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* gnu: gd: Fix-CVE-2016-3074.Leo Famulari2016-05-17
| | | | | | * gnu/packages/patches/gd-CVE-2016-3074.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd)[source]: Use it.
* gnu: gd: Specify 'cpe-name'.Ludovic Courtès2016-05-17
| | | | * gnu/packages/gd.scm (gd)[properties]: New field.
* lint: Honor 'cpe-name' and 'cpe-version' package properties.Ludovic Courtès2016-05-17
| | | | | | | | | | * guix/scripts/lint.scm (package-name->cpe-name): Remove. (package-vulnerabilities): Honor 'cpe-name' and 'cpe-version' properties. * gnu/packages/grub.scm (grub)[properties]: New field. * gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and 'cpe-version'. * doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
* gnu: emacs-constants: Remove old patch.Federico Beffa2016-05-17
| | | | | * gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it. * gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
* store: Clarify 'query-path-hash' docstring.Ludovic Courtès2016-05-17
| | | | * guix/store.scm (query-path-hash): Clarify docstring.
* import: Gracefully report import failures.Ludovic Courtès2016-05-17
| | | | | | | | | | | | Previously, something like 'guix import gnu which' would spit out a backtrace if, say, the 'which' tarball could not be authenticated. * guix/upstream.scm (download-tarball): Mention failure modes in docstring. * guix/import/gnu.scm (gnu-package->sexp): Return #f when 'download-tarball' returns #f. * guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does not return a (package ...) sexp.
* import: Exit with non-zero when an unknown importer is asked.Ludovic Courtès2016-05-17
| | | | | * guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format' when IMPORTER is unknown.
* gnu: emacs-constants: Update to 2.6.Federico Beffa2016-05-17
| | | | | * gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and update to 2.6.
* gnu: sortmerna: Update to 2.1b.Ben Woodcroft2016-05-17
| | | | | * gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b. [inputs]: New field.
* gnu: vsearch: Update to 1.11.1.Ben Woodcroft2016-05-17
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
* gnu: diamond: Update to 0.8.1.Ben Woodcroft2016-05-17
| | | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1. [source]: Remove 'snippet'. [build-system]: Use cmake-build-system. [arguments]: Remove modifications to phases. [native-inputs]: Remove field. [inputs]: Remove 'boost'.
* gnu: emacs-constants: Factorize home-page in source URL.Ludovic Courtès2016-05-17
| | | | | * gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above. Use it in 'uri'.
* gnu: 'uncompressed-file-fetch' no longer depends on gzip.Ludovic Courtès2016-05-17
| | | | | * gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on GZIP.
* gnu: cflow: Update to 1.5.Efraim Flashner2016-05-17
| | | | * gnu/packages/code.scm (cflow): Update to 1.5.
* gnu: Add geiser-next.Christopher Allan Webber2016-05-16
| | | | | | | Also, I previously committed to this repository in 2015; add self to copyright headers for that year too. * gnu/packages/emacs.scm (geiser-next): New variable.
* import cran: latest-bioconductor-release: Wrap Bioconductor URL in list.Ricardo Wurmus2016-05-16
| | | | | * guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor URL in list in the "urls" field of the "upstream-source" value.
* gnu: r-zlibbioc: Update to 1.18.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
* gnu: r-motifrg: Update to 1.16.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
* gnu: r-seqlogo: Update to 1.38.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
* gnu: r-genomation: Update to 1.4.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
* gnu: r-seqpattern: Update to 1.4.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
* gnu: r-impute: Update to 1.46.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
* gnu: r-bsgenome: Update to 1.40.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
* gnu: r-topgo: Update to 2.24.0.Ricardo Wurmus2016-05-16
| | | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0. [propagated-inputs]: Add r-matrixstats.
* gnu: r-graph: Update to 1.50.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
* gnu: r-genomicfeatures: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
* gnu: r-rtracklayer: Update to 1.32.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
* gnu: r-genomicalignments: Update to 1.8.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
* gnu: r-summarizedexperiment: Update to 1.2.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
* gnu: r-rsamtools: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
* gnu: r-biostrings: Update to 2.40.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
* gnu: r-biocparallel: Update to 1.6.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
* gnu: r-biomart: Update to 2.28.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
* gnu: r-annotationdbi: Update to 1.34.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
* gnu: r-biobase: Update to 2.32.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
* gnu: r-genomicranges: Update to 1.24.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
* gnu: r-xvector: Update to 0.12.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
* gnu: r-variantannotation: Update to 1.18.0.Ricardo Wurmus2016-05-16
| | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.0.
* gnu: r-genomeinfodb: Update to 1.8.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
* gnu: r-iranges: Update to 2.6.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
* gnu: r-s4vectors: Update to 0.10.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
* gnu: r-dnacopy: Update to 1.46.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
* gnu: r-biocgenerics: Update to 0.18.0.Ricardo Wurmus2016-05-16
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
* import cran: Use URL for Bioconductor 3.3.Ricardo Wurmus2016-05-16
| | | | | * guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.3.
* gnu: imagemagick: Update to 6.9.4-1.Leo Famulari2016-05-16
| | | | * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-1.
* gnu: libgit2: Update to 0.24.1.Efraim Flashner2016-05-16
| | | | * gnu/packages/version-control.scm (libgit2): Update to 0.24.1.
* gnu: tmux: Update to 2.2.Efraim Flashner2016-05-16
| | | | * gnu/packages/tmux.scm (tmux): Update to 2.2.
* build: Accept dates with space-padded hour field.Ricardo Wurmus2016-05-16
| | | | | * guix/build/download.scm: Replace "parse-rfc-822-date" from the (web http) module.
* gnu: Add ledger.Alex Griffin2016-05-16
| | | | | | * gnu/packages/finance.scm (ledger): New variable. Co-authored-by: Alex Kost <alezost@gmail.com>
* gnu: Add utfcpp.Alex Griffin2016-05-16
| | | | | | * gnu/packages/textutils.scm (utfcpp): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
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