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* Update .mailmap.Alex Kost2017-01-01
| | | | | | | | * .mailmap: Add new entries for Alex Sassmannshausen, Ben Woodcroft, Daniel Pimentel, David Hashe, George Clemmer, Ivan Vilata i Balaguer, Jeff Mickey, John J. Foerch, Marek Benc, Pjotr Prins, Raoul Jean Pierre Bonnal, Rene Saavedra, 宋文武, Stefan Reichör, Thomas Danckaert and Vincent Legoll.
* gnu: manaplus: Update to 1.6.12.24.Alex Kost2017-01-01
| | | | * gnu/packages/games.scm (manaplus): Update to 1.6.12.24.
* gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft2017-01-01
| | | | | | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0. [source]: Remove patch. (python2-dendropy)[source]: Use the same source as python-dendropy. * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: diamond: Update to 0.8.31.Ben Woodcroft2017-01-01
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
* gnu: nagios: Update to 4.2.4 [fixes CVE-2016-{9565,9566}].Ludovic Courtès2016-12-31
| | | | | * gnu/packages/monitoring.scm (nagios): Update to 4.2.4. [native-inputs]: New field.
* Add 'guix copy'.Ludovic Courtès2016-12-31
| | | | | | | | * 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.
* ssh: 'retrieve-files' detects remote export failures.Ludovic Courtès2016-12-31
| | | | | * guix/ssh.scm (retrieve-files): Call 'lookahead-u8' and raise a '&message' condition when it returns EOF.
* ssh: 'send-files' returns the list of items sent.Ludovic Courtès2016-12-31
| | | | * guix/ssh.scm (send-files): Return MISSING.
* ssh: Allow transfers of complete closures.Ludovic Courtès2016-12-31
| | | | | | * guix/ssh.scm (store-export-channel, send-files) (file-retrieval-port, retrieve-files): Add #:recursive? parameter and honor it.
* git-download: Use a single download script for all derivations.Ludovic Courtès2016-12-31
| | | | | | | | | | | 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 ced200328ca6337ac446e4557c645629e7d7a997. * guix/git-download.scm (git-fetch)[build]: Get the URL, commit, and recursive parameter using 'getenv'. Pass #:script-name and #:env-vars arguments to 'gexp->derivation'.
* gnu: python-graphql-relay: Update to 0.4.5.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-graphql-relay): Update to 0.4.5.
* gnu: python-freezegun: Update to 0.3.8.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-freezegun): Update to 0.3.8.
* gnu: python-ply: Update to 3.9.Tobias Geerinckx-Rice2016-12-31
| | | | | * gnu/packages/python.scm (python-ply): Update to 3.9. [source]: Use pypi-uri.
* gnu: python-pyquery: Update to 1.2.17.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-pyquery): Update to 1.2.17.
* gnu: python-click-log: Update to 0.1.8.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-click-log): Update to 0.1.8.
* gnu: python-ndg-httpsclient: Update to 0.4.2.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-ndg-httpsclient): Update to 0.4.2.
* gnu: python-ipykernel: Update to 4.5.2.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-ipykernel): Update to 4.5.2.
* gnu: python-jupyter-core: Update to 4.2.1.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-jupyter-core): Update to 4.2.1.
* gnu: python2-fastlmm: Update to 0.2.26.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python2-fastlmm): Update to 0.2.26.
* gnu: python-pytz: Update to 2016.10.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-pytz): Update to 2016.10.
* gnu: python-pyyaml: Update to 3.12.Tobias Geerinckx-Rice2016-12-31
| | | | | * gnu/packages/python.scm (python-pyyaml): Update to 3.12. [source]: Use pypi-uri.
* gnu: python-pygments: Update to 2.1.3.Tobias Geerinckx-Rice2016-12-31
| | | | * gnu/packages/python.scm (python-pygments): Update to 2.1.3.
* gnu: tiled: Update to 0.18.0.Kei Kebreau2016-12-30
| | | | * gnu/packages/game-development.scm (tiled): Update to 0.18.0.
* hydra: Remove 'qemu-image' job.Ludovic Courtès2016-12-31
| | | | | | | | | 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.
* 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.
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