322a583fcf
gnu: diamond: Update to 0.8.31.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
2017-01-01 16:47:47 +10:00
7fc2d377d1
gnu: nagios: Update to 4.2.4 [fixes CVE-2016-{9565,9566}].
...
* gnu/packages/monitoring.scm (nagios): Update to 4.2.4.
[native-inputs]: New field.
2016-12-31 20:02:59 +01:00
f11c444d44
Add 'guix copy'.
...
* guix/scripts/copy.scm: New file.
* guix/scripts/archive.scm (options->derivations+files): Export.
* doc/guix.texi (Invoking guix copy): New node.
* Makefile.am (MODULES) [HAVE_GUILE_SSH]: Add guix/scripts/copy.scm.
* po/guix/POTFILES.in: Likewise.
2016-12-31 18:35:29 +01:00
13164a2102
ssh: 'retrieve-files' detects remote export failures.
...
* guix/ssh.scm (retrieve-files): Call 'lookahead-u8' and raise a
'&message' condition when it returns EOF.
2016-12-31 18:35:29 +01:00
23973e4fbf
ssh: 'send-files' returns the list of items sent.
...
* guix/ssh.scm (send-files): Return MISSING.
2016-12-31 18:35:29 +01:00
e9629e8221
ssh: Allow transfers of complete closures.
...
* guix/ssh.scm (store-export-channel, send-files)
(file-retrieval-port, retrieve-files): Add #:recursive? parameter and
honor it.
2016-12-31 18:35:29 +01:00
c0b2d08bf4
git-download: Use a single download script for all derivations.
...
That way, we have only one /gnu/store/…-git-download instead of one
/gnu/store/…-PACKAGE-checkout-builder for each package.
This is a followup to ced200328c
2016-12-31 18:35:29 +01:00
b13a5b4d16
gnu: python-graphql-relay: Update to 0.4.5.
...
* gnu/packages/python.scm (python-graphql-relay): Update to 0.4.5.
2016-12-31 16:51:56 +01:00
0c315fb394
gnu: python-freezegun: Update to 0.3.8.
...
* gnu/packages/python.scm (python-freezegun): Update to 0.3.8.
2016-12-31 16:51:56 +01:00
234ade2d7b
gnu: python-ply: Update to 3.9.
...
* gnu/packages/python.scm (python-ply): Update to 3.9.
[source]: Use pypi-uri.
2016-12-31 16:51:55 +01:00
ab0c342924
gnu: python-pyquery: Update to 1.2.17.
...
* gnu/packages/python.scm (python-pyquery): Update to 1.2.17.
2016-12-31 16:51:55 +01:00
42734b9a88
gnu: python-click-log: Update to 0.1.8.
...
* gnu/packages/python.scm (python-click-log): Update to 0.1.8.
2016-12-31 16:51:54 +01:00
ae476d01da
gnu: python-ndg-httpsclient: Update to 0.4.2.
...
* gnu/packages/python.scm (python-ndg-httpsclient): Update to 0.4.2.
2016-12-31 16:51:54 +01:00
f165648e1b
gnu: python-ipykernel: Update to 4.5.2.
...
* gnu/packages/python.scm (python-ipykernel): Update to 4.5.2.
2016-12-31 16:51:53 +01:00
45cc957c72
gnu: python-jupyter-core: Update to 4.2.1.
...
* gnu/packages/python.scm (python-jupyter-core): Update to 4.2.1.
2016-12-31 16:51:53 +01:00
594358f5b6
gnu: python2-fastlmm: Update to 0.2.26.
...
* gnu/packages/python.scm (python2-fastlmm): Update to 0.2.26.
2016-12-31 16:51:40 +01:00
a5f92ca04f
gnu: python-pytz: Update to 2016.10.
...
* gnu/packages/python.scm (python-pytz): Update to 2016.10.
2016-12-31 16:36:20 +01:00
bf5e4bc42a
gnu: python-pyyaml: Update to 3.12.
...
* gnu/packages/python.scm (python-pyyaml): Update to 3.12.
[source]: Use pypi-uri.
2016-12-31 15:27:24 +01:00
7d2e758df5
gnu: python-pygments: Update to 2.1.3.
...
* gnu/packages/python.scm (python-pygments): Update to 2.1.3.
2016-12-31 15:27:23 +01:00
c055a37c8c
gnu: tiled: Update to 0.18.0.
...
* gnu/packages/game-development.scm (tiled): Update to 0.18.0.
2016-12-30 21:45:51 -05:00
a3a2774501
hydra: Remove 'qemu-image' job.
...
As per the discussion at
<https://lists.gnu.org/archive/html/guix-devel/2016-12/msg01098.html >.
* build-aux/hydra/gnu-system.scm (demo-os): Remove.
(qemu-jobs): Remove 'qemu-image' job.
* build-aux/hydra/demo-os.scm: Remove.
2016-12-31 01:44:04 +01:00
da62a4a19e
gnu: mc: Partially fix absolute file paths.
...
Partially fixes <http://bugs.gnu.org/25273 >.
* gnu/packages/mc.scm (mc)[arguments]: Add new phase 'fix-absolutism.
This substitutes absolute file paths with functional file paths.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-31 01:44:04 +01:00
0f391063d9
gnu: pius: Update to 2.2.2-0.891687c.
...
* gnu/packages/gnupg.scm (pius): Update to 2.2.2-0.891687c.
[inputs]: Change GNUPG-2.0 to GNUPG (2.1).
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-31 01:44:04 +01:00
987a29ba43
Add (guix ssh) module.
