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2019-05-29gnu: r-edger: Update to 3.26.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
2019-05-29gnu: r-variantannotation: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
2019-05-28import: cran: Ignore invalid packages from the system requirements.Ricardo Wurmus
* guix/import/cran.scm (description->package): Filter invalid packages from the list of system requirements.
2019-05-28gnu: r-atacseqqc: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.1.
2019-05-28gnu: r-icobra: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.12.1.
2019-05-28gnu: r-chippeakanno: Update to 3.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.1.
2019-05-28gnu: r-geosphere: Update to 1.5-10.Ricardo Wurmus
* gnu/packages/cran.scm (r-geosphere): Update to 1.5-10.
2019-05-28gnu: r-ggfortify: Update to 0.4.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.7.
2019-05-28gnu: r-wgcna: Update to 1.68.Ricardo Wurmus
* gnu/packages/cran.scm (r-wgcna): Update to 1.68.
2019-05-28gnu: r-bookdown: Update to 0.11.Ricardo Wurmus
* gnu/packages/cran.scm (r-bookdown): Update to 0.11. [propagated-inputs]: Add ghc-pandoc; remove r-yaml.
2019-05-28gnu: r-upsetr: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-upsetr): Update to 1.4.0.
2019-05-28gnu: r-epi: Update to 2.37.Ricardo Wurmus
* gnu/packages/cran.scm (r-epi): Update to 2.37.
2019-05-28gnu: r-etm: Update to 1.0.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-etm): Update to 1.0.5.
2019-05-28gnu: r-cmprsk: Update to 2.2-8.Ricardo Wurmus
* gnu/packages/cran.scm (r-cmprsk): Update to 2.2-8.
2019-05-28gnu: r-ks: Update to 1.11.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-ks): Update to 1.11.5.
2019-05-28gnu: r-bayesplot: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-bayesplot): Update to 1.7.0. [propagated-inputs]: Add r-glue, r-tibble, and r-tidyselect.
2019-05-28gnu: r-refgenome: Update to 1.7.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-refgenome): Update to 1.7.7.
2019-05-28gnu: r-snakecase: Update to 0.11.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-snakecase): Update to 0.11.0.
2019-05-28gnu: r-openxlsx: Update to 4.1.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-openxlsx): Update to 4.1.0.1.
2019-05-28gnu: r-pillar: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-pillar): Update to 1.4.1.
2019-05-28gnu: r-tsp: Update to 1.1-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-tsp): Update to 1.1-7.
2019-05-28gnu: r-jomo: Update to 2.6-8.Ricardo Wurmus
* gnu/packages/cran.scm (r-jomo): Update to 2.6-8.
2019-05-28gnu: r-ksamples: Update to 1.2-9.Ricardo Wurmus
* gnu/packages/cran.scm (r-ksamples): Update to 1.2-9.
2019-05-28gnu: r-lpsolve: Update to 5.6.13.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-lpsolve): Update to 5.6.13.1.
2019-05-28gnu: r-car: Update to 3.0-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 3.0-3.
2019-05-28gnu: r-fpc: Update to 2.2-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fpc): Update to 2.2-1. [propagated-inputs]: Remove r-trimcluster.
2019-05-28gnu: r-prabclus: Update to 2.2-7.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-prabclus): Update to 2.2-7.1.
2019-05-28gnu: r-zoo: Update to 1.8-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-6.
2019-05-28gnu: r-rmarkdown: Update to 1.13.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.13. [propagated-inputs]: Add r-xfun.
2019-05-28gnu: r-evaluate: Update to 0.14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-evaluate): Update to 0.14.
2019-05-28self: Fix unquoting.Ricardo Wurmus
This is a follow-up to commit dfc69e4b6d4bbc41a4d37b3cc6ea12adb34aaafa. * guix/self.scm (whole-package): Unquote %storedir in the daemon wrapper.
