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path: root/gnu/packages/bioinformatics.scm
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* Merge branch 'master' into core-updatesMark H Weaver2019-08-22
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| * gnu: edirect: Update to 12.1.20190819.Efraim Flashner2019-08-20
| | | | | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819.
| * gnu: r-gviz: Update to 1.28.1.Ricardo Wurmus2019-08-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1.
| * gnu: r-edger: Update to 3.26.7.Ricardo Wurmus2019-08-16
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.7.
* | Merge branch 'master' into core-updatesMarius Bakke2019-08-13
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| * gnu: freebayes: Simplify and enable tests.Ricardo Wurmus2019-08-09
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles" phase; move build of tabixpp and vcflib to separate phase "build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build" phase.
| * gnu: freebayes: Move bamtools to inputs.Ricardo Wurmus2019-08-09
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools from here... [inputs]: ...to here.
| * gnu: Add freebayes.Pierre Neidhardt2019-08-09
| | | | | | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
| * gnu: Add vcflib.Pierre Neidhardt2019-08-09
| | | | | | | | | | * gnu/packages/bioinformatics.scm (vcflib): New variable. (tabixpp-freebayes): New private variable.
| * gnu: r-hdf5array: Update to 1.12.2.Ricardo Wurmus2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2.
| * gnu: r-biocparallel: Update to 1.18.1.Ricardo Wurmus2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1.
| * Revert "gnu: Add vcflib."Efraim Flashner2019-08-08
| | | | | | | | | | | | This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master
| * Revert "gnu: Add freebayes."Efraim Flashner2019-08-08
| | | | | | | | This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843.
| * gnu: Add freebayes.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (freebayes): New variable.
| * gnu: Add vcflib.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (vcflib): New variable.
| * gnu: Add fastahack.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (fastahack): New variable.
| * gnu: Add fsom.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (fsom): New variable.
| * gnu: Add multichoose.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (multichoose): New variable.
| * gnu: Add smithwaterman.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (smithwaterman): New variable.
| * gnu: Add tabixpp.Pierre Neidhardt2019-08-08
| | | | | | | | * gnu/packages/bioinformatics.scm (tabixpp): New variable.
| * gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml.Robert Vollmert2019-08-07
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | These are ghc-8.4-bundled packages, removing to avoid build conflicts. * gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove. * gnu/packages/haskell-web.scm (ghc-xhtml): Remove. * gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text. * gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and ghc-text. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec. (git-annex)[inputs]: Remove ghc-stm and ghc-text. (ghc-sdl2)[inputs]: Remove ghc-text. (ghc-sdl2-image)[inputs]: Remove ghc-text. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm. (ghc-tasty)[inputs]: Remove ghc-stm. (ghc-tasty-rerun)[inputs]: Same. (ghc-quickcheck-instances)[inputs]: Remove ghc-text. (ghc-hedgehog)[inputs]: Remove ghc-stm. * gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove ghc-text. * gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text. (ghc-cookie)[inputs]: Same. (ghc-http-types)[inputs]: Same. (ghc-http)[inputs]: Remove ghc-parsec. (ghc-http-client)[inputs]: Remove ghc-text. (ghc-http2)[inputs]: Remove ghc-stm. (ghc-http-conduit)[native-inputs]: Remove ghc-text. (ghc-wai)[inputs]: Same. (ghc-wai-extra)[inputs]: Same. (ghc-warp)[inputs]: Remove ghc-stm and ghc-text. (ghc-xss-sanitize)[native-inputs]: Remove ghc-text. (ghc-css-text)[inputs]: Same. (ghc-mime-types)[inputs]: Same. (ghc-blaze-html)[inputs]: Same. (ghc-aeson)[inputs]: Same. (ghc-aeson-pretty)[inputs]: Same. (ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec. (ghc-multipart)[inputs]: Remove ghc-parsec. (ghc-uri-encode)[inputs]: Remove ghc-text. (ghc-path-pieces)[inputs]: Same. (ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec. (ghc-yesod-persistent)[inputs]: Remove ghc-text. (ghc-yesod-form)[inputs]: Same. (ghc-yesod)[inputs]: