da62a4a19e
gnu: mc: Partially fix absolute file paths.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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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.
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* 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'.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/statistics.scm (r-base64): New variable.
2016-12-29 21:49:12 +01:00
ca380feb37
gnu: r-rmarkdown: Update to 1.3.
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* 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.
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* gnu/packages/statistics.scm (r-rprojroot): New variable.
2016-12-29 21:49:12 +01:00
a8e45b3240
gnu: r-rcpparmadillo: Update to 0.7.600.1.0.
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* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.600.1.0.
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to
7.600.1.
2016-12-29 21:49:12 +01:00
b1c1f4d012
gnu: armadillo: Update to 7.600.2.
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* gnu/packages/maths.scm (armadillo): Update to 7.600.2.
2016-12-29 21:49:12 +01:00
c729d3dc0e
gnu: r-zoo: Update to 1.7-14.
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* gnu/packages/statistics.scm (r-zoo): Update to 1.7-14.
[propagated-inputs]: Remove r-lattice.
2016-12-29 21:49:11 +01:00
53941eb7a5
gnu: r-fastcluster: Update to 1.1.22.
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* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.22.
2016-12-29 21:49:11 +01:00
3a181dc46e
gnu: r-plotly: Update to 4.5.6.
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* gnu/packages/statistics.scm (r-plotly): Update to 4.5.6.
2016-12-29 21:49:11 +01:00
54aa6eb6ee
gnu: r-r-rsp: Update to 0.40.0.
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* gnu/packages/statistics.scm (r-r-rsp): Update to 0.40.0.
2016-12-29 21:49:11 +01:00
1a44753b95
gnu: r-r-utils: Update to 2.5.0.
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* gnu/packages/statistics.scm (r-r-utils): Update to 2.5.0.
2016-12-29 21:49:11 +01:00
62350c0797
gnu: r-coda: Update to 0.19-1.
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* gnu/packages/statistics.scm (r-coda): Update to 0.19-1.
[propagated-inputs]: Remove r-lattice.
2016-12-29 21:49:11 +01:00
3607afbe4c
gnu: r-chron: Update to 2.3-48.
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* gnu/packages/statistics.scm (r-chron): Update to 2.3-48.
2016-12-29 21:49:11 +01:00
eaec5506ad
gnu: r-knitr: Update to 1.15.1.
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* gnu/packages/statistics.scm (r-knitr): Update to 1.15.1.
[propagated-inputs]: Remove r-formatr.
2016-12-29 21:49:10 +01:00
fd7810d323
gnu: r-bh: Update to 1.62.0-1.
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* gnu/packages/statistics.scm (r-bh): Update to 1.62.0-1.
2016-12-29 21:49:10 +01:00
dd4ae2950a
gnu: r-svglite: Update to 1.2.0.
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* gnu/packages/statistics.scm (r-svglite): Update to 1.2.0.
2016-12-29 21:49:10 +01:00
48a87bbe3b
gnu: r-gdtools: Update to 0.1.3.
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* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.3.
2016-12-29 21:49:10 +01:00
ab01f1cdb1
gnu: r-ggplot2: Update to 2.2.0.
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* gnu/packages/statistics.scm (r-ggplot2): Update to 2.2.0.
[propagated-inputs]: Remove r-proto and r-svglite; add r-lazyeval and
r-tibble.
2016-12-29 21:49:10 +01:00
b94b03b7fa
gnu: r-scales: Update to 0.4.1.
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* gnu/packages/statistics.scm (r-scales): Update to 0.4.1.
2016-12-29 21:49:10 +01:00
8a8fc31c6a
gnu: r-mgcv: Update to 1.8-16.
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* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-16.
2016-12-29 21:49:10 +01:00
421f7772b4
gnu: r-qtl: Update to 1.40-8.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
2016-12-29 21:49:09 +01:00
2a1c1b8074
gnu: r-hms: Update to 0.3.
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* gnu/packages/statistics.scm (r-hms): Update to 0.3.
2016-12-29 21:49:09 +01:00
85455a08f4
gnu: r-git2r: Update to 0.17.0.
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* gnu/packages/statistics.scm (r-git2r): Update to 0.17.0.
2016-12-29 21:49:09 +01:00
abb6f0540e
gnu: r-ade4: Update to 1.7-5
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* gnu/packages/statistics.scm (r-ade4): Update to 1.7-5.
2016-12-29 21:49:09 +01:00
db1b38af4e
gnu: r-xml: Update to 3.98-1.5.
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* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.5.
[propagated-inputs]: Remove r-rcurl.
2016-12-29 21:49:09 +01:00
ng0