2019-05-28gnu: python-attrs: Update to 19.1.0.h.nasajpour
* gnu/packages/python-xyz.scm (python-attrs): Update to 19.1.0. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
2019-05-28gnu: python-flask: Update to 1.0.3.h.nasajpour
* gnu/packages/python-web.scm (python-flask): Update to 1.0.3. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
2019-05-28gnu: d-feet: Fix missing input and update to 0.3.14.Pierre Neidhardt
* gnu/packages/gnome.scm (d-feet): Update to 0.3.14. [inputs]: Add hicolor-icon-theme since d-feet won't list anything without it.
2019-05-28gnu: guix: Update to 35d1354.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to 35d1354.
2019-05-27gnu: emacs-relint: Update to 1.8.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.8.
2019-05-27gnu: emacs-xr: Update to 1.12.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.12.
2019-05-27publish: Display the compression method and level in use.Ludovic Courtès
* guix/scripts/publish.scm (guix-publish): Use 'info' instead of 'format' for the initial message. When COMPRESSION is true, display the method and level in use.
2019-05-27lzlib: 'lzread!' never returns more than it was asked for.Ludovic Courtès
Fixes a bug whereby 'lzread!' could return more than COUNT. * guix/lzlib.scm (lzread!): Rewrite in a semi-functional style.
2019-05-27gnu: guix: Add dependency on lzlib.Ludovic Courtès
* gnu/packages/package-management.scm (guix)[inputs]: Add LZLIB.
2019-05-27self: Add dependency on lzlib.Ludovic Courtès
* guix/self.scm (compiled-guix): Pass #:lzlib to 'make-config.scm'. (make-config.scm): Add #:lzlib and honor it. (specification->package): Add "lzlib".
2019-05-27publish: Add support for lzip.Ludovic Courtès
* guix/scripts/publish.scm (show-help, %options): Support '-C METHOD' and '-C METHOD:LEVEL'. (default-compression): New procedure. (bake-narinfo+nar): Add lzip. (nar-response-port): Likewise. (string->compression-type): New procedure. (make-request-handler): Generalize /nar/gzip handler to handle /nar/lzip as well. * tests/publish.scm ("/nar/lzip/*"): New test. ("/*.narinfo with lzip compression"): New test. * doc/guix.texi (Invoking guix publish): Document it. (Requirements): Mention lzlib.
2019-05-27utils: Support compression and decompression with lzip.Ludovic Courtès
* guix/utils.scm (lzip-port): New procedure. (decompressed-port, compressed-port, compressed-output-port): Add 'lzip case. * tests/utils.scm <top level>: Call 'test-compression/decompression' for 'lzip as well.
2019-05-27utils: Test 'compressed-port' and 'decompressed-port' for both gzip and xz.Ludovic Courtès
* tests/utils.scm (test-compression/decompression): New procedure. <top level>: Call it for both 'xz and 'gzip.
2019-05-27lzlib: Add 'make-lzip-input-port/compressed'.Ludovic Courtès
* guix/lzlib.scm (lzwrite!, make-lzip-input-port/compressed): New procedures. * tests/lzlib.scm ("make-lzip-input-port/compressed"): New test. * guix/tests.scm (%seed): Export.
2019-05-27lzlib: Adjust 'lz-compress-read' docstring.Ludovic Courtès
* guix/lzlib.scm (lz-compress-read): The integer return can be zero; adjust docstring accordingly.
2019-05-27gnu: r-shiny: Fix JavaScript minification.Ricardo Wurmus
Fixes <https://bugs.gnu.org/35923>. * gnu/packages/cran.scm (r-shiny)[native-inputs]: Add uglify-js.
2019-05-27gnu: Add osmctoolsGuillaume LE VAILLANT
* gnu/packages/geo.scm (osmctools): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-05-27gnu: go@1.4: Update to 1.4-bootstrap-20171003.Alex Griffin
* gnu/packages/golang.scm (go-1.4): Use the bootstrap branch that is still supported upstream. [version]: Update to 1.4-bootstrap-20171003. [arguments]: Remove obsolete fix for timezone test which is now included upstream. Don't manually disable cgo because it is disabled by default. Manually enable test suite because future releases will disable tests by default. Signed-off-by: Leo Famulari <leo@famulari.name>
2019-05-27gnu: python-alembic: Update to 1.0.10.Danny Milosavljevic
* gnu/packages/databases.scm (python-alembic): Update to 1.0.10.
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