1d65b5379b
gnu: r-vegan: Update to 2.4-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-3.
[arguments]: Remove build phase "revert-test-deletion".
[native-inputs]: Remove "r-vegan-delete-tests-patch".
2017-04-08 10:25:50 +02:00
1c8ee3fcc2
gnu: r-stringi: Update to 1.1.5.
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* gnu/packages/statistics.scm (r-stringi): Update to 1.1.5.
2017-04-08 10:25:50 +02:00
4653341b23
gnu: khal: Update to 0.9.5.
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* gnu/packages/calendar.scm (khal): Update to 0.9.5.
2017-04-07 22:04:51 -04:00
abf0880a67
vm: Add missing module.
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* gnu/build/vm.scm (define-module): Use module (guix build syscalls).
It fixes the following warnings during guix build :
gnu/build/vm.scm:233:3: warning: possibly unbound variable `mount'
gnu/build/vm.scm:238:3: warning: possibly unbound variable `umount'
gnu/build/vm.scm:268:8: warning: possibly unbound variable `mount'
gnu/build/vm.scm:276:8: warning: possibly unbound variable `umount'
gnu/build/vm.scm:315:4: warning: possibly unbound variable `mount'
gnu/build/vm.scm:323:4: warning: possibly unbound variable `umount'
This was not possible until the previous commit because we had to be sure
that Guile core implementation of 'mount' and 'umount' was used in
initrd context.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-07 23:30:39 +02:00
f91fcd9c42
syscalls: Allow mount and umount use from static Guile.
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* guix/build/syscalls.scm (mount): Use Guile core mount if called from
static Guile, otherwise use FFI based mount implementation.
(umount): Ditto.
This allows to use (guix build syscalls) from a module independently
of calling context.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-07 23:30:39 +02:00
cf47a8a51d
gnu: dovecot-trees: Update to 2.1.0.
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* gnu/packages/mail.scm (dovecot-trees): Update to 2.1.0.
(source): Change to use 'url-fetch'.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-07 23:30:38 +02:00
1165b08f86
build: Include 'glibc-utf8-locales' in the binary tarball.
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* Makefile.am (guix-binary.%.tar.xz): Add 'glibc-utf8-locales' and
'glibc-final' to the 'guix pack' command line.
* doc/guix.texi (Binary Installation): Mention 'etc/profile'.
2017-04-07 23:30:38 +02:00
5537f2d279
profiles: Slightly improve the instructions in 'etc/profile'.
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* guix/build/profiles.scm (build-etc/profile): Fix typo in comment.
Add backslash in the generated shell comment.
2017-04-07 23:30:38 +02:00
83cfa0247b
pack: Add '--expression'.
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* guix/scripts/pack.scm (%options, show-help): Add '--expression'.
(guix-pack)[maybe-package-argument]: New procedure.
Use it, and remove variable 'specs'.
* doc/guix.texi (Invoking guix pack): Document '--expression'.
2017-04-07 23:30:38 +02:00
d10fa5c7ff
gnu: Add intel-gpu-tools.
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* gnu/packages/admin.scm (intel-gpu-tools): New variable.
2017-04-07 23:00:53 +02:00
d71b758f3a
gnu: emacs-symon: Update to 20160630.
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* gnu/packagages/emacs.scm (emacs-symon): Update to 20160630 (this is
the latest tag available from the upstream).
[source]: Use github instead of melpa.
[home-page]: Update.
Signed-off-by: Alex Kost <alezost@gmail.com>
2017-04-07 20:22:29 +03:00
350cfccb06
gnu: Add emacs-adaptive-wrap.
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Suggested-by Ivan Vilata i Balaguer <ivan@selidor.net>.
Fixes <https://bugs.gnu.org/26367 >.
* gnu/packages/emacs.scm (emacs-adaptive-wrap): New variable.
Signed-off-by: Alex Kost <alezost@gmail.com>
2017-04-07 20:22:29 +03:00
b0dd3436ed
gnu: emacs-debbugs: Update to 0.14.
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* gnu/packages/emacs.scm (emacs-debbugs): Update to 0.14.
2017-04-07 20:22:29 +03:00
b25d3bd973
gnu: perf: Add support for C++ symbol demangling.
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* gnu/packages/linux.scm (perf)[inputs]: Add libiberty.
2017-04-07 17:37:46 +02:00
f214d470d7
gnu: ratpoison: Update to 1.4.9.
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* gnu/packages/ratpoison.scm (ratpoison): Update to 1.4.9.
[inputs]: Remove libxinerama. Add libxrandr.
Signed-off-by: Leo Famulari <leo@famulari.name>
2017-04-07 10:01:54 -04:00
6cfb860a7a
gnu: guitarix: Disable webkit features.
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The only version of webkit supported by guitarix is unmaintained and contains a
large number of security vulnerabilities, and should be removed from Guix.
* gnu/packages/audio.scm (guitarix)[inputs]: Remove webkitgtk/gtk+-2.
2017-04-07 09:37:14 -04:00
d5a3e8f019
gnu: myrepos: Use 'modify-phases' syntax.
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* gnu/packages/version-control.scm (myrepos)[arguments]: Use
'modify-phases' syntax.
2017-04-07 16:16:14 +03:00
d46e9fcb2c
gnu: myrepos: Update to 1.20170129.
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* gnu/packages/version-control.scm (myrepos): Update to 1.20170129.
[source]: Source tarballs have been removed from Github, use
git-download to download from upstream repository.
[home-page]: Use https.
2017-04-07 16:16:13 +03:00
ecc39b3f55
gnu: gnubik: Update to 2.4.3.
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* gnu/packages/games.scm (gnubik): Update to 2.4.3.