Same. (ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text. (ghc-hxt)[inputs]: Remove ghc-parsec. * gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text. (ghc-double-conversion)[inputs]: Same. (ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text. [native-inputs]: Remove ghc-parsec. (ghc-cgi)[inputs]: Remove ghc-parsec. (hlint)[inputs]: Remove ghc-text. (ghc-openglraw)[inputs]: Remove ghc-text. (ghc-opengl)[inputs]: Same. (ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text. (ghc-hackage-security)[inputs]: Remove ghc-parsec. (cabal-install)[inputs]: Remove ghc-stm. (ghc-parsec-numbers)[inputs]: Remove ghc-parsec. (ghc-safesemaphore)[inputs]: Remove ghc-stm. (ghc-text-binary)[inputs]: Remove ghc-text. (ghc-hashable)[inputs]: Remove ghc-text. (ghc-transformers-base)[inputs]: Remove ghc-stm. (ghc-indents)[inputs]: Remove ghc-parsec. (ghc-regex-tdfa-rc)[inputs]: Same. (ghc-regex-tdfa-text)[inputs]: Same. (ghc-regex)[inputs]: Remove ghc-text. (ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text. (ghc-attoparsec)[inputs]: Remove ghc-text. (ghc-attoparsec-bootstrap)[inputs]: Same. (ghc-zip-archive)[inputs]: Same. (ghc-polyparse)[inputs]: Same. (ghc-reducers)[inputs]: Same. (ghc-xml)[inputs]: Same. (ghc-feed)[inputs]: Same. (ghc-exceptions)[inputs]: Remove ghc-stm. (ghc-case-insensitive)[inputs]: Remove ghc-text. (ghc-megaparsec)[inputs]: Same. (ghc-network-uri)[inputs]: Remove ghc-parsec. (ghc-monad-control)[inputs]: Remove ghc-stm. (ghc-blaze-builder)[inputs]: Remove ghc-text. (ghc-blaze-markup)[inputs]: Same. (ghc-async)[inputs]: Remove ghc-stm. (ghc-invariant)[inputs]: Same. (ghc-statevar)[inputs]: Same. (ghc-lens)[inputs]: Remove ghc-text. (ghc-cheapskate)[inputs]: Same. (ghc-semigroups)[inputs]: Same. (ghc-semigroups-bootstrap)[inputs]: Same. (ghc-fast-logger)[inputs]: Same. (ghc-scientific)[inputs]: Same. (ghc-scientific-bootstrap)[inputs]: Same. (ghc-texmath)[inputs]: Remove ghc-parsec. (ghc-highlighting-kate)[inputs]: Same. (ghc-cmark)[inputs]: Remove ghc-text. (ghc-cmark-gfm)[inputs]: Same. (ghc-th-lift-instances)[inputs]: Same. (ghc-yaml)[inputs]: Same. (ghc-hslua)[inputs]: Same. (ghc-hslua-module-text)[inputs]: Same. (ghc-skylighting-core)[inputs]: Same. (ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec. (ghc-pandoc)[inputs]: Same. (ghc-typed-process)[inputs]: Remove ghc-stm. (ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text. (ghc-xml-types)[inputs]: Remove ghc-text. (ghc-xml-conduit)[inputs]: Same. (ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec. (ghc-regex-tdfa)[inputs]: Remove ghc-parsec. (ghc-wl-pprint-text)[inputs]: Remove ghc-text. (ghc-graphviz)[inputs]: Same. (ghc-system-filepath-bootstrap)[inputs]: Same. (ghc-system-fileio-bootstrap)[inputs]: Same. (ghc-shelly)[inputs]: Same. (ghc-chell)[inputs]: Same. (ghc-system-filepath)[inputs]: Same. (ghc-system-fileio)[inputs]: Same. (ghc-fsnotify)[inputs]: Same. (ghc-json)[inputs]: Remove ghc-text and ghc-parsec. (ghc-esqueleto)[inputs]: Remove ghc-text. (shellcheck)[inputs]: Remove ghc-parsec. (ghc-errors)[inputs]: Remove ghc-text. (ghc-chunked-data)[inputs]: Same. (ghc-uuid-types)[inputs]: Same. (ghc-uuid)[inputs]: Same. (ghc-rebase)[inputs]: Remove ghc-stm and ghc-text. (ghc-foldl)[inputs]: Remove ghc-text. (ghc-mono-traversable)[inputs]: Same. (ghc-conduit-combinators)[inputs]: Same. (ghc-aws)[inputs]: Same. (ghc-stm-chans)[inputs]: Remove ghc-stm. (ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm. (ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text. (ghc-resource-pool)[inputs]: Remove ghc-stm. (ghc-attoparsec-iso8601)[inputs]: Remove ghc-text. (ghc-http-api-data)[inputs]: Same. (ghc-persistent)[inputs]: Same. (ghc-aeson-compat)[inputs]: Same. (ghc-persistent-template)[inputs]: Same. (ghc-unliftio)[inputs]: Remove ghc-stm. (ghc-persistent-sqlite)[native-inputs]: Remove ghc-text. (ghc-bytes)[inputs]: Same. (ghc-missingh)[inputs]: Remove ghc-parsec. (ghc-rio)[inputs]: Remove ghc-text. (ghc-cairo)[inputs]: Same. (ghc-atomic-write)[inputs]: Remove ghc-text. [native-inputs]: Same. (ghc-stm-conduit)[inputs]: Remove ghc-stm. (ghc-conduit-algorithms)[inputs]: Same. (ghc-interpolate)[native-inputs]: Remove ghc-text. (ghc-hpack)[inputs]: Same. (ghc-inline-c)[inputs]: Remove ghc-parsec. (ghc-configurator)[inputs]: Remove ghc-text. (ghc-c2hs)[native-inputs]: Same. (ghc-libmpd)[inputs]: Same. (ghc-concurrent-output)[inputs]: Remove ghc-stm. * gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text. * gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: r-msnid: Update to 1.18.1.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1.
