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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.
2018-09-05gnu: r-graph: Move from bioinformatics to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05gnu: r-ggpubr: Update to 0.1.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8. [propagated-inputs]: Add r-glue and r-polynom.
2018-09-05gnu: r-codedepends: Update to 0.6.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5. [propagated-inputs]: Add r-graph.
2018-09-05gnu: r-later: Update to 0.7.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
2018-09-05gnu: r-maptools: Update to 0.9-3.Ricardo Wurmus
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
2018-09-05gnu: r-fnn: Update to 1.1.2.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
2018-09-05gnu: r-heatmaply: Update to 0.15.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
2018-09-05gnu: r-tsa: Update to 1.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-tsa): Update to 1.2. [propagated-inputs]: Remove r-tseries.
2018-09-05gnu: r-statnet-common: Update to 4.1.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
2018-09-05gnu: r-metap: Update to 1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-metap): Update to 1.0. [propagated-inputs]: Add r-rdpack.
2018-09-05gnu: r-tinytex: Update to 0.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
2018-09-05gnu: r-pillar: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0. [propagated-inputs]: Add r-fansi.
2018-09-05gnu: r-xts: Update to 0.11-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-xts): Update to 0.11-0. [native-inputs]: Remove.
2018-09-05gnu: r-mice: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
2018-09-05gnu: r-pan: Update to 1.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-pan): Update to 1.6.
2018-09-05gnu: r-jomo: Update to 2.6-4.Ricardo Wurmus
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4. [propagated-inputs]: Add r-ordinal.
2018-09-05gnu: Add r-ordinal.Ricardo Wurmus
* gnu/packages/cran.scm (r-ordinal): New variable.
2018-09-05gnu: Add r-ucminf.Ricardo Wurmus
* gnu/packages/cran.scm (r-ucminf): New variable.
2018-09-05gnu: r-broom: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-broom): Update to 0.5.0. [propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove r-plyr and r-psych.
2018-09-05gnu: r-ipred: Update to 0.9-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
2018-09-05gnu: r-pls: Update to 2.7-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
2018-09-05gnu: r-glue: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-glue): Update to 1.3.0.
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