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* gnu: perl: Improve description.宋文武2018-09-09
| | | | | | Fixes <https://bug.gnu.org/32650>. * gnu/packages/perl.scm (perl)[description]: Use description from 'perlintro'.
* tests: base: Add Guile-Gcrypt & co. to the search path.Ludovic Courtès2018-09-08
| | | | | | | | | | Fixes a regression introduced in ca719424455465fca4b872c371daf2a46de88b33, whereby (gcrypt hash) would not be found in the system under test, leading to a failure of the "/run/current-system is a GC root" test. * gnu/tests/base.scm (run-basic-test)[guix&co]: New variable. [test]: Add all of GUIX&CO to %LOAD-PATH.
* services: nginx: 'stop' returns #f.Ludovic Courtès2018-09-08
| | | | | | | | Previously we'd return #t, which the Shepherd would consider a failure to stop the service. * gnu/services/web.scm (nginx-shepherd-service): In 'nginx-action', return #f when stopping the service.
* services: nginx: Don't read PID file when passed a custom config file.Ludovic Courtès2018-09-08
| | | | | | | | Fixes <https://bugs.gnu.org/32665>. * gnu/services/web.scm (nginx-shepherd-service): Check whether FILE is true and don't read the PID file if it is; use 'read-pid-file' instead of a potentially endless loop.
* gnu: mes: Update to 0.17.1.Jan Nieuwenhuizen2018-09-08
| | | | | | | * gnu/packages/patches/mes-nyacc-0.86.0.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0. (nyacc-for-mes): Remove.
* gnu: nyacc: Update to 0.86.0.Jan Nieuwenhuizen2018-09-08
| | | | | | * gnu/packages/patches/nyacc-binary-literals.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch.
* gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl.Benjamin Slade2018-09-08
| | | | | | | * gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New variables. Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
* gnu: linux-libre: Update to 4.18.6.Mark H Weaver2018-09-07
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.68.Mark H Weaver2018-09-07
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.125.Mark H Weaver2018-09-07
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125.
* gnu: linux-libre@4.4: Update to 4.4.154.Mark H Weaver2018-09-07
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154.
* services: 'instantiate-missing-services' reaches fixed point.Ludovic Courtès2018-09-07
| | | | | | | | | Fixes a bug whereby services indirectly depended on would not be automatically instantiated. * gnu/services.scm (instantiate-missing-services): Loop back when the length of ADJUSTED is greater than that of INSTANCES. * tests/services.scm ("instantiate-missing-services, indirect"): New test.
* gnu: diffoscope: Update to 100.Ludovic Courtès2018-09-07
| | | | * gnu/packages/package-management.scm (diffoscope): Update to 100.
* gnu: indent: Add version 2.2.12.Ludovic Courtès2018-09-07
| | | | * gnu/packages/code.scm (indent-2.2.12): New variable.
* gnu: gdb: Update to 8.2.Ludovic Courtès2018-09-07
| | | | * gnu/packages/gdb.scm (gdb): Update to 8.2.
* gnu: guile-json: Update to 1.2.0.Ludovic Courtès2018-09-07
| | | | | * gnu/packages/guile.scm (guile-json): Update to 1.2.0. [license]: Change to GPL3+.
* gnu: Add r-ggformula.pimi2018-09-07
| | | | | | * gnu/packages/cran.scm (r-ggformula): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-mosaiccore.pimi2018-09-07
| | | | | | * gnu/packages/cran.scm (r-mosaiccore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-ggstance.pimi2018-09-07
| | | | | | gnu/packages/cran.scm (r-ggstance): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-abctools.pimi2018-09-07
| | | | | | * gnu/packages/cran.scm (r-abctools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-abcrf.pimi2018-09-07
| | | | | | * gnu/packages/cran.scm (r-abcrf): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-abcp2.pimi2018-09-07
| | | | | | * gnu/packages/cran.scm (r-abcp2): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: emacs-ess: Update to 17.11.Alex Branham2018-09-07
| | | | | | | | | | | * gnu/packages/emacs.scm (emacs-ess): Update to 17.11 [url]: Use github for https [snippet]: update julia-mode substitution, only build info doc, bypass failing test [propagated-inputs]: Add emacs-julia-mode [description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS) [arguments]: Remove 'set-home' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* vm: Make UUID computation really deterministic.Ludovic Courtès2018-09-07
| | | | | | | | | Fixes <https://bugs.gnu.org/32652>. * gnu/system/vm.scm (operating-system-uuid)[service-name, file-system-digest]: New procedures. Map these over services and file systems and hash the result. * tests/guix-system.sh: Add test.