...
* guix/scripts/offload.scm (connect-to-remote-daemon)
(store-import-channel, store-export-channel, send-files)
(retrieve-files): Move to (guix ssh).
(nonce): Add optional 'name' parameter and use it.
(retrieve-files*): New procedure.
(transfer-and-offload): Use it instead of 'retrieve-files', and add
first parameter to 'send-files'.
(assert-node-can-import): Likewise.
(assert-node-can-export): Use 'retrieve-files' instead of
'store-export-channel'.
* guix/ssh.scm: New file.
* configure.ac: Use 'GUIX_CHECK_GUILE_SSH' and define 'HAVE_GUILE_SSH'
Automake conditional.
* Makefile.am (MODULES) [HAVE_GUILE_SSH]: Add guix/ssh.scm.
2016-12-31 01:44:04 +01:00
68415aa4e1
gnu: libtermkey: Update to 0.19.
...
* gnu/packages/terminals.scm (libtermkey): Update to 0.19.
Co-authored-by: Leo Famulari <leo@famulari.name>
2016-12-30 16:15:25 -05:00
858b9afeaf
gnu: libpng: Mention CVE-2016-10087.
...
* gnu/packages/patches/libpng-fix-null-ptr-dereference.patch: Rename to ...
* gnu/packages/patches/libpng-CVE-2016-10087.patch: ... this.
* gnu/local.mk (dist_patch_DATA): Adjust.
* gnu/packages/image.scm (libpng/fixed)[source]: Use renamed patch.
2016-12-30 14:33:21 -05:00
6023041346
import: crate: Do not build when guile-json is not available.
...
* Makefile.am (MODULES): Add 'guix/import/crate.scm' and
'guix/scripts/import/crate.scm' only when HAVE_GUILE_JSON.
2016-12-30 14:15:35 -05:00
4037e5f52b
gnu: linux-libre@4.1: Update to 4.1.37.
...
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.37.
2016-12-30 04:26:11 -05:00
a29929b32c
gnu: multiqc: Update to 0.9.
...
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>.
* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-12-30 17:22:43 +10:00
95d7d0c57f
gnu: elogind: Enable ACL support.
...
* gnu/packages/freedesktop.scm (elogind) [inputs]: Add acl.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-29 23:42:23 +01:00
3547a5effe
services: Add libmtp's udev rules to '%desktop-services'.
...
Suggested by Chris Marusich <cmmarusich@gmail.com>.
* gnu/services/desktop.scm (%desktop-services): Add 'mtp' service via
call to 'simple-service'.
2016-12-29 23:35:42 +01:00
87b5209558
gnu: mpd: Install systemd service files.
...
* gnu/packages/mpd.scm (mpd)[arguments]: Add 'install-service-files' phase.
2016-12-29 17:28:34 -05:00
76b64381cb
gnu: r-genomicfeatures: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
2016-12-29 22:24:12 +01:00
2f642e5229
gnu: r-biostrings: Update to 2.42.1.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
2016-12-29 22:24:11 +01:00
72c2693b9e
gnu: r-limma: Update to 3.30.7.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
2016-12-29 22:24:11 +01:00
5796af9981
gnu: r-variantannotation: Update to 1.20.2.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
2016-12-29 22:24:11 +01:00
5d3acc0b36
gnu: r-edger: Update to 3.16.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
2016-12-29 22:24:11 +01:00
81a17b61e7
gnu: r-genomeinfodb: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
2016-12-29 22:24:11 +01:00
54d9b568fc
gnu: r-iranges: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
2016-12-29 22:24:11 +01:00
86fc9c4a2c
gnu: r-s4vectors: Update to 0.12.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
2016-12-29 22:24:11 +01:00
c8ad8b6976
gnu: r-biocstyle: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
2016-12-29 22:24:10 +01:00
007ee80277
gnu: r-deseq2: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
2016-12-29 22:24:10 +01:00
d0f0579e6f
gnu: r-annotate: Update to 1.52.1.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
2016-12-29 22:24:10 +01:00
a57495e27a
gnu: khard: Update to 0.11.3.
...
* gnu/packages/mail.scm (khard): Update to 0.11.3.
[arguments]: Build with python instead of python-2. Remove
'disable-egg-compression' phase.
[propagated-inputs]: Don't use python-2 variants of propagated-inputs.
2016-12-29 16:12:13 -05:00
35bb2ff88a
gnu: r-rsqlite: Update to 1.1-1.
...
* gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-1.
[propagated-inputs]: Add r-bh, r-memoise, r-plogr, and r-rcpp.
2016-12-29 21:49:13 +01:00
28c041afe8
gnu: Add r-plogr.
...
* gnu/packages/statistics.scm (r-plogr): New variable.
2016-12-29 21:49:13 +01:00
ab607061cd
gnu: r-hmisc: Update to 4.0-1.
...
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-1.
[propagated-inputs]: Remove r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart; add r-base64.
2016-12-29 21:49:12 +01:00
0811f0f9d2
gnu: Add r-base64.
...
* gnu/packages/statistics.scm (r-base64): New variable.
2016-12-29 21:49:12 +01:00
ca380feb37
gnu: r-rmarkdown: Update to 1.3.
...
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.3.
[propagated-inputs]: Remove r-tibble; add r-rprojroot.
2016-12-29 21:49:12 +01:00
046e27e3f5
gnu: Add r-rprojroot.
...
* gnu/packages/statistics.scm (r-rprojroot): New variable.
2016-12-29 21:49:12 +01:00
Ben Woodcroft