| * gnu: r-rcas: Update to 1.10.1.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1.
| * gnu: r-genomicfeatures: Update to 1.36.4.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4.
| * gnu: r-rtracklayer: Update to 1.44.2.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2.
| * gnu: r-summarizedexperiment: Update to 1.14.1.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1.
| * gnu: r-biomart: Update to 2.40.3.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3.
| * gnu: r-limma: Update to 3.40.6.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6.
| * gnu: r-edger: Update to 3.26.6.Ricardo Wurmus2019-08-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6.
| * gnu: khmer: Make gzip timestamps writable.Brian Leung2019-08-05
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase to make gzip timestamps writable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* | gnu: prank: Update to 170427.Marius Bakke2019-07-31
| | | | | | | | * gnu/packages/bioinformatics.scm (prank): Update to 170427.
* | Merge branch 'master' into core-updatesMarius Bakke2019-07-31
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| * gnu: Explicitly refer to 'guile-json-1' when needed.Ludovic Courtès2019-07-25
| | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change 'guile-json' to 'guile-json-1'. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise. * gnu/packages/mail.scm (mumi)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise. * gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.
* | Merge branch 'master' into core-updatesMarius Bakke2019-07-22
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| * gnu: htslib: Propagate zlib.Ricardo Wurmus2019-07-22
| | | | | | | | | | | | | | Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here.
* | gnu: bpp: Use the default GCC.Marius Bakke2019-07-18
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bpp-core, bpp-phyl, bpp-popgen, bpp-seq, bppsuite)[inputs]: Remove GCC-5.
* | Merge branch 'master' into core-updatesLudovic Courtès2019-07-17
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| * gnu: Add python-ont-fast5-api.Ricardo Wurmus2019-07-15
| | | | | | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): New variable.
| * gnu: pigx-rnaseq: Update to 0.0.10.Ricardo Wurmus2019-07-13
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.10.
* | gnu: nanopolish: Fix build with GCC 7.Marius Bakke2019-07-17
| | | | | | | | | | * gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Preserve the existing CPATH variable, if any.
* | gnu: salmon: Fix build with GCC 7.Marius Bakke2019-07-15
| | | | | | | | | | * gnu/packages/bioinformatics.scm (salmon)[arguments]: Do not read from CPLUS_INCLUDE_PATH, and add headers to CPATH only.
* | gnu: Adjust uses of C{,PLUS}_INCLUDE_PATH for GCC 7.Marius Bakke2019-07-14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | These variables are no longer set in the build environment by default. GCC still respects these search paths and treats them as "system headers" so we can continue to use them, just not expect them to be available. * gnu/packages/mpi.scm (openmpi)[arguments]: Do not attempt to read from C_INCLUDE_PATH, nor CPLUS_INCLUDE_PATH. * gnu/packages/games.scm (kiki)[arguments]: Likewise. * gnu/packages/networking.scm (hcxtools)[arguments]: Likewise. * gnu/packages/synergy.scm (synergy)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (gemma, sailfish)[arguments]: Likewise. * gnu/packages/maths.scm (dune-alugrid)[arguments]: Likewise.