* gnu: knot: Update to 2.7.2.Tobias Geerinckx-Rice2018-09-07
| | | | * gnu/packages/dns.scm (knot): Update to 2.7.2.
* gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}].Leo Famulari2018-09-06
| | | | * gnu/packages/networking.scm (wireshark): Update to 2.6.3.
* gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618].Leo Famulari2018-09-06
| | | | | | * gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1. (curl-7.61.0): Replace variable with ... (curl-7.61.1): ... new variable.
* gnu: libgme: Update to 0.6.2.Kei Kebreau2018-09-06
| | | | | * gnu/packages/music.scm (libgme): Update to 0.6.2. [native-inputs]: Add gcc-4.9.
* services: hpcguix-web: Set SSL_CERT_DIR.Ludovic Courtès2018-09-06
| | | | | | | | | | | Previously Git pulls over HTTPS would fail with: guix/git.scm:132:7: In procedure update-cached-checkout: Throw to key `git-error' with args `(#<<git-error> code: -17 message: "the SSL certificate is invalid" class: 16>)'. * gnu/services/web.scm (hpcguix-web-shepherd-service): Pass "SSL_CERT_DIR=/etc/ssl/certs". * doc/guix.texi (Web Services): Mention certificates.
* gnu: gfortran, gcc-objc, gcc-objc++: Add version 8.Eric Brown2018-09-06
| | | | | | | * gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: guile-present: Install .go files to libdir.Ludovic Courtès2018-09-06
| | | | | * gnu/packages/plotutils.scm (guile-present)[source](modules, snippet): Remove.
* gnu: guile-charting: Install .go files to libdir.Ludovic Courtès2018-09-06
| | | | | * gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet): Remove.
* gnu: hpcguix-web: Update to 9ff40fc.Ludovic Courtès2018-09-06
| | | | | | * gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc. [arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and guile-bytestructures to DEPS.
* gnu: guile-commonmark: Install .go files to libdir.Ludovic Courtès2018-09-06
| | | | | | * gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the "modir = " and "godir = " line separately, allowing .go files to be installed to $(libdir).
* Add missing use-modules clause.Ricardo Wurmus2018-09-06
| | | | | | | | This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
* gnu: ccache: Update to 3.4.3.Tobias Geerinckx-Rice2018-09-06
| | | | | * gnu/packages/ccache.scm (ccache): Update to 3.4.3. [arguments]: Remove obsolete 'munge-failing-test' phase.
* gnu: font-fira-code: Update to 1.205.Tobias Geerinckx-Rice2018-09-06
| | | | * gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
* gnu: libmpdclient: Update to 2.15.Tobias Geerinckx-Rice2018-09-06
| | | | * gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
* gnu: pigx-scrnaseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-bsseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-chipseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: pigx-rnaseq: Use latest version of Pandoc.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and "ghc-pandoc-1" with "ghc-pandoc".
* gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
* gnu: r-modelmetrics: Update to 1.2.0.Ricardo Wurmus2018-09-05
| | | | | * gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0. [propagated-inputs]: Add r-data-table.
* gnu: r-robustbase: Update to 0.93-2.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
* gnu: r-rann: Update to 2.6.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/statistics.scm (r-rann): Update to 2.6.
* gnu: r-ggthemes: Update to 4.0.1.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1. [propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr, r-stringr, and r-tibble.
* gnu: r-ztable: Update to 0.2.0.Ricardo Wurmus2018-09-05
| | | | | | * gnu/packages/statistics.scm (r-ztable): Update to 0.2.0. [propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer, r-rcolorbrewer, r-scales, and r-stringr.
* gnu: r-zoo: Update to 1.8-3.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
* gnu: r-gtools: Update to 3.8.1.Ricardo Wurmus2018-09-05
| | | | * gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
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