| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2019-05-16 | gnu: star: Update to 2.7.1a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.7.1a.
| Ricardo Wurmus |
| 2019-05-14 | gnu: Add ataqv.•••* gnu/packages/bioinformatics.scm (ataqv): New variable.
| Ricardo Wurmus |
| 2019-05-11 | gnu: r-hdf5array: Update to 1.12.1.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.1.
| Ricardo Wurmus |
| 2019-05-06 | gnu: r-systempiper: Update to 1.18.0.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0.
[propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
| Ricardo Wurmus |
| 2019-05-06 | gnu: r-rsamtools: Update to 2.0.0.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0.
[propagated-inputs]: Add r-rhtslib.
| Ricardo Wurmus |
| 2019-05-06 | gnu: r-impute: Update to 1.58.0.•••* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
| Ricardo Wurmus |
| 2019-05-06 | gnu: r-rcas: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0.
[propagated-inputs]: Add ghc-pandoc.
| Ricardo Wurmus |