2017-04-07 16:16:13 +03:00
37982693ca
gnu: vsearch: Update to 2.4.3.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
2017-04-07 21:35:07 +10:00
fbd6fb1a9d
gnu: qemu: Update to 2.8.1 [security fixes].
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Fixes CVE-2016-{9602,9603} and CVE-2017-{2615,2620,2630,5667,5931}.
* gnu/packages/qemu.scm (qemu): Update to 2.8.1.
* gnu/packages/patches/qemu-CVE-2017-2615.patch,
gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch,
gnu/packages/patches/qemu-CVE-2017-5667.patch,
gnu/packages/patches/qemu-CVE-2017-5931.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
2017-04-07 00:53:02 -04:00
0715c0e69c
gnu: surf: Update to 2.0.
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* gnu/packages/suckless.scm (surf): Update to 2.0.
[inputs]: Replace webkitgtk/gtk+-2 with webkitgtk.
2017-04-06 22:44:07 -04:00
c923f83116
size: Add test to multiple 'store-profile' arguments.
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* tests/size.scm ("store-profile with multiple items"): New test.
2017-04-07 00:17:16 +02:00
9a3762a768
size: Avoid '_' as a pattern variable in 'match'.
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* guix/scripts/size.scm (display-profile, profile->page-map): Don't use
'_' as a 'match' pattern variable.
2017-04-07 00:17:16 +02:00
6b6aca9b36
gnu: flann: Move .mex file to a separate "octave" output.
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That way the closure of flann:out is down from 1 GiB
to 290 MiB.
* gnu/packages/maths.scm (flann)[outputs]: New field.
[arguments]: Add 'set-octave-directory' phase.
2017-04-07 00:17:16 +02:00
3be437398e
gnu: webkitgtk: Update to 2.16.1.
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* gnu/packages/webkit.scm (webkitgtk): Update to 2.16.1.
2017-04-06 17:24:57 -04:00
fe418cc5b2
gnu: armadillo: Change license to ASL 2.0.
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Armadillo versions 7.800 and onwards are licensed under the Apache License
2.0.
* gnu/packages/maths.scm (armadillo)[license]: Change to ASL 2.0.
2017-04-06 15:42:18 +02:00
2aa78c8f04
gnu: re2: Update to 2017-04-01.
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* gnu/packages/regex.scm (re2): Update to 2017-04-01.
2017-04-06 15:07:55 +02:00
fdcc9163d5
gnu: feh: Update to 2.18.3.
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* gnu/packages/image-viewers.scm (feh): Update to 2.18.3.
2017-04-06 15:05:40 +02:00
2c273a82f3
gnu: libusb: Update to 1.0.21.
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* gnu/packages/libusb.scm (libusb): Update to 1.0.21.
[home-page]: Update to new URL.
2017-04-06 15:03:07 +02:00
05b662663d
gnu: libmtp: Update to 1.1.13 [security fixes].
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* gnu/packages/libusb.scm (libmtp): Update to 1.1.13.
2017-04-06 14:58:05 +02:00
c9dccf7917
gnu: r-sourcetools: Update to 0.1.6.
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* gnu/packages/statistics.scm (r-sourcetools): Update to 0.1.6.
2017-04-06 14:39:23 +02:00
e18c731ba0
gnu: r-seqinr: Update to 3.3-6.
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* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
2017-04-06 14:39:22 +02:00
498d2553ed
gnu: Remove armadillo-for-rcpparmadillo.
...
This package is no longer useful, because upstream does not keep the tarballs
of older releases. We use the bundled armadillo sources in the
r-rccparmadillo package instead.
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Remove variable.
2017-04-06 14:39:22 +02:00
0685fe3c86
gnu: r-rcpparmadillo: Update to 0.7.700.0.0.
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* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.
2017-04-06 14:39:22 +02:00
133cba8cb5
gnu: armadillo: Update to 7.800.2.
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* gnu/packages/maths.scm (armadillo): Update to 7.800.2.
2017-04-06 14:39:22 +02:00
a3656b11d2
gnu: r-annotationforge: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
2017-04-06 14:39:22 +02:00
e0d7b31820
gnu: r-shortread: Update to 1.32.1.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
2017-04-06 14:39:21 +02:00
2cea968e41
gnu: r-s4vectors: Update to 0.12.2.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
2017-04-06 14:39:21 +02:00
7d05eb2dcc
gnu: r-iranges: Update to 2.8.2.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
2017-04-06 14:39:21 +02:00
e89cf15091
gnu: r-variantannotation: Update to 1.20.3.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
2017-04-06 14:39:21 +02:00
3506a62762
gnu: r-limma: Update to 3.30.13.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
2017-04-06 14:39:21 +02:00
4cd4721dbb
gnu: r-genomicranges: Update to 1.26.4.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
69b356efce
gnu: r-annotationdbi: Update to 1.36.2.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
2017-04-06 14:39:20 +02:00
5cc3b7a548
gnu: r-genomicalignments: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
2017-04-06 14:39:20 +02:00
25d8854723
gnu: r-rtracklayer: Update to 1.34.2.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
2017-04-06 14:39:20 +02:00
9ce6cb082e
gnu: r-genomicfeatures: Update to 1.26.4.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
57ac1d2f03
gnu: r-seqminer: Update to 5.7.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
2017-04-06 14:39:19 +02:00
e8bec95e69
gnu: r-maldiquant: Update to 1.16.2.
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* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
2017-04-06 14:39:19 +02:00
20e97759bf
gnu: r-ranger: Update to 0.7.0.
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* gnu/packages/statistics.scm (r-ranger): Update to 0.7.0.
2017-04-06 14:39:19 +02:00
Ricardo Wurmus