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2018-09-08services: nginx: Don't read PID file when passed a custom config file.Ludovic Courtès
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.
2018-09-08gnu: mes: Update to 0.17.1.Jan Nieuwenhuizen
* 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.
2018-09-08gnu: nyacc: Update to 0.86.0.Jan Nieuwenhuizen
* 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.
2018-09-08gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl.Benjamin Slade
* gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New variables. Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
2018-09-07gnu: linux-libre: Update to 4.18.6.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6. (%linux-libre-hash): Update hash.
2018-09-07gnu: linux-libre@4.14: Update to 4.14.68.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68. (%linux-libre-4.14-hash): Update hash.
2018-09-07gnu: linux-libre@4.9: Update to 4.9.125.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125.
2018-09-07gnu: linux-libre@4.4: Update to 4.4.154.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154.
2018-09-07services: 'instantiate-missing-services' reaches fixed point.Ludovic Courtès
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.
2018-09-07gnu: diffoscope: Update to 100.Ludovic Courtès
* gnu/packages/package-management.scm (diffoscope): Update to 100.
2018-09-07gnu: indent: Add version 2.2.12.Ludovic Courtès
* gnu/packages/code.scm (indent-2.2.12): New variable.
2018-09-07gnu: gdb: Update to 8.2.Ludovic Courtès
* gnu/packages/gdb.scm (gdb): Update to 8.2.
2018-09-07gnu: guile-json: Update to 1.2.0.Ludovic Courtès
* gnu/packages/guile.scm (guile-json): Update to 1.2.0. [license]: Change to GPL3+.
2018-09-07gnu: Add r-ggformula.pimi
* gnu/packages/cran.scm (r-ggformula): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: Add r-mosaiccore.pimi
* gnu/packages/cran.scm (r-mosaiccore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: Add r-ggstance.pimi
gnu/packages/cran.scm (r-ggstance): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: Add r-abctools.pimi
* gnu/packages/cran.scm (r-abctools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: Add r-abcrf.pimi
* gnu/packages/cran.scm (r-abcrf): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: Add r-abcp2.pimi
* gnu/packages/cran.scm (r-abcp2): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-07gnu: emacs-ess: Update to 17.11.Alex Branham
* 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>
2018-09-07vm: Make UUID computation really deterministic.Ludovic Courtès
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.
2018-09-07gnu: knot: Update to 2.7.2.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (knot): Update to 2.7.2.
2018-09-06gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}].Leo Famulari
* gnu/packages/networking.scm (wireshark): Update to 2.6.3.
2018-09-06gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618].Leo Famulari
* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1. (curl-7.61.0): Replace variable with ... (curl-7.61.1): ... new variable.
2018-09-06gnu: libgme: Update to 0.6.2.Kei Kebreau
* gnu/packages/music.scm (libgme): Update to 0.6.2. [native-inputs]: Add gcc-4.9.
2018-09-06services: hpcguix-web: Set SSL_CERT_DIR.Ludovic Courtès
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.
2018-09-06gnu: gfortran, gcc-objc, gcc-objc++: Add version 8.Eric Brown
* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-06gnu: guile-present: Install .go files to libdir.Ludovic Courtès
* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet): Remove.
2018-09-06gnu: guile-charting: Install .go files to libdir.Ludovic Courtès
* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet): Remove.
2018-09-06gnu: hpcguix-web: Update to 9ff40fc.Ludovic Courtès
* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc. [arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and guile-bytestructures to DEPS.
2018-09-06gnu: guile-commonmark: Install .go files to libdir.Ludovic Courtès
* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the "modir = " and "godir = " line separately, allowing .go files to be installed to $(libdir).
2018-09-06Add missing use-modules clause.Ricardo Wurmus
This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
2018-09-06gnu: ccache: Update to 3.4.3.Tobias Geerinckx-Rice
* gnu/packages/ccache.scm (ccache): Update to 3.4.3. [arguments]: Remove obsolete 'munge-failing-test' phase.
2018-09-06gnu: font-fira-code: Update to 1.205.Tobias Geerinckx-Rice
* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
2018-09-06gnu: libmpdclient: Update to 2.15.Tobias Geerinckx-Rice
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
2018-09-05gnu: pigx-scrnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-bsseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-chipseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: pigx-rnaseq: Use latest version of Pandoc.Ricardo Wurmus
* 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".
2018-09-05gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05gnu: r-modelmetrics: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0. [propagated-inputs]: Add r-data-table.
2018-09-05gnu: r-robustbase: Update to 0.93-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
2018-09-05gnu: r-rann: Update to 2.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rann): Update to 2.6.
2018-09-05gnu: r-ggthemes: Update to 4.0.1.Ricardo Wurmus
* 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.
2018-09-05gnu: r-ztable: Update to 0.2.0.Ricardo Wurmus
* 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.
2018-09-05gnu: r-zoo: Update to 1.8-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
2018-09-05gnu: r-gtools: Update to 3.8.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
2018-09-05gnu: r-kernlab: Update to 0.9-27.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
2018-09-05gnu: r-adaptivesparsity: Update to 1.6.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6. [propagated-inputs]: Add r-mass and r-matrix.
2018-09-05gnu: r-codedepends: Move from cran to bioconductor.Ricardo Wurmus
* gnu/packages/cran.scm (r-codedepends): Move from here... * gnu/packages/bioconductor.scm (r-codedepends): ...to here.
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