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2017-11-30gnu: r-annotationhub: Update to 2.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
2017-11-30gnu: r-msnid: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
2017-11-30gnu: r-maldiquant: Update to 1.17.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
2017-11-30gnu: r-genomicalignments: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
2017-11-30gnu: r-limma: Update to 3.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
2017-11-30gnu: r-variantannotation: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
2017-11-30gnu: r-getopt: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
2017-11-30gnu: r-gseabase: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
2017-11-30gnu: r-dexseq: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
2017-11-30gnu: r-deseq2: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
2017-11-30gnu: r-annotate: Update to 1.56.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
2017-11-30gnu: r-circlize: Update to 0.4.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-circlize): Update to 0.4.2.
2017-11-30gnu: r-rcpp: Update to 0.12.14.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.14.
2017-11-30gnu: r-timedate: Update to 3042.101.Ricardo Wurmus
* gnu/packages/cran.scm (r-timedate): Update to 3042.101.
2017-11-30gnu: r-stringi: Update to 1.1.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-stringi): Update to 1.1.6.
2017-11-30gnu: r-devtools: Update to 1.13.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.4.
2017-11-30gnu: r-mclust: Update to 5.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mclust): Update to 5.4.
2017-11-30gnu: r-rcppeigen: Update to 0.3.3.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.3.1.
2017-11-30gnu: r-car: Update to 2.1-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 2.1-6.
2017-11-30gnu: r-sn: Update to 1.5-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sn): Update to 1.5-1.
2017-11-30gnu: r-openssl: Update to 0.9.9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.9.
2017-11-30gnu: r-hms: Update to 0.4.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hms): Update to 0.4.0. [propagated-inputs]: Add r-rlang and r-pkgconfig.
2017-11-30gnu: r-dendextend: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-dendextend): Update to 1.6.0.
2017-11-30gnu: r-recipes: Update to 0.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-recipes): Update to 0.1.1. [propagated-inputs]: Add r-broom and r-matrix.
2017-11-30gnu: Add r-broom.Ricardo Wurmus
* gnu/packages/cran.scm (r-broom): New variable.
2017-11-30gnu: Add r-psych.Ricardo Wurmus
* gnu/packages/cran.scm (r-psych): New variable.
2017-11-30gnu: mongodb: Use scons-build-system.Arun Isaac
* gnu/packages/databases.scm (mongodb): Switch to scons-build-system.
2017-11-30gnu: klick: Use scons-build-system.Arun Isaac
* gnu/packages/music.scm (klick): Switch to scons-build-system.
2017-11-30gnu: pingus: Use scons-build-system.Arun Isaac
* gnu/packages/games.scm (pingus): Switch to scons-build-system.
2017-11-30gnu: godot: Use scons-build-system.Arun Isaac
* gnu/packages/game-development.scm (godot): Switch to scons-build-system.
2017-11-30gnu: metabat: Use scons-build-system.Arun Isaac
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
2017-11-30gnu: serf: Use scons-build-system.Arun Isaac
* gnu/packages/web.scm (serf): Switch to scons-build-system.
2017-11-30gnu: gpick: Use scons-build-system.Arun Isaac
* gnu/packages/image.scm (gpick): Switch to scons-build-system.
2017-11-30gnu: linuxdcpp: Use scons-build-system.Arun Isaac
* gnu/packages/direct-connect.scm (linuxdcpp): Switch to scons-build-system.
2017-11-30build-system: Add scons-build-system.Arun Isaac
* guix/build-system/scons.scm: New file. * guix/build/scons-build-system.scm: New file. * Makefile.am (MODULES): Register them. * doc/guix.texi (Build Systems): Add scons-build-system.
2017-11-30gnu: scons: Update to 3.0.1.Arun Isaac
* gnu/packages/python.scm (scons): Update to 3.0.1. (scons-python2): New variable.
