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2017-08-02gnu: r-category: Update to 2.42.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
2017-08-02gnu: r-biocstyle: Update to 2.4.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
2017-08-02gnu: r-dnacopy: Update to 1.50.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
2017-08-02gnu: r-iranges: Update to 2.10.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
2017-08-02gnu: r-genomeinfodb: Update to 1.12.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
2017-08-02gnu: r-variantannotation: Update to 1.22.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02gnu: r-limma: Update to 3.32.5.Roel Janssen
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
2017-08-02gnu: r-biobase: Update to 2.36.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
2017-08-02gnu: r-annotationdbi: Update to 1.38.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
2017-08-02gnu: r-biomart: Update to 2.32.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
2017-08-02gnu: r-biocparallel: Update to 1.10.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
2017-08-02gnu: r-biostrings: Update to 2.44.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
2017-08-02gnu: r-delayedarray: Update to 0.2.7.Roel Janssen
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
2017-08-02gnu: r-summarizedexperiment: Update to 1.6.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
2017-08-02gnu: r-genomicalignments: Update to 1.12.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
2017-08-02gnu: r-rtracklayer: Update to 1.36.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
2017-08-02gnu: r-genomicfeatures: Update to 1.28.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
2017-08-02gnu: r-copywriter: Update to 2.8.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
2017-08-02gnu: r-sva: Update to 3.24.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
2017-08-02gnu: r-rsqlite: Update to 2.0.Roel Janssen
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.0.
2017-08-02gnu: Add r-blob.Roel Janssen
* gnu/packages/statistics.scm (r-blob): New variable.
2017-08-02gnu: Add r-pkgconfig.Roel Janssen
* gnu/packages/statistics.scm (r-pkgconfig): New variable.
2017-08-02pull: Honor '--no-grafts'.Ludovic Courtès
* guix/scripts/pull.scm (guix-pull): Parameterize %GRAFT? as a function of OPTS.
2017-08-02pull: Use the commit ID as the version string.Ludovic Courtès
* guix/scripts/pull.scm (build-from-source): Add #:commit parameter. Pass it to BUILD. (build-and-install): Add #:commit and pass it to 'build-from-source'. (guix-pull): Pass #:commit to 'build-and-install'.
2017-08-02pull: Fetch source code from Git.Ludovic Courtès
* guix/scripts/pull.scm (%snapshot-url, with-environment-variable) (with-PATH): Remove. (ensure-guile-git!): New procedure. (%repository-url): New variable. (%default-options): Add 'repository-url' and 'ref'. (show-help, %options): Add '--commit' and '--url'. (temporary-directory, first-directory, interned-then-deleted) (unpack): Remove. (build-from-source): Rename 'tarball' to 'source'. Remove call to 'unpack'. (build-and-install): Rename 'tarball' to 'source'. (honor-lets-encrypt-certificates!, report-git-error): New procedures. (with-git-error-handling): New macro. (guix-pull)[fetch-tarball]: Remove. Wrap body in 'with-git-error-handling'. Rewrite to use 'latest-repository-commit'. * build-aux/build-self.scm (build): Print an error message and exit when GUILE-GIT is #f. * doc/guix.texi (Invoking guix pull): Mention Git. Document '--commit' and '--branch'.
2017-08-02build: Make Guile-Git a hard requirement.Ludovic Courtès
* configure.ac: Error out when (git) is missing. * doc/guix.texi (Requirements): Mention Guile-Git. * Makefile.am (MODULES): Add guix/git.scm unconditionally.
2017-08-01gnu: re2: Update to 2017-08-01.Marius Bakke
* gnu/packages/regex.scm (re2): Update to 2017-08-01.
2017-08-01gnu: maim: Update to 5.4.66.Marius Bakke
* gnu/packages/xdisorg.scm (maim): Update to 5.4.66.
2017-08-01gnu: slop: Update to 7.3.48.Marius Bakke
* gnu/packages/xdisorg.scm (slop): Update to 7.3.48.
2017-08-01gnu: git: Update to 2.13.4.Marius Bakke
* gnu/packages/version-control.scm (git): Update to 2.13.4.
