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25164 Commits

Author SHA1 Message Date
Julien Lepiller 3ffd180cc5
gnu: Update coq-coquelicot to 3.0.1. 
* gnu/packages/ocaml.scm (coq-coquelicot): Update to 3.0.1.
 2017-10-22 10:21:19 +02:00
Julien Lepiller 2e331c9c43
gnu: Update coq-mathcomp to 1.6.2. 
* gnu/packages/ocaml.scm (coq-mathcomp): Update to 1..6.2.
 2017-10-22 10:21:16 +02:00
Julien Lepiller b44f13e04c
gnu: Update coq-flocq to 2.6.0. 
* gnu/packages/ocaml.scm (coq-flocq): Update to 2.6.0.
 2017-10-22 10:21:14 +02:00
Julien Lepiller 6e4da73710
gnu: Update coq to 8.7.0. 
* gnu/packages/ocaml.scm (coq): Update to 8.7.0.
[build-system]: Use ocaml-build-system.
[inputs]: Add python-2.
[arguments]: Disable two failing tests.
 2017-10-22 10:21:11 +02:00
Julien Lepiller 07b4cd3a48
gnu: camlp5: install META file. 
* gnu/packages/ocaml.scm (camlp5) [phases]: New install-meta phase.
 2017-10-22 10:20:50 +02:00
Marius Bakke 3d679ab1e5
gnu: lame: Update to 3.100. 
* gnu/packages/mp3.scm (lame): Update to 3.100.
[source]: Don't hard-code version.
 2017-10-22 00:39:26 +02:00
Marius Bakke 28d0b52164
gnu: python-pyqt: Update to 5.9. 
* gnu/packages/qt.scm (python-pyqt): Update to 5.9.
 2017-10-21 22:38:55 +02:00
Marius Bakke 079e679219
gnu: python-sip: Update to 4.19.3. 
* gnu/packages/qt.scm (python-sip): Update to 4.19.3.
 2017-10-21 22:38:55 +02:00
Tobias Geerinckx-Rice a4194d1684
gnu: rest: Update to 0.8.1. 
* gnu/packages/gnome.scm (rest): Update to 0.8.1.
 2017-10-21 17:43:46 +02:00
Tobias Geerinckx-Rice 4b9a65bf6e
gnu: gnome-disk-utility: Update to 3.26.1. 
* gnu/packages/gnome.scm (gnome-disk-utility): Update to 3.26.1.
[build-system]: Use meson-build-system.
[native-inputs]: Add gtk+:bin.
 2017-10-21 17:43:46 +02:00
Tobias Geerinckx-Rice b27991179e
gnu: perl-geo-ip: Update to 1.51. 
* gnu/packages/networking.scm (perl-geo-ip): Update to 1.51.
 2017-10-21 17:43:46 +02:00
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