* | Merge branch 'master' into core-updatesMarius Bakke2019-07-12
|\| | | | | | | | | | | | | | | | | Conflicts: gnu/local.mk gnu/packages/python-xyz.scm gnu/packages/xml.scm guix/gexp.scm po/guix/POTFILES.in
| * gnu: r-biocinstaller: Remove entirely.Tobias Geerinckx-Rice2019-07-09
| | | | | | | | | | | | | | | | This follows up on commit 0971f8bd884b6e92b77d9e12030cd58279699183, which led to ‘r-biocmanager: unbound variable’ errors. See <https://lists.gnu.org/archive/html/guix-devel/2019-07/msg00120.html>. * gnu/packages/bioinformatics.scm (r-biocinstaller): Remove variable.
| * gnu: Remove r-biocinstaller.Tobias Geerinckx-Rice2019-07-08
| | | | | | | | | | | | | | It requires R < 3.6 and is no longer supported. * gnu/packages/bioinformatics.scm (r-biocinstaller): Define as deprecated in favour of r-biocmanager.
| * gnu: r-xbioc: Update to 0.1.16-1.6ff0670.Tobias Geerinckx-Rice2019-07-08
| | | | | | | | | | | | | | | | | | This is needed to deprecate r-biocinstaller, which is no longer distributed. * gnu/packages/bioinformatics.scm (r-xbioc): Update to 0.1.16-1.6ff0670. [propagated-inputs]: Replace deprecated r-biocinstaller with r-biocmanager.
| * gnu: nanopolish: Update to 0.11.1-1.6331dc4.Ricardo Wurmus2019-07-05
| | | | | | | | * gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
* | gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml.Robert Vollmert2019-07-04
|/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | These are ghc-8.4-bundled packages, removing to avoid build conflicts. * gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove. * gnu/packages/haskell-web.scm (ghc-xhtml): Remove. * gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text. * gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and ghc-text. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec. (git-annex)[inputs]: Remove ghc-stm and ghc-text. (ghc-sdl2)[inputs]: Remove ghc-text. (ghc-sdl2-image)[inputs]: Remove ghc-text. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm. (ghc-tasty)[inputs]: Remove ghc-stm. (ghc-tasty-rerun)[inputs]: Same. (ghc-quickcheck-instances)[inputs]: Remove ghc-text. (ghc-hedgehog)[inputs]: Remove ghc-stm. * gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove ghc-text. * gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text. (ghc-cookie)[inputs]: Same. (ghc-http-types)[inputs]: Same. (ghc-http)[inputs]: Remove ghc-parsec. (ghc-http-client)[inputs]: Remove ghc-text. (ghc-http2)[inputs]: Remove ghc-stm. (ghc-http-conduit)[native-inputs]: Remove ghc-text. (ghc-wai)[inputs]: Same. (ghc-wai-extra)[inputs]: Same. (ghc-warp)[inputs]: Remove ghc-stm and ghc-text. (ghc-xss-sanitize)[native-inputs]: Remove ghc-text. (ghc-css-text)[inputs]: Same. (ghc-mime-types)[inputs]: Same. (ghc-blaze-html)[inputs]: Same. (ghc-aeson)[inputs]: Same. (ghc-aeson-pretty)[inputs]: Same. (ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec. (ghc-multipart)[inputs]: Remove ghc-parsec. (ghc-uri-encode)[inputs]: Remove ghc-text. (ghc-path-pieces)[inputs]: Same. (ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec. (ghc-yesod-persistent)[inputs]: Remove ghc-text. (ghc-yesod-form)[inputs]: Same. (ghc-yesod)[inputs]: Same. (ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text. (ghc-hxt)[inputs]: Remove ghc-parsec. * gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text. (ghc-double-conversion)[inputs]: Same. (ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text. [native-inputs]: Remove ghc-parsec. (ghc-cgi)[inputs]: Remove ghc-parsec. (hlint)[inputs]: Remove ghc-text. (ghc-openglraw)[inputs]: Remove ghc-text. (ghc-opengl)[inputs]: Same. (ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text. (ghc-hackage-security)[inputs]: Remove ghc-parsec. (cabal-install)[inputs]: Remove ghc-stm. (ghc-parsec-numbers)[inputs]: Remove ghc-parsec. (ghc-safesemaphore)[inputs]: Remove ghc-stm. (ghc-text-binary)[inputs]: Remove ghc-text. (ghc-hashable)[inputs]: Remove ghc-text. (ghc-transformers-base)[inputs]: Remove ghc-stm. (ghc-indents)[inputs]: Remove ghc-parsec. (ghc-regex-tdfa-rc)[inputs]: Same. (ghc-regex-tdfa-text)[inputs]: Same. (ghc-regex)[inputs]: Remove ghc-text. (ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text. (ghc-attoparsec)[inputs]: Remove ghc-text. (ghc-attoparsec-bootstrap)[inputs]: Same. (ghc-zip-archive)[inputs]: Same. (ghc-polyparse)[inputs]: Same. (ghc-reducers)[inputs]: Same. (ghc-xml)[inputs]: Same. (ghc-feed)[inputs]: Same. (ghc-exceptions)[inputs]: Remove ghc-stm. (ghc-case-insensitive)[inputs]: Remove ghc-text. (ghc-megaparsec)[inputs]: Same. (ghc-network-uri)[inputs]: Remove ghc-parsec. (ghc-monad-control)[inputs]: Remove ghc-stm. (ghc-blaze-builder)[inputs]: Remove ghc-text. (ghc-blaze-markup)[inputs]: Same. (ghc-async)[inputs]: Remove ghc-stm. (ghc-invariant)[inputs]: Same. (ghc-statevar)[inputs]: Same. (ghc-lens)[inputs]: Remove ghc-text. (ghc-cheapskate)[inputs]: Same. (ghc-semigroups)[inputs]: Same. (ghc-semigroups-bootstrap)[inputs]: Same. (ghc-fast-logger)[inputs]: Same. (ghc-scientific)[inputs]: Same. (ghc-scientific-bootstrap)[inputs]: Same. (ghc-texmath)[inputs]: Remove ghc-parsec. (ghc-highlighting-kate)[inputs]: Same. (ghc-cmark)[inputs]: Remove ghc-text. (ghc-cmark-gfm)[inputs]: Same. (ghc-th-lift-instances)[inputs]: Same. (ghc-yaml)[inputs]: Same. (ghc-hslua)[inputs]: Same. (ghc-hslua-module-text)[inputs]: Same. (ghc-skylighting-core)[inputs]: Same. (ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec. (ghc-pandoc)[inputs]: Same. (ghc-typed-process)[inputs]: Remove ghc-stm. (ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text. (ghc-xml-types)[inputs]: Remove ghc-text. (ghc-xml-conduit)[inputs]: Same. (ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec. (ghc-regex-tdfa)[inputs]: Remove ghc-parsec. (ghc-wl-pprint-text)[inputs]: Remove ghc-text. (ghc-graphviz)[inputs]: Same. (ghc-system-filepath-bootstrap)[inputs]: Same. (ghc-system-fileio-bootstrap)[inputs]: Same. (ghc-shelly)[inputs]: Same. (ghc-chell)[inputs]: Same. (ghc-system-filepath)[inputs]: Same. (ghc-system-fileio)[inputs]: Same. (ghc-fsnotify)[inputs]: Same. (ghc-json)[inputs]: Remove ghc-text and ghc-parsec. (ghc-esqueleto)[inputs]: Remove ghc-text. (shellcheck)[inputs]: Remove ghc-parsec. (ghc-errors)[inputs]: Remove ghc-text. (ghc-chunked-data)[inputs]: Same. (ghc-uuid-types)[inputs]: Same. (ghc-uuid)[inputs]: Same. (ghc-rebase)[inputs]: Remove ghc-stm and ghc-text. (ghc-foldl)[inputs]: Remove ghc-text. (ghc-mono-traversable)[inputs]: Same. (ghc-conduit-combinators)[inputs]: Same. (ghc-aws)[inputs]: Same. (ghc-stm-chans)[inputs]: Remove ghc-stm. (ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm. (ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text. (ghc-resource-pool)[inputs]: Remove ghc-stm. (ghc-attoparsec-iso8601)[inputs]: Remove ghc-text. (ghc-http-api-data)[inputs]: Same. (ghc-persistent)[inputs]: Same. (ghc-aeson-compat)[inputs]: Same. (ghc-persistent-template)[inputs]: Same. (ghc-unliftio)[inputs]: Remove ghc-stm. (ghc-persistent-sqlite)[native-inputs]: Remove ghc-text. (ghc-bytes)[inputs]: Same. (ghc-missingh)[inputs]: Remove ghc-parsec. (ghc-rio)[inputs]: Remove ghc-text. (ghc-cairo)[inputs]: Same. (ghc-atomic-write)[inputs]: Remove ghc-text. [native-inputs]: Same. (ghc-stm-conduit)[inputs]: Remove ghc-stm. (ghc-conduit-algorithms)[inputs]: Same. (ghc-interpolate)[native-inputs]: Remove ghc-text. (ghc-hpack)[inputs]: Same. (ghc-inline-c)[inputs]: Remove ghc-parsec. (ghc-configurator)[inputs]: Remove ghc-text. (ghc-c2hs)[native-inputs]: Same. (ghc-libmpd)[inputs]: Same. (ghc-concurrent-output)[inputs]: Remove ghc-stm. * gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text. * gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: pigx-rnaseq: Update to 0.0.8.Ricardo Wurmus2019-07-04
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
* gnu: r-phangorn: Update to 2.5.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-31 17:18:35 +0000