES.  Add call to 'download-nar'.
* guix/git-download.scm (git-fetch): Likewise.
* guix/hg-download.scm (hg-fetch): Likewise.
 2017-10-19 23:21:49 +02:00
Ludovic Courtès 8c3488259e
Add (guix progress). 
Among other things, this removes (guix utils), (guix ui), (guix config),
etc. from the closure of (guix build download), as was the case since
798648515b.

* guix/utils.scm (<progress-reporter>, call-with-progress-reporter):
Move to...
* guix/progress.scm: ... here.  New file.
* Makefile.am (MODULES): Add it.
* guix/build/download.scm (current-terminal-columns)
(nearest-exact-integer, duration->seconds, seconds->string)
(byte-count->string, progress-bar, string-pad-middle)
(rate-limited, progress-reporter/file, dump-port*)
(time-monotonic): Move to progress.scm.
* guix/scripts/download.scm: Adjust accordingly.
* guix/scripts/substitute.scm: Likewise.
 2017-10-19 23:21:49 +02:00
Ludovic Courtès 347fa4aebf
download: Make 'http-fetch' public. 
* guix/build/download.scm (http-fetch): Remove 'file' parameter.  Change
to return an input port and the content-length.  Make public.
(url-fetch): Adjust accordingly.
 2017-10-19 23:21:49 +02:00
Ludovic Courtès b3ac341d4e
download: Remove old-Guile leftovers. 
This is a followup to 36626c556e.

* guix/build/download.scm (http-fetch): Rename 'port-or-bv' to 'port'.
Assume (port? port) is always true, and remove other branch.
 2017-10-19 23:21:49 +02:00
Ludovic Courtès 9b396c0cab
vm: Always use GRUB/i386. 
Fixes <https://bugs.gnu.org/28768>.
Reported by Oleg Pykhalov <go.wigust@gmail.com>.

* gnu/system/vm.scm (virtualized-operating-system): Override the
'bootloader' field.
 2017-10-19 23:21:49 +02:00
Mark H Weaver b11962067b
gnu: linux-libre: Update to 4.13.8. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.13.8.
(%linux-libre-hash): Update hash.
 2017-10-19 15:31:47 -04:00
Mark H Weaver 7a402621ec
gnu: linux-libre@4.9: Update to 4.9.57. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.57.
 2017-10-19 15:31:02 -04:00
Mark H Weaver a7c3dfeb6c
gnu: linux-libre@4.4: Update to 4.4.93. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.93.
 2017-10-19 15:30:30 -04:00
Mark H Weaver a8401c4ef1
gnu: linux-libre@4.1: Update to 4.1.45. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.45.
Remove patch that is now included upstream.
 2017-10-19 15:29:09 -04:00
Marius Bakke 8c1db4fc58
gnu: yadifa: Update to 2.2.6. 
* gnu/packages/dns.scm (yadifa): Update to 2.2.6.
 2017-10-19 21:21:01 +02:00
Marius Bakke 43dc47fa24
gnu: Add zathura-pdf-mupdf. 
* gnu/packages/pdf.scm (zathura-pdf-mupdf): New variable.
 2017-10-19 21:21:01 +02:00
Marius Bakke 513885b54e
gnu: qemu: Build with libjpeg-turbo. 
This gets rid of a compile warning since SPICE uses libjpeg-turbo, and reduces
the closure size by 0.8MiB.

* gnu/packages/virtualization.scm (qemu)[inputs]: Replace LIBJPEG-8 with
LIBJPEG-TURBO.
 2017-10-19 21:20:56 +02:00
Oleg Pykhalov d1c11418e7
gnu: emacs: Fix Man default C header file search path. 
* gnu/packages/emacs.scm (emacs): Make sure Man looks for C header files in
  the right places.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:47 +02:00
宋文武 b79813a19a
gnu: speex: Build and install 'speexdec' and 'speexenc'. 
* gnu/packages/xiph.scm (speex)[native-inputs]: Add 'pkg-config'.
[inputs]: Add 'speexdsp'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:44 +02:00
Andy Patterson 4ad8fbd185
gnu: virt-manager: Fix default URI check. 
Allows virt-manager to connect to qemu://system by default.

* gnu/packages/virtualization.scm (virt-manager)[arguments]<#:phases>: Add
'fix-default-uri.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:44 +02:00
Andy Patterson b764a9f5e0
gnu: virt-manager: Enable statistics graphing support. 
* gnu/packages/virtualization.scm (virt-manager)[inputs]: Add
python2-pycairo.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:44 +02:00
Andy Patterson 9a187b39b7
gnu: qemu: Add OpenGL support. 
Enables virgl support with spice 0.13+.

* gnu/packages/virtualization.scm (qemu)[arguments]<#:configure-flags>: Add
--enable-opengl.
[inputs]: Add libdrm and libepoxy.
(qemu-minimal)[inputs]: Remove libdrm and libepoxy.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:44 +02:00
Andy Patterson 8da7f79281
gnu: virt-manager: Enable spice-gtk support. 
* gnu/packages/virtualization.scm (virt-manager)[inputs]: Add spice-gtk.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:43 +02:00
Andy Patterson c44dd0d676
gnu: spice-gtk: Enable GObject introspection support. 
Allows virt-manager to use the spice-gtk widget.

* gnu/packages/spice.scm (spice-gtk)[inputs]: Add gobject-introspection.
[arguments]<#:configure-flags>: Add --enable-introspection.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:43 +02:00
Andy Patterson b376ec57f9
gnu: qemu: Enable spice usb redirection support. 
* gnu/packages/virtualization.scm (qemu)[arguments]<#:configure-flags>: New
argument.
[inputs]: Add usbredir.
(qemu-minimal)[arguments]<#:configure-flags>: Restrict them even when they are
set by qemu.
[inputs]: Remove usbredir.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-10-19 12:17:43 +02:00
Ricardo Wurmus ad3c61fcd3
gnu: python-hy: Update to 0.13.0. 
* gnu/packages/python.scm (python-hy): Update to 0.13.0.
 2017-10-19 01:37:52 +02:00
ng0 909f02dd70
gnu: Order module imports in (gnu packages mate) alphabetically. 
* gnu/packages/mate.scm: Order module imports alphabetically.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-19 01:22:18 +02:00
Christopher Allan Webber 0ff4425cea
gnu: Add dirvish. 
* gnu/packages/backup.scm (dirvish): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2017-10-19 01:14:28 +02:00
Christopher Allan Webber a1777c77f0
gnu: Add perl-libtime-period. 
* gnu/packages/perl.scm (perl-libtime-period): New variable.
 2017-10-19 01:13:40 +02:00