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2020-06-13gnu: r-topgo: Update to 2.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.40.0.
2020-06-13gnu: r-genomicfeatures: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rtracklayer: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.48.0.
2020-06-13gnu: r-genomicalignments: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.24.0.
2020-06-13gnu: r-summarizedexperiment: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-delayedarray: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.0. [propagated-inputs]: Remove r-biocparallel.
2020-06-13gnu: r-rsamtools: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.4.0.
2020-06-13gnu: r-biostrings: Update to 2.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm ( r-biostrings): Update to 2.56.0. [propagated-inputs]: Add r-crayon.
2020-06-13gnu: r-biocparallel: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.22.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biomart: Update to 2.44.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
2020-06-13gnu: r-annotationdbi: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biobase: Update to 2.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
2020-06-13gnu: r-genomicranges: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-xvector: Update to 0.28.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
2020-06-13gnu: r-limma: Update to 3.44.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
2020-06-13gnu: r-variantannotation: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
2020-06-13gnu: r-edger: Update to 3.30.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
2020-06-13gnu: r-genomeinfodb: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
2020-06-13gnu: r-iranges: Update to 2.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
2020-06-13gnu: r-s4vectors: Update to 0.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
2020-06-13gnu: r-bioccheck: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocstyle: Update to 2.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocviews: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
2020-06-13gnu: r-grohmm: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
2020-06-13gnu: r-systempiper: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0. [propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and r-stringr; remove r-biocgenerics. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-shortread: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
2020-06-13gnu: r-gostats: Update to 2.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
2020-06-13gnu: r-category: Update to 2.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
2020-06-13gnu: r-gseabase: Update to 1.50.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rbgl: Update to 1.64.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
2020-06-13gnu: r-annotationforge: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-dexseq: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-deseq2: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1. [propagated-inputs]: Remove r-hmisc. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-genefilter: Update to 1.70.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rgraphviz: Update to 2.32.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
2020-06-13gnu: r-preprocesscore: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
2020-06-13gnu: Add r-dot.Ricardo Wurmus
* gnu/packages/cran.scm (r-dot): New variable.
2020-06-13gnu: Add r-v8.Ricardo Wurmus
* gnu/packages/cran.scm (r-v8): New variable.
2020-06-13gnu: Add r-scatterpie.Ricardo Wurmus
* gnu/packages/cran.scm (r-scatterpie): New variable.
2020-06-13gnu: Add r-gprofiler2.Ricardo Wurmus
* gnu/packages/cran.scm (r-gprofiler2): New variable.
2020-06-13gnu: node: Build shared library.Ricardo Wurmus
* gnu/packages/node.scm (node)[arguments]: Build shared library.
2020-06-13gnu: r-gprofiler: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here... * gnu/packages/cran.scm (r-gprofiler): ...to here.
2020-06-12gnu: guile-sqlite3: Update to 0.1.1.Ludovic Courtès
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.1. [source]: Remove 'patches', 'modules', and 'snippet'. * gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch: Remove. * gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2020-06-12gnu: Add liblogging.Katherine Cox-Buday
* gnu/packages/c.scm (liblogging): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add libfastjson.Katherine Cox-Buday
* gnu/packages/c.scm (libfastjson): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add libestr.Katherine Cox-Buday
* gnu/packages/c.scm (libestr): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add emacs-shell-pop.Ryan Desfosses
* gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Fix apache mirror URIs.Efraim Flashner
* gnu/packages/web.scm (serf)[source]: Remove redundant part of URI. * gnu/packages/java.scm (ant-bootstrap, java-commons-httpclient, java-jakarta-oro)[source]: Same. * gnu/packages/maven.scm (maven-shared-utils, maven-plugin-annotations, maven-wagon-provider-api, maven-artifact)[source]: Same.
2020-06-12system: image: Do not produce an HFS tree when building an ISO.Mathieu Othacehe
Use "mbr_only" mode to make sure that no HFS+ tree are generated. * gnu/system/image.scm (system-image): Set MKRESCUE_SED_MODE to "mbr_only".
2020-06-12gnu: xf86-input-libinput: Reduce closure size.Pierre Neidhardt
* gnu/packages/xorg.scm (xf86-input-libinput)[inputs]: Replace libinput by libinput-minimal.
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