2017-08-01gnu: r-foreign: Update hash after upstream tarball change.Roel Janssen
* gnu/packages/statistics.scm (r-foreign): Update hash. The only difference in the tarball is the metadata. The contents are identical.
2017-08-01gnu: r-foreign: Remove duplicate recipe.Roel Janssen
* gnu/packages/statistics.scm (r-foreign): Remove duplicate recipe.
2017-08-01graph: Provide access to the package record in the emit functions.Roel Janssen
* guix/graph.scm (export-graph): Pass the node to the emit functions, instead of the node's label.
2017-08-01guix package: Allow `guix package -u' to fuction as before.Efraim Flashner
This is a follow up to 6ddf97f81bb99a73f00e30ad5fc19577872b5b49 * guix/scripts/package.scm (%options) <"-u">: Only check for a flag when there is an ARG after '-u'.
2017-08-01gnu: rapidjson: Update to 1.1.0.Leo Famulari
* gnu/packages/web.scm (rapidjson): Update to 1.1.0. [source]: Remove snippet.
2017-08-01gnu: Add pidentd.ng0
* gnu/packages/networking.scm (pidentd): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2017-08-01gnu: hyperrogue: Update to 10.0e.Kei Kebreau
* gnu/packages/games.scm (hyperrogue): Update to 10.0e. [arguments]: Adjust accordingly.
2017-08-01gnu: metabat: Limit to x86_64 and i686 only.Efraim Flashner
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
2017-08-01gnu: Add emacs-yasnippet-snippets.Kyle Meyer
* gnu/packages/emacs.scm (emacs-yasnippet-snippets): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-01gnu: emacs-yasnippet: Upgrade to 0.12.0.Kyle Meyer
* gnu/packages/emacs.scm (emacs-yasnippet): Upgrade to 0.12.0. [source]: Remove an uninstalled directory from yas-snippet-dirs. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-01gnu: guile-ssh: Update to 0.11.2.Ludovic Courtès
* gnu/packages/ssh.scm (guile-ssh): Update to 0.11.2. [source]: Remove 'patches', 'modules', and 'snippet'. * gnu/packages/patches/guile-ssh-channel-finalization.patch, gnu/packages/patches/guile-ssh-double-free.patch, gnu/packages/patches/guile-ssh-rexec-bug.patch: Remove. * gnu/local.mk (dist_patch_DATA): Remove them.
2017-08-01gnu: artanis: Unbundled guile-json and version according to documentation.Adonay Felipe Nogueira
* gnu/packages/guile.scm (artanis): Unbundled guile-json and version according to documentation. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-01lint: formatting: Detect sexp boundaries.Ludovic Courtès
* guix/scripts/lint.scm (report-formatting-issues)[last-line]: Remove. [sexp-last-line]: New procedure. Use it.
2017-08-01gnu: python-pbr-minimal: Update to 3.0.1Muriithi Frederick Muriuki
* gnu/packages/python.scm (python-pbr-minimal): Update to 3.0.1 [source]: Update hash and remove patch. * gnu/packages/patches/python-pbr-fix-man-page-support.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2017-08-01gnu: libgit2: Enable SHA-1 collision detection.Leo Famulari
* gnu/packages/version-control.scm (libgit2)[arguments]: Enable '-DUSE_SHA1DC' in #:configure-flags.
2017-08-01gnu: ruby-bio-commandeer: Update to 0.2.0.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-bio-commandeer): Update to 0.2.0.
2017-07-31gnu: libmicrohttpd: Update to 0.9.55.Ludovic Courtès
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.55. [arguments]: Add 'add-missing-LDFLAGS' phase.
2017-07-31guix package: Warn when invoked with '-u -something'.Ludovic Courtès
Fixes <https://bugs.gnu.org/27820>. Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>. * guix/scripts/package.scm (%options) <"-u">: Emit a warning when ARG starts with "-".
2017-07-31gnu: xf86-video-intel: Update snapshot.Ludovic Courtès
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2100efa. Introduce 'revision' variable.
2017-07-31gnu: guile-bytestructures: Install .go files to lib/guile/X.Y.Ludovic Courtès
* gnu/packages/guile.scm (guile-bytestructures)[arguments]: Install .go files to OBJECT-DIR, defined as OUT/lib/guile/X.Y/site-ccache.
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