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* 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.
* gnu: r-tximport: Update to 1.12.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
* gnu: r-genomicfeatures: Update to 1.36.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
* gnu: r-genomicalignments: Update to 1.20.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
* gnu: r-biomart: Update to 2.40.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
* gnu: r-edger: Update to 3.26.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
* gnu: r-systempiper: Update to 1.18.2.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
* gnu: pigx-scrnaseq: Update to 0.0.8.Ricardo Wurmus2019-06-27
| | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
* gnu: khmer: Update to 3.0.0a3.Ricardo Wurmus2019-06-21
| | | | | | | | * gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3. [source]: Remove patch; remove seqan in snippet. [inputs]: Add seqan-1. * gnu/packages/patches/khmer-use-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: pigx-rnaseq: Update to 0.0.7.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed.
* gnu: ngs-sdk: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
* gnu: sra-tools: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
* gnu: ncbi-vdb: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
* gnu: Add tbsp.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (tbsp): New variable.
* gnu: r-seurat: Update to 3.0.2.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
* gnu: r-tximport: Update to 1.12.1.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
* gnu: r-systempiper: Update to 1.18.1.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
* gnu: Remove r-loomr.Ricardo Wurmus2019-06-14
| | | | | | | The loomR package is actually non-free software according to its author. See https://github.com/mojaveazure/loomR/pull/24. * gnu/packages/bioinformatics.scm (r-loomr): Remove variable.
* gnu: pigx-rnaseq: Update to 0.0.6.Ricardo Wurmus2019-06-12
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.6. [inputs]: Remove bedtools.
* gnu: Add r-psiplot.Ricardo Wurmus2019-06-11
| | | | * gnu/packages/bioinformatics.scm (r-psiplot): New variable.
* gnu: r-msnbase: Update to 2.10.1.Ricardo Wurmus2019-06-09
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.1.
* gnu: r-iranges: Update to 2.18.1.Ricardo Wurmus2019-06-09
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.1.
* gnu: r-biocviews: Update to 1.52.2.Ricardo Wurmus2019-06-01
| | | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.2. [propagated-inputs]: Add r-biocmanager.
* gnu: r-biocviews: Update to 1.52.1.Ricardo Wurmus2019-05-30
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.1.
* gnu: r-scran: Update to 1.12.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.1.
* gnu: r-scater: Update to 1.12.2.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.2.
* gnu: r-sva: Update to 3.32.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.1.
* 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.
* gnu: pigx-chipseq: Update to 0.0.41.Ricardo Wurmus2019-05-26
| | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.41.
* gnu: Move Sphinx and friends to (gnu packages sphinx).Marius Bakke2019-05-24
| | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python-xyz.scm (python-sphinxcontrib-websupport, python2-sphinxcontrib-websupport, python-sphinx, python2-sphinx, python-sphinx-gallery, python2-sphinx-gallery, python-sphinx-rtd-theme, python2-sphinx-rtd-theme, python-guzzle-sphinx-theme, python2-guzzle-sphinx-theme, python-sphinxcontrib-newsfeed, python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput, python-sphinx-repoze-interface, python2-sphinx-repoze-interface, python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme, python-sphinx-alabaster-theme, python2-sphinx-alabaster-theme, python-sphinx-me, python-sphinxcontrib-svg2pdfconverter): Move to ... (gnu): * gnu/packages/sphinx.scm: ... here. New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly. * gnu/packages/admin.scm, gnu/packages/bioinformatics.scm, gnu/packages/calendar.scm, gnu/packages/cluster.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/elf.scm, gnu/packages/emacs-xyz.scm, gnu/packages/emulators.scm, gnu/packages/finance.scm, gnu/packages/image.scm, gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm, gnu/packages/openstack.scm, gnu/packages/pdf.scm, gnu/packages/python-web.scm, gnu/packages/search.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/tls.scm, gnu/packages/web.scm: Adjust module imports.
* gnu: salmon: Update to 0.13.1.Ricardo Wurmus2019-05-23
| | | | | | | | | * gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1. [arguments]: Adjust "do-not-look-for-boost" build phase; adjust "prepare-rapmap" phase; adjust "use-system-libraries" phase. [inputs]: Remove bwa, jellyfish, spdlog-for-salmon. [native-inputs]: Add pkg-config. (spdlog-for-salmon, bwa-for-salmon): Remove variables.
* gnu: umi-tools: Fix typo "containing".Vagrant Cascadian2019-05-22
| | | | * gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
* gnu: r-gage: Fix typo "functions".Vagrant Cascadian2019-05-22
| | | | * gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
* gnu: r-limma: Update to 3.40.2.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
* gnu: r-edger: Update to 3.26.3.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
* gnu: r-scater: Update to 1.12.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
* gnu: r-seurat: Update to 3.0.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
* gnu: r-maldiquant: Update to 1.19.3.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
* gnu: r-edger: Update to 3.26.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
* gnu: star: Update to 2.7.1a.Ricardo Wurmus2019-05-16
| | | | * gnu/packages/bioinformatics.scm (star): Update to 2.7.1a.
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-07 04:59:47 +0000