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* gnu: r-genomicfeatures: Update to 1.36.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.1.
* gnu: r-edger: Update to 3.26.4.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
* gnu: r-variantannotation: Update to 1.30.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
* import: cran: Ignore invalid packages from the system requirements.Ricardo Wurmus2019-05-28
| | | | | * guix/import/cran.scm (description->package): Filter invalid packages from the list of system requirements.
* gnu: r-atacseqqc: Update to 1.8.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.1.
* gnu: r-icobra: Update to 1.12.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/bioconductor.scm (r-icobra): Update to 1.12.1.
* gnu: r-chippeakanno: Update to 3.18.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.1.
* gnu: r-geosphere: Update to 1.5-10.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-geosphere): Update to 1.5-10.
* gnu: r-ggfortify: Update to 0.4.7.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-ggfortify): Update to 0.4.7.
* gnu: r-wgcna: Update to 1.68.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-wgcna): Update to 1.68.
* gnu: r-bookdown: Update to 0.11.Ricardo Wurmus2019-05-28
| | | | | * gnu/packages/cran.scm (r-bookdown): Update to 0.11. [propagated-inputs]: Add ghc-pandoc; remove r-yaml.
* gnu: r-upsetr: Update to 1.4.0.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-upsetr): Update to 1.4.0.
* gnu: r-epi: Update to 2.37.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-epi): Update to 2.37.
* gnu: r-etm: Update to 1.0.5.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-etm): Update to 1.0.5.
* gnu: r-cmprsk: Update to 2.2-8.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-cmprsk): Update to 2.2-8.
* gnu: r-ks: Update to 1.11.5.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-ks): Update to 1.11.5.
* gnu: r-bayesplot: Update to 1.7.0.Ricardo Wurmus2019-05-28
| | | | | * gnu/packages/cran.scm (r-bayesplot): Update to 1.7.0. [propagated-inputs]: Add r-glue, r-tibble, and r-tidyselect.
* gnu: r-refgenome: Update to 1.7.7.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-refgenome): Update to 1.7.7.
* gnu: r-snakecase: Update to 0.11.0.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-snakecase): Update to 0.11.0.
* gnu: r-openxlsx: Update to 4.1.0.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-openxlsx): Update to 4.1.0.1.
* gnu: r-pillar: Update to 1.4.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-pillar): Update to 1.4.1.
* gnu: r-tsp: Update to 1.1-7.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-tsp): Update to 1.1-7.
* gnu: r-jomo: Update to 2.6-8.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-jomo): Update to 2.6-8.
* gnu: r-ksamples: Update to 1.2-9.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-ksamples): Update to 1.2-9.
* gnu: r-lpsolve: Update to 5.6.13.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/cran.scm (r-lpsolve): Update to 5.6.13.1.
* gnu: r-car: Update to 3.0-3.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/statistics.scm (r-car): Update to 3.0-3.
* gnu: r-fpc: Update to 2.2-1.Ricardo Wurmus2019-05-28
| | | | | * gnu/packages/statistics.scm (r-fpc): Update to 2.2-1. [propagated-inputs]: Remove r-trimcluster.
* gnu: r-prabclus: Update to 2.2-7.1.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/statistics.scm (r-prabclus): Update to 2.2-7.1.
* gnu: r-zoo: Update to 1.8-6.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/statistics.scm (r-zoo): Update to 1.8-6.
* gnu: r-rmarkdown: Update to 1.13.Ricardo Wurmus2019-05-28
| | | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.13. [propagated-inputs]: Add r-xfun.
* gnu: r-evaluate: Update to 0.14.Ricardo Wurmus2019-05-28
| | | | * gnu/packages/statistics.scm (r-evaluate): Update to 0.14.
* self: Fix unquoting.Ricardo Wurmus2019-05-28
| | | | | | This is a follow-up to commit dfc69e4b6d4bbc41a4d37b3cc6ea12adb34aaafa. * guix/self.scm (whole-package): Unquote %storedir in the daemon wrapper.
* gnu: python-attrs: Update to 19.1.0.h.nasajpour2019-05-28
| | | | | | * gnu/packages/python-xyz.scm (python-attrs): Update to 19.1.0. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
* gnu: python-flask: Update to 1.0.3.h.nasajpour2019-05-28
| | | | | | * gnu/packages/python-web.scm (python-flask): Update to 1.0.3. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
* gnu: d-feet: Fix missing input and update to 0.3.14.Pierre Neidhardt2019-05-28
| | | | | * 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.
* gnu: guix: Update to 35d1354.Ludovic Courtès2019-05-28
| | | | * gnu/packages/package-management.scm (guix): Update to 35d1354.
* gnu: emacs-relint: Update to 1.8.Nicolas Goaziou2019-05-27
| | | | * gnu/packages/emacs-xyz.scm (emacs-relint): Update to 1.8.
* gnu: emacs-xr: Update to 1.12.Nicolas Goaziou2019-05-27
| | | | * gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.12.
* publish: Display the compression method and level in use.Ludovic Courtès2019-05-27
| | | | | | * 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.
* lzlib: 'lzread!' never returns more than it was asked for.Ludovic Courtès2019-05-27
| | | | | | Fixes a bug whereby 'lzread!' could return more than COUNT. * guix/lzlib.scm (lzread!): Rewrite in a semi-functional style.
* gnu: guix: Add dependency on lzlib.Ludovic Courtès2019-05-27
| | | | * gnu/packages/package-management.scm (guix)[inputs]: Add LZLIB.
* self: Add dependency on lzlib.Ludovic Courtès2019-05-27
| | | | | | * guix/self.scm (compiled-guix): Pass #:lzlib to 'make-config.scm'. (make-config.scm): Add #:lzlib and honor it. (specification->package): Add "lzlib".
* publish: Add support for lzip.Ludovic Courtès2019-05-27
| | | | | | | | | | | | | | | * 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.
* utils: Support compression and decompression with lzip.Ludovic Courtès2019-05-27
| | | | | | | | * 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.
* utils: Test 'compressed-port' and 'decompressed-port' for both gzip and xz.Ludovic Courtès2019-05-27
| | | | | * tests/utils.scm (test-compression/decompression): New procedure. <top level>: Call it for both 'xz and 'gzip.
* lzlib: Add 'make-lzip-input-port/compressed'.Ludovic Courtès2019-05-27
| | | | | | | * 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.
* lzlib: Adjust 'lz-compress-read' docstring.Ludovic Courtès2019-05-27
| | | | | * guix/lzlib.scm (lz-compress-read): The integer return can be zero; adjust docstring accordingly.
* gnu: r-shiny: Fix JavaScript minification.Ricardo Wurmus2019-05-27
| | | | | | Fixes <https://bugs.gnu.org/35923>. * gnu/packages/cran.scm (r-shiny)[native-inputs]: Add uglify-js.
* gnu: Add osmctoolsGuillaume LE VAILLANT2019-05-27
| | | | | | * gnu/packages/geo.scm (osmctools): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: go@1.4: Update to 1.4-bootstrap-20171003.Alex Griffin2019-05-27
| | | | | | | | | | | | * 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>
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