2017-11-30gnu: dtc: Fix build on 32 bits platforms.Mathieu Othacehe
* gnu/packages/bootloaders.scm (dtc)[patches]: Add dtc-32-bits-check.patch and dtc-format-modifier.patch to fix build and tests on 32 bits platforms. * gnu/packages/patches/dtc-32-bits-check.patch : New file. * gnu/packages/patches/dtc-format-modifier.patch : New file. * gnu/local.mk (dist_patch_DATA): Add two above patches.
2017-11-30gnu: Update r-matrix to 1.2-12.Roel Janssen
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-12.
2017-11-30gnu: Update r-cluster to 2.0.6.Roel Janssen
* gnu/packages/statistics.scm (r-cluster): Update to 2.0.6.
2017-11-30gnu: Update r-minimal to 3.4.3.Roel Janssen
* gnu/packages/statistics.scm (r-minimal): Update to 3.4.3.
2017-11-30gnu: guix: Move 'bootstrap' phase after 'unpack'.Ludovic Courtès
Suggested by Mark H Weaver <mhw@netris.org> at <https://lists.gnu.org/archive/html/guix-devel/2017-11/msg00389.html>. * gnu/packages/package-management.scm (guix)[arguments]: Move 'bootstrap' phase back after 'unpack'.
2017-11-30doc: Give the absolute file name of 'hydra.gnu.org.pub' in snippets.Ludovic Courtès
* doc/guix.texi (Substitute Server Authorization): Give the absolute file name of 'hydra.gnu.org.pub' in the snippet.
2017-11-30gnu: grub-efi: Disable tests on all platforms.Efraim Flashner
This is a follow-up to 56f0feb6781e3680541d7adc21d6b3b4746a33ca and 63087721bb54a14dc04ec424474386ae98f7771b, which accidentally enabled tests for grub-efi on other platforms. * gnu/packages/bootloaders.scm (grub-efi)[arguments]: Override inherited tests field and disable on all platforms.
2017-11-30gnu: exim: Update to 4.89.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (exim): Update to 4.89.1. [source]: Remove patches for fixed CVEs (all of them). * gnu/packages/patches/exim-CVE-2017-16943.patch: Delete file... * gnu/packages/patches/exim-CVE-2017-16944.patch: ...as well as this file... * gnu/packages/patches/exim-CVE-2017-1000369.patch: ...and this file. * gnu/local.mk (dist_patch_DATA): Remove all of them.
2017-11-29gnu: libgit2: Avoid dependency on cURL.Ludovic Courtès
This reduces the closure size from 225 MiB to 80 MiB, while still supporting HTTP(S) access. * gnu/packages/version-control.scm (libgit2)[source](modules, snippet): New fields. [inputs]: Remove CURL; add HTTP-PARSER.
2017-11-29gexp: Default to 'guile-2.2' for 'program-file'.Ludovic Courtès
Previously things returned by 'program-file', such as %MODPROBE-WRAPPER in (gnu services), would refer to 'guile-final'. This would introduce 'guile-final' in the system closure, which is otherwise absent. By referring to 'guile-2.2' we remove that extra Guile. * guix/gexp.scm (default-guile): Refer to GUILE-2.2 instead of GUILE-FINAL.
2017-11-29gnu: spectrwm: Fix description.Tobias Geerinckx-Rice
* gnu/packages/wm.scm (spectrwm)[description]: Fix typo and use @dfn.
2017-11-29gnu: ghc-happy: Update to 1.19.8.Tobias Geerinckx-Rice
* gnu/packages/haskell.scm (ghc-happy): Update to 1.19.8. [arguments]: Delete; run all tests.
2017-11-29gnu: curl: Update to 7.57.0 [fixes CVE-2017-{8816,8817,8818}].Leo Famulari
* gnu/packages/curl.scm (curl): Update replacement to 7.57.0. (curl-7.56.1): Replace with ... (curl-7.57.0): ... new variable.
2017-11-29gnu: libtorrent-rasterbar: Update to 1.1.5.Leo Famulari
* gnu/packages/bittorrent.scm (libtorrent-rasterbar): Update to 1.1.5.
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