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2018-09-07gnu: linux-libre: Update to 4.18.6....* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6. (%linux-libre-hash): Update hash. Mark H Weaver
2018-09-07gnu: linux-libre@4.14: Update to 4.14.68....* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68. (%linux-libre-4.14-hash): Update hash. Mark H Weaver
2018-09-07gnu: linux-libre@4.9: Update to 4.9.125....* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125. Mark H Weaver
2018-09-07gnu: linux-libre@4.4: Update to 4.4.154....* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154. Mark H Weaver
2018-09-07services: 'instantiate-missing-services' reaches fixed point....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. Ludovic Courtès
2018-09-07gnu: diffoscope: Update to 100....* gnu/packages/package-management.scm (diffoscope): Update to 100. Ludovic Courtès
2018-09-07gnu: indent: Add version 2.2.12....* gnu/packages/code.scm (indent-2.2.12): New variable. Ludovic Courtès
2018-09-07gnu: gdb: Update to 8.2....* gnu/packages/gdb.scm (gdb): Update to 8.2. Ludovic Courtès
2018-09-07gnu: guile-json: Update to 1.2.0....* gnu/packages/guile.scm (guile-json): Update to 1.2.0. [license]: Change to GPL3+. Ludovic Courtès
2018-09-07gnu: Add r-ggformula....* gnu/packages/cran.scm (r-ggformula): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: Add r-mosaiccore....* gnu/packages/cran.scm (r-mosaiccore): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: Add r-ggstance....gnu/packages/cran.scm (r-ggstance): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: Add r-abctools....* gnu/packages/cran.scm (r-abctools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: Add r-abcrf....* gnu/packages/cran.scm (r-abcrf): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: Add r-abcp2....* gnu/packages/cran.scm (r-abcp2): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> pimi
2018-09-07gnu: emacs-ess: Update to 17.11....* 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> Alex Branham
2018-09-07vm: Make UUID computation really deterministic....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. Ludovic Courtès
2018-09-07gnu: guile: Remove "share/guile/site" from GUILE_LOAD_COMPILED_PATH.....go files should always go to lib/guile/2.x/site-ccache, and in practice, we no longer have packages that don't do that. * gnu/packages/guile.scm (guile-2.2)[native-search-paths]: Remove "share/guile/site/2.2" from GUILE_LOAD_COMPILED_PATH spec. (guile-2.0)[native-search-paths]: Likewise. Ludovic Courtès
2018-09-07gnu: knot: Update to 2.7.2....* gnu/packages/dns.scm (knot): Update to 2.7.2. Tobias Geerinckx-Rice
2018-09-06gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}]....* gnu/packages/networking.scm (wireshark): Update to 2.6.3. Leo Famulari
2018-09-06gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618]....* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1. (curl-7.61.0): Replace variable with ... (curl-7.61.1): ... new variable. Leo Famulari
2018-09-06gnu: libgme: Update to 0.6.2....* gnu/packages/music.scm (libgme): Update to 0.6.2. [native-inputs]: Add gcc-4.9. Kei Kebreau
2018-09-06services: hpcguix-web: Set SSL_CERT_DIR....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. Ludovic Courtès
2018-09-06gnu: gfortran, gcc-objc, gcc-objc++: Add version 8....* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Eric Brown
2018-09-06gnu: guile-present: Install .go files to libdir....* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet): Remove. Ludovic Courtès
2018-09-06gnu: guile-charting: Install .go files to libdir....* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet): Remove. Ludovic Courtès
2018-09-06gnu: hpcguix-web: Update to 9ff40fc....* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc. [arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and guile-bytestructures to DEPS. Ludovic Courtès
2018-09-06gnu: guile-commonmark: Install .go files to libdir....* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the "modir = " and "godir = " line separately, allowing .go files to be installed to $(libdir). Ludovic Courtès
2018-09-06Add missing use-modules clause....This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor). Ricardo Wurmus
2018-09-06gnu: ccache: Update to 3.4.3....* gnu/packages/ccache.scm (ccache): Update to 3.4.3. [arguments]: Remove obsolete 'munge-failing-test' phase. Tobias Geerinckx-Rice
2018-09-06gnu: font-fira-code: Update to 1.205....* gnu/packages/fonts.scm (font-fira-code): Update to 1.205. Tobias Geerinckx-Rice
2018-09-06gnu: libmpdclient: Update to 2.15....* gnu/packages/mpd.scm (libmpdclient): Update to 2.15. Tobias Geerinckx-Rice
2018-09-05gnu: pigx-scrnaseq: Use latest version of Pandoc....* 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". Ricardo Wurmus
2018-09-05gnu: pigx-bsseq: Use latest version of Pandoc....* 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". Ricardo Wurmus
2018-09-05gnu: pigx-chipseq: Use latest version of Pandoc....* 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". Ricardo Wurmus
2018-09-05gnu: pigx-rnaseq: Use latest version of Pandoc....* 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". Ricardo Wurmus
2018-09-05gnu: r-rcas: Use standard version of ghc-pandoc-citeproc....* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace "ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc". Ricardo Wurmus
2018-09-05gnu: r-modelmetrics: Update to 1.2.0....* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0. [propagated-inputs]: Add r-data-table. Ricardo Wurmus
2018-09-05gnu: r-robustbase: Update to 0.93-2....* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2. Ricardo Wurmus
2018-09-05gnu: r-rann: Update to 2.6....* gnu/packages/statistics.scm (r-rann): Update to 2.6. Ricardo Wurmus
2018-09-05gnu: r-ggthemes: Update to 4.0.1....* 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. Ricardo Wurmus
2018-09-05gnu: r-ztable: Update to 0.2.0....* 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. Ricardo Wurmus
2018-09-05gnu: r-zoo: Update to 1.8-3....* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3. Ricardo Wurmus
2018-09-05gnu: r-gtools: Update to 3.8.1....* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1. Ricardo Wurmus
2018-09-05gnu: r-kernlab: Update to 0.9-27....* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27. Ricardo Wurmus
2018-09-05gnu: r-adaptivesparsity: Update to 1.6....* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6. [propagated-inputs]: Add r-mass and r-matrix. Ricardo Wurmus
2018-09-05gnu: r-codedepends: Move from cran to bioconductor....* gnu/packages/cran.scm (r-codedepends): Move from here... * gnu/packages/bioconductor.scm (r-codedepends): ...to here. Ricardo Wurmus
2018-09-05gnu: r-graph: Move from bioinformatics to bioconductor....* gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here. Ricardo Wurmus
2018-09-05gnu: r-ggpubr: Update to 0.1.8....* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8. [propagated-inputs]: Add r-glue and r-polynom. Ricardo Wurmus
2018-09-05gnu: r-codedepends: Update to 0.6.5....* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5. [propagated-inputs]: Add r-graph. Ricardo Wurmus
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