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* gnu: mc: Partially fix absolute file paths.ng02016-12-31
| | | | | | | | | 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>
* gnu: pius: Update to 2.2.2-0.891687c.Troy Sankey2016-12-31
| | | | | | | * 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>
* Add (guix ssh) module.Ludovic Courtès2016-12-31
| | | | | | | | | | | | | | | | | * 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.
* gnu: libtermkey: Update to 0.19.José Miguel Sánchez García2016-12-30
| | | | | | * gnu/packages/terminals.scm (libtermkey): Update to 0.19. Co-authored-by: Leo Famulari <leo@famulari.name>
* gnu: libpng: Mention CVE-2016-10087.Leo Famulari2016-12-30
| | | | | | | * 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.
* import: crate: Do not build when guile-json is not available.David Thompson2016-12-30
| | | | | * Makefile.am (MODULES): Add 'guix/import/crate.scm' and 'guix/scripts/import/crate.scm' only when HAVE_GUILE_JSON.
* gnu: linux-libre@4.1: Update to 4.1.37.Mark H Weaver2016-12-30
| | | | * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.37.
* gnu: multiqc: Update to 0.9.Ben Woodcroft2016-12-30
| | | | | | | | | 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.
* gnu: elogind: Enable ACL support.Chris Marusich2016-12-29
| | | | | | * gnu/packages/freedesktop.scm (elogind) [inputs]: Add acl. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: Add libmtp's udev rules to '%desktop-services'.Ludovic Courtès2016-12-29
| | | | | | | Suggested by Chris Marusich <cmmarusich@gmail.com>. * gnu/services/desktop.scm (%desktop-services): Add 'mtp' service via call to 'simple-service'.
* gnu: mpd: Install systemd service files.Leo Famulari2016-12-29
| | | | * gnu/packages/mpd.scm (mpd)[arguments]: Add 'install-service-files' phase.
* gnu: r-genomicfeatures: Update to 1.26.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
* gnu: r-biostrings: Update to 2.42.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
* gnu: r-limma: Update to 3.30.7.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
* gnu: r-variantannotation: Update to 1.20.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
* gnu: r-edger: Update to 3.16.5.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
* gnu: r-genomeinfodb: Update to 1.10.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
* gnu: r-iranges: Update to 2.8.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
* gnu: r-s4vectors: Update to 0.12.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
* gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
* gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
* gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
* gnu: khard: Update to 0.11.3.Leo Famulari2016-12-29
| | | | | | | * 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.
* gnu: r-rsqlite: Update to 1.1-1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-1. [propagated-inputs]: Add r-bh, r-memoise, r-plogr, and r-rcpp.
* gnu: Add r-plogr.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-plogr): New variable.
* gnu: r-hmisc: Update to 4.0-1.Ricardo Wurmus2016-12-29
| | | | | | * 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.
* gnu: Add r-base64.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-base64): New variable.
* gnu: r-rmarkdown: Update to 1.3.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.3. [propagated-inputs]: Remove r-tibble; add r-rprojroot.
* gnu: Add r-rprojroot.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-rprojroot): New variable.
* gnu: r-rcpparmadillo: Update to 0.7.600.1.0.Ricardo Wurmus2016-12-29
| | | | | | * 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.
* gnu: armadillo: Update to 7.600.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/maths.scm (armadillo): Update to 7.600.2.
* gnu: r-zoo: Update to 1.7-14.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-zoo): Update to 1.7-14. [propagated-inputs]: Remove r-lattice.
* gnu: r-fastcluster: Update to 1.1.22.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.22.
* gnu: r-plotly: Update to 4.5.6.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-plotly): Update to 4.5.6.
* gnu: r-r-rsp: Update to 0.40.0.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-r-rsp): Update to 0.40.0.
* gnu: r-r-utils: Update to 2.5.0.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-r-utils): Update to 2.5.0.
* gnu: r-coda: Update to 0.19-1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-coda): Update to 0.19-1. [propagated-inputs]: Remove r-lattice.
* gnu: r-chron: Update to 2.3-48.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-chron): Update to 2.3-48.
* gnu: r-knitr: Update to 1.15.1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-knitr): Update to 1.15.1. [propagated-inputs]: Remove r-formatr.
* gnu: r-bh: Update to 1.62.0-1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-bh): Update to 1.62.0-1.
* gnu: r-svglite: Update to 1.2.0.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-svglite): Update to 1.2.0.
* gnu: r-gdtools: Update to 0.1.3.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-gdtools): Update to 0.1.3.
* gnu: r-ggplot2: Update to 2.2.0.Ricardo Wurmus2016-12-29
| | | | | | * 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.
* gnu: r-scales: Update to 0.4.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-scales): Update to 0.4.1.
* gnu: r-mgcv: Update to 1.8-16.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-16.
* gnu: r-qtl: Update to 1.40-8.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
* gnu: r-hms: Update to 0.3.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-hms): Update to 0.3.
* gnu: r-git2r: Update to 0.17.0.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-git2r): Update to 0.17.0.
* gnu: r-ade4: Update to 1.7-5Ricardo Wurmus2016-12-29
| | | | * gnu/packages/statistics.scm (r-ade4): Update to 1.7-5.
* gnu: r-xml: Update to 3.98-1.5.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/statistics.scm (r-xml): Update to 3.98-1.5. [propagated-inputs]: Remove r-rcurl.
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