| Age | Commit message (Expand) | Author |
|---|
| 2019-07-15 | gnu: salmon: Fix build with GCC 7.•••* gnu/packages/bioinformatics.scm (salmon)[arguments]: Do not read from
CPLUS_INCLUDE_PATH, and add headers to CPATH only.
| Marius Bakke |
| 2019-07-14 | gnu: Adjust uses of C{,PLUS}_INCLUDE_PATH for GCC 7.•••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.
| Marius Bakke |
| 2019-07-12 | Merge branch 'master' into core-updates••• Conflicts:
gnu/local.mk
gnu/packages/python-xyz.scm
gnu/packages/xml.scm
guix/gexp.scm
po/guix/POTFILES.in
| Marius Bakke |
| 2019-07-09 | gnu: r-biocinstaller: Remove entirely.•••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.
| Tobias Geerinckx-Rice |
| 2019-07-08 | gnu: Remove r-biocinstaller.•••It requires R < 3.6 and is no longer supported.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Define as
deprecated in favour of r-biocmanager.
| Tobias Geerinckx-Rice |
| 2019-07-08 | gnu: r-xbioc: Update to 0.1.16-1.6ff0670.•••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.
| Tobias Geerinckx-Rice |
| 2019-07-05 | gnu: nanopolish: Update to 0.11.1-1.6331dc4.•••* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
| Ricardo Wurmus |
| 2019-07-04 | gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml.•••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>
| Robert Vollmert |
| 2019-07-04 | gnu: pigx-rnaseq: Update to 0.0.8.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-phangorn: Update to 2.5.5.•••* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-tximport: Update to 1.12.3.•••* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-genomicfeatures: Update to 1.36.3.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-genomicalignments: Update to 1.20.1.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-biomart: Update to 2.40.1.•••* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-edger: Update to 3.26.5.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
| Ricardo Wurmus |
| 2019-06-29 | gnu: r-systempiper: Update to 1.18.2.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
| Ricardo Wurmus |
| 2019-06-27 | gnu: pigx-scrnaseq: Update to 0.0.8.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2019-06-21 | gnu: khmer: Update to 3.0.0a3.•••* 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.
| Ricardo Wurmus |
| 2019-06-20 | gnu: pigx-rnaseq: Update to 0.0.7.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7.
[inputs]: Add coreutils and sed.
| Ricardo Wurmus |
| 2019-06-20 | gnu: ngs-sdk: Update to 2.9.6.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
| Ricardo Wurmus |
| 2019-06-20 | gnu: sra-tools: Update to 2.9.6.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
| Ricardo Wurmus |
| 2019-06-20 | gnu: ncbi-vdb: Update to 2.9.6.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6.
[arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
| Ricardo Wurmus |
| 2019-06-17 | gnu: Add tbsp.•••* gnu/packages/bioinformatics.scm (tbsp): New variable.
| Ricardo Wurmus |
| 2019-06-17 | gnu: r-seurat: Update to 3.0.2.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
| Ricardo Wurmus |
| 2019-06-17 | gnu: r-tximport: Update to 1.12.1.•••* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
| Ricardo Wurmus |
| 2019-06-17 | gnu: r-systempiper: Update to 1.18.1.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
| Ricardo Wurmus |
| 2019-06-14 | gnu: Remove r-loomr.•••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.
| Ricardo Wurmus |
| 2019-06-12 | gnu: pigx-rnaseq: Update to 0.0.6.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.6.
[inputs]: Remove bedtools.
| Ricardo Wurmus |
| 2019-06-11 | gnu: Add r-psiplot.•••* gnu/packages/bioinformatics.scm (r-psiplot): New variable.
| Ricardo Wurmus |
| 2019-06-09 | gnu: r-msnbase: Update to 2.10.1.•••* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.1.
| Ricardo Wurmus |
| 2019-06-09 | gnu: r-iranges: Update to 2.18.1.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.1.
| Ricardo Wurmus |
| 2019-06-01 | gnu: r-biocviews: Update to 1.52.2.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.2.
[propagated-inputs]: Add r-biocmanager.
| Ricardo Wurmus |
| 2019-05-30 | gnu: r-biocviews: Update to 1.52.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.1.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-scran: Update to 1.12.1.•••* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.1.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-scater: Update to 1.12.2.•••* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.2.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-sva: Update to 3.32.1.•••* gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.1.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-genomicfeatures: Update to 1.36.1.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.1.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-edger: Update to 3.26.4.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
| Ricardo Wurmus |
| 2019-05-29 | gnu: r-variantannotation: Update to 1.30.1.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
| Ricardo Wurmus |
| 2019-05-26 | gnu: pigx-chipseq: Update to 0.0.41.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.41.
| Ricardo Wurmus |
| 2019-05-24 | gnu: Move Sphinx and friends to (gnu packages sphinx).•••* 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.
| Marius Bakke |
| 2019-05-23 | gnu: salmon: Update to 0.13.1.•••* 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.
| Ricardo Wurmus |
| 2019-05-22 | gnu: umi-tools: Fix typo "containing".•••* gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
| Vagrant Cascadian |
| 2019-05-22 | gnu: r-gage: Fix typo "functions".•••* gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
| Vagrant Cascadian |
| 2019-05-20 | gnu: r-limma: Update to 3.40.2.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
| Ricardo Wurmus |
| 2019-05-20 | gnu: r-edger: Update to 3.26.3.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
| Ricardo Wurmus |
| 2019-05-20 | gnu: r-scater: Update to 1.12.1.•••* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
| Ricardo Wurmus |
| 2019-05-20 | gnu: r-seurat: Update to 3.0.1.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
| Ricardo Wurmus |
| 2019-05-20 | gnu: r-maldiquant: Update to 1.19.3.•••* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
| Ricardo Wurmus |
| 2019-05-20 | gnu: r-edger: Update to 3.26.1.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
| Ricardo Wurmus |
