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28499 Commits

Author SHA1 Message Date
Ricardo Wurmus 5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus c37b361e44
gnu: r-summarizedexperiment: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 373430672d
gnu: r-biomart: Update to 2.34.2. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 024f19c68b
gnu: r-genomicranges: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0674657908
gnu: r-limma: Update to 3.34.8. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5fb1fee67b
gnu: r-variantannotation: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus d22abe1e5d
gnu: r-edger: Update to 3.20.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 66ae706c24
gnu: r-bookdown: Update to 0.6. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6.
[propagated-inputs]: Add r-xfun and ghc-pandoc.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 2e9da3390c
gnu: r-vegan: Update to 2.4-6. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 0f001b3c5a
gnu: r-drr: Update to 0.0.3. 
* gnu/packages/cran.scm (r-drr): Update to 0.0.3.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 92e4534ca8
gnu: r-lava: Update to 1.6. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.
[propagated-inputs]: Add r-squarem.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 093acd0de1
gnu: r-sp: Update to 1.2-7. 
* gnu/packages/cran.scm (r-sp): Update to 1.2-7.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus de1c0332d9
gnu: r-proxy: Update to 0.4-21. 
* gnu/packages/cran.scm (r-proxy): Update to 0.4-21.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus e30b878ec8
gnu: r-hexbin: Update to 1.27.2. 
* gnu/packages/statistics.scm (r-hexbin): Update to 1.27.2.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 64fe220cbe
gnu: r-dendextend: Update to 1.7.0. 
* gnu/packages/cran.scm (r-dendextend): Update to 1.7.0.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus cb471b7eaa
gnu: r-ddalpha: Update to 1.3.1.1. 
* gnu/packages/cran.scm (r-ddalpha): Update to 1.3.1.1.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 1d13426bed
gnu: r-recipes: Update to 0.1.2. 
* gnu/packages/cran.scm (r-recipes): Update to 0.1.2.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 637584253f
gnu: r-pracma: Update to 2.1.4. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.4.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 1c7919251a
gnu: Add r-uuid. 
* gnu/packages/cran.scm (r-uuid): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus c555ccabcf
gnu: Add r-pillar. 
* gnu/packages/cran.scm (r-pillar): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus f244296822
gnu: Add r-utf8. 
* gnu/packages/cran.scm (r-utf8): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus c5f033e0f6
gnu: Add r-squarem. 
* gnu/packages/cran.scm (r-squarem): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus fe5b889365
gnu: r-shape: Update to 1.4.4. 
* gnu/packages/cran.scm (r-shape): Update to 1.4.4.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 33d8699da5
gnu: r-rcpp: Update to 0.12.15. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.15.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus f6d2b45ca8
gnu: Add r-xfun. 
* gnu/packages/cran.scm (r-xfun): New variable.
 2018-02-13 16:18:41 +01:00
Leo Famulari 77737e0354
gnu: unzip: Mitigate CVE-2018-1000035. 
* gnu/packages/compression.scm (unzip)[replacement]: New field.
(unzip/fixed): New variable.
 2018-02-13 09:51:07 -05:00
Ricardo Wurmus ad5de226e7
gnu: Add ghc-megaparsec. 
* gnu/packages/haskell.scm (ghc-megaparsec): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus aeecabd43c
gnu: Add ghc-parser-combinators. 
* gnu/packages/haskell.scm (ghc-parser-combinators): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus f941a52a14
gnu: Add ghc-text-binary. 
* gnu/packages/haskell.scm (ghc-text-binary): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 183d1b1aaf
gnu: ghc-trifecta: Update to 1.7.1.1. 
* gnu/packages/haskell.scm (ghc-trifecta): Update to 1.7.1.1.
[inputs]: Add ghc-doctest.
[native-inputs]: Add cabal-doctest.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 2815963b8d
gnu: ghc-reducers: Update to 3.12.2. 
* gnu/packages/haskell.scm (ghc-reducers): Update to 3.12.2.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 67e86e58e0
gnu: ghc-directory: Add note. 
* gnu/packages/haskell.scm (ghc-directory): Add comment not to use this
package as an input.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 0498d1689d
gnu: darcs: Update to 2.12.5. 
* gnu/packages/version-control.scm (darcs): Update to 2.12.5.
[arguments]: Relax version constraint on shelly.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 97bfe0d759
gnu: darcs: Remove ghc-directory from inputs. 
* gnu/packages/version-control.scm (darcs)[inputs]: Remove ghc-directory.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 4b1f2166fe
gnu: ghc-graphviz: Fix build with newer QuickCheck. 
* gnu/packages/haskell.scm (ghc-graphviz)[arguments]: Allow building with
newer QuickCheck.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus f25c95d384
gnu: ghc-tar: Disable tests. 
* gnu/packages/haskell.scm (ghc-tar)[arguments]: Disable tests.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 1b58d289fd
gnu: ghc-system-filepath: Update to 0.4.14. 
* gnu/packages/haskell.scm (ghc-system-filepath): Update to 0.4.14.
[arguments]: Disable tests.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus da76c6de87
gnu: darcs: Remove ghc-process from inputs. 
* gnu/packages/version-control.scm (darcs)[inputs]: Remove ghc-process.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 831cb41906
gnu: ghc-hslogger: Remove ghc-process from inputs. 
* gnu/packages/haskell.scm (ghc-hslogger)[inputs]: Remove ghc-process.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 64f597a611
gnu: ghc-process: Update to 1.6.3.0. 
* gnu/packages/haskell.scm (ghc-process): Update to 1.6.3.0.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 973075a091
gnu: ghc-haskeline: Update to 0.7.4.2. 
* gnu/packages/haskell.scm (ghc-haskeline): Update to 0.7.4.2.
[inputs]: Add ghc-stm.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus 54afb52e1f
gnu: ghc-fgl-arbitrary: Fix build with newer QuickCheck. 
* gnu/packages/haskell.scm (ghc-fgl-arbitrary)[arguments]: Allow building with
newer QuickCheck.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus c0a541cba8
gnu: ghc-fgl: Fix build with newer QuickCheck. 
* gnu/packages/haskell.scm (ghc-fgl)[arguments]: Allow building with newer
QuickCheck.
 2018-02-13 13:37:40 +01:00
Ricardo Wurmus a49bb332a1
gnu: ghc-pandoc-citeproc: Update to 0.12.2.5. 
* gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.12.2.5.
 2018-02-13 13:37:40 +01:00
Ricardo Wurmus 1ddcb5e300
gnu: ghc-hs-bibutils: Update to 6.2.0.1. 
* gnu/packages/haskell.scm (ghc-hs-bibutils): Update to 6.2.0.1.
 2018-02-13 13:37:40 +01:00
Ricardo Wurmus 1afa5abbe8
gnu: ghc-pandoc: Update to 2.0.6. 
* gnu/packages/haskell.scm (ghc-pandoc): Update to 2.0.6.
[inputs]: Add ghc-aeson-pretty, ghc-cmark-gfm, ghc-doctemplates, ghc-glob,
ghc-hslua-module-text, ghc-old-locale, ghc-skylighting, and ghc-split; remove
ghc-ansi-terminal, ghc-cmark, ghc-extensible-exceptions, ghc-filemanip,
ghc-highlighting-kate, and ghc-old-time.
[native-inputs]: Remove ghc-test-framework, ghc-test-framework-hunit, and
ghc-test-framework-quickcheck2; add ghc-tasty, ghc-tasty-golden,
ghc-tasty-hunit, and ghc-tasty-quickcheck.
 2018-02-13 13:37:40 +01:00