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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+.
2018-09-07guix describe: Display information about the current generation.Ludovic Courtès
* guix/scripts/describe.scm (display-profile-info)[number]: Use the current generation number instead of the last generation number.
2018-09-07guix package: Record package provenance in manifest entries.Ludovic Courtès
* guix/profiles.scm (package->manifest-entry): Add #:properties and honor it. * guix/scripts/package.scm (package-provenance) (package->manifest-entry*): New procedures. (transaction-upgrade-entry, options->installable): Use 'package->manifest-entry*' instead of 'package->manifest-entry'.
2018-09-07Add 'guix describe'.Ludovic Courtès
* guix/scripts/describe.scm: New file. * Makefile.am (MODULES): Add it. (SH_TESTS): Add tests/guix-describe.sh. * po/guix/POTFILES.in: Add it. * guix/scripts/pull.scm (display-profile-content): Export. * guix/describe.scm (current-profile, current-profile-entries): Export. * tests/guix-describe.sh: New file. * doc/guix.texi (Features): Mention 'guix pull' and provenance tracking. (Invoking guix pull): Link to 'guix describe'. (Channels): Likewise. (Invoking guix describe): New node.
2018-09-07pull: Add '--profile'.Ludovic Courtès
* guix/scripts/pull.scm (show-help, %options): Add '--profile'. (build-and-install): Change 'config-dir' argument to 'profile'. (guix-pull): Honor '--profile'. * doc/guix.texi (Invoking guix pull): Document it.
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.
2018-09-06doc: Update hpcguix-web configuration documentation.Ludovic Courtès
* doc/guix.texi (Web Services): Document 'channels' and 'package-list-expiration'.
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.
2018-09-06build-self: Accomodate upgrades from May 2016 and earlier.Ludovic Courtès
Reported by Paul Garlick <pgarlick@tourbillion-technology.com>. Fixes a bug whereby "old" Guix instances (before mid-May 2018) would fail to pull to current master. Specifically, Paul reported being unable to upgrade from 6f84dc4314cd84550d9fc7e7afa11c495edc45a5 (a commit that predates that addition of the 'bootstrap' phase on gnu-build-system on 'master' and that also predates the new 'guix pull'.) * build-aux/build-self.scm (guile-gcrypt)[arguments]: New field.
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>
2018-09-06build: Remove -L flag when $LIBGCRYPT_LIBDIR is empty.Ludovic Courtès
Reported by Alex Vong <alexvong1995@gmail.com>. * config-daemon.ac: Do not add "-L$LIBGCRYPT_LIBDIR" to LIBGCRYPT_LIBS when "$LIBGCRYPT_LIBDIR" is empty.
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.
2018-09-05git: Don't require users to specifiy "origin/" for branches.Ludovic Courtès
Fixes <https://bugs.gnu.org/32618>. Reported by Eric Brown <brown@fastmail.com>. * guix/git.scm (update-cached-checkout): Remove "origin/" from default REF. Define CANONICAL-REF and use it instead of REF. (latest-repository-commit): Remove "origin/" from default REF. * guix/channels.scm (%default-channels): Remove "origin/" from 'branch'.
2018-09-05channels: Fix external channel builds.Ludovic Courtès
This fixes a regression introduced in ca719424455465fca4b872c371daf2a46de88b33 whereby external channels would fail to build due to the lack of (gcrypt …) modules. * guix/channels.scm (channel-instance-derivations): Add 'guile-gcrypt'. Pass it along CORE to 'build-channel-instance'.
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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