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2019-10-20gnu: Remove more GCC < 7 workarounds....* gnu/packages/abiword.scm (abiword)[arguments]: Do not pass "-std=c++11" to the GCC command line. * gnu/packages/aidc.scm (zbar)[arguments]: Likewise. * gnu/packages/android.scm (android-libbase, android-libcutils, android-libziparchive, fastboot)[arguments]: Likewise. * gnu/packages/audio.scm (azr3, guitarix, suil)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (bless)[arguments]: Likewise. * gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Likewise. * gnu/packages/code.scm (rtags)[arguments]: Likewise. * gnu/packages/coq.scm (coq-gappa)[arguments]: Likewise. * gnu/packages/emulators.scm (dolphin-emu)[arguments]: Likewise. * gnu/packages/engineering.scm (xyce-serial, xyce-parallel)[arguments]: Likewise. * gnu/packages/gnupg.scm (pinentry-qt)[arguments]: Likewise. * gnu/packages/gobby.scm (libnet6, obby)[arguments]: Likewise. * gnu/packages/graph.scm (python-faiss)[arguments]: Likewise. * gnu/packages/graphics.scm (povray)[arguments]: Likewise. * gnu/packages/image-processing.scm (opencv, itk-snap)[arguments]: Likewise. * gnu/packages/image.scm (freeimage)[arguments]: Likewise. * gnu/packages/kodi.scm (crossguid)[arguments]: Likewise. * gnu/packages/music.scm (amsynth, qmidiarp, qmidiroute, seq24)[arguments]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[arguments]: Likewise. * gnu/packages/sagemath.scm (lcalc)[arguments]: Likewise. * gnu/packages/video.scm (vlc, mlt, v4l-utils)[arguments]: Likewise. Marius Bakke
2019-10-18gnu: r-rhdf5lib: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3. Ricardo Wurmus
2019-10-18gnu: r-hdf5array: Update to 1.12.3....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3. Ricardo Wurmus
2019-10-18gnu: r-gwascat: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1. Ricardo Wurmus
2019-10-18gnu: r-ldblock: Update to 1.14.3....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3. Ricardo Wurmus
2019-10-18gnu: r-ensembldb: Update to 2.8.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1. Ricardo Wurmus
2019-10-18gnu: r-keggrest: Update to 1.24.1....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1. Ricardo Wurmus
2019-10-18gnu: r-rhdf5: Update to 2.28.1....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1. Ricardo Wurmus
2019-10-18gnu: r-rhtslib: Update to 1.16.3....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3. Ricardo Wurmus
2019-10-18gnu: r-rsamtools: Update to 2.0.3....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3. Ricardo Wurmus
2019-10-18gnu: bowtie1: Update to 1.2.3....* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3. Ricardo Wurmus
2019-10-14gnu: Add methyldackel....* gnu/packages/bioinformatics.scm (methyldackel): New variable. Ricardo Wurmus
2019-10-14gnu: Add r-velocyto....* gnu/packages/bioinformatics.scm (r-velocyto): New variable. Ricardo Wurmus
2019-10-07Merge branch 'master' into core-updatesLudovic Courtès
2019-10-06gnu: r-seurat: Update to 3.1.1....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1. [propagated-inputs]: Add r-httr. Ricardo Wurmus
2019-10-06gnu: r-rsamtools: Update to 2.0.2....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2. Ricardo Wurmus
2019-10-06gnu: r-biomart: Update to 2.40.5....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5. Ricardo Wurmus
2019-10-06Merge branch 'master' into core-updatesRicardo Wurmus
2019-10-03gnu: rcas-web: Fix build with RCAS > 1.3.x....* gnu/packages/bioinformatics.scm (rcas-web)[arguments]: Add ‘find-RCAS’ phase. Tobias Geerinckx-Rice
2019-10-01Merge branch 'master' into core-updatesLudovic Courtès
2019-09-28gnu: r-gviz: Update to 1.28.3....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.3. Ricardo Wurmus
2019-09-28gnu: r-mzr: Update to 2.18.1....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.1. Ricardo Wurmus
2019-09-28gnu: r-rhtslib: Update to 1.16.2....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.2. Ricardo Wurmus
2019-09-28gnu: r-rsamtools: Update to 2.0.1....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.1. Ricardo Wurmus
2019-09-28gnu: r-iranges: Update to 2.18.3....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.3. Ricardo Wurmus
2019-09-17Merge branch 'master' into core-updatesLudovic Courtès
2019-09-14gnu: r-delayedmatrixstats: Update to 1.6.1....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1. Ricardo Wurmus
2019-09-14gnu: r-rhdf5lib: Update to 1.6.1....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1. Ricardo Wurmus
2019-09-14gnu: r-rtracklayer: Update to 1.44.4....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4. Ricardo Wurmus
2019-09-14gnu: r-genomicranges: Update to 1.36.1....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1. Ricardo Wurmus
2019-09-14gnu: r-s4vectors: Update to 0.22.1....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1. Ricardo Wurmus
2019-09-08gnu: r-gprofiler: Update to 0.6.8....* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8. Ricardo Wurmus
2019-09-08gnu: r-annotationhub: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1. Ricardo Wurmus
2019-09-08gnu: r-edger: Update to 3.26.8....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8. Ricardo Wurmus
2019-09-06Merge branch 'master' into core-updatesMark H Weaver
2019-09-06gnu: Add samblaster....* gnu/packages/bioinformatics.scm (samblaster): New variable. Ricardo Wurmus
2019-09-05gnu: libbigwig: Update to 0.4.4....* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4. Ricardo Wurmus
2019-09-05gnu: python-pyfaidx: Remove python-setuptools as an input....As this is provided by the build system, and I'm assuming that it's not necessary to have it as a propagated input. * gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove python-setuptools. Christopher Baines
2019-09-05gnu: umi-tools: Remove python-setuptools as an input....As this is provided by the build system. * gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove python-setuptools. Christopher Baines
2019-09-05gnu: bwa-meth: Capture one more reference to "bwa"....Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de> * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of "bwa index" to retain reference to "bwa" package. Ricardo Wurmus
2019-09-02gnu: r-ldblock: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2. [propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and r-httr. Ricardo Wurmus
2019-09-02gnu: r-seurat: Update to 3.1.0....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0. [propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot. Ricardo Wurmus
2019-09-02gnu: r-rtracklayer: Update to 1.44.3....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3. Ricardo Wurmus
2019-09-02gnu: r-biomart: Update to 2.40.4....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4. Ricardo Wurmus
2019-09-02gnu: r-annotationdbi: Update to 1.46.1....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1. Ricardo Wurmus
2019-09-02gnu: r-iranges: Update to 2.18.2....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2. Ricardo Wurmus
2019-08-31gnu: Move non-compilers out of haskell.scm....* gnu/packages/haskell.scm (ghc-abstract-deque, ghc-abstract-par, ghc-adjunctions, ghc-aeson-compat, ghc-alex, ghc-alsa-core, ghc-annotated-wl-pprint, ghc-ansi-terminal, ghc-ansi-wl-pprint, ghc-appar, ghc-async, ghc-atomic-write, ghc-attoparsec, ghc-attoparsec-bootstrap, ghc-attoparsec-iso8601, ghc-auto-update, ghc-aws, ghc-base16-bytestring, ghc-base64-bytestring, ghc-base-compat, ghc-basement, ghc-base-orphans, ghc-base-prelude, ghc-base-unicode-symbols, ghc-bifunctors, ghc-bindings-dsl, ghc-blaze-builder, ghc-blaze-markup, ghc-bloomfilter, ghc-boxes, ghc-byteable, ghc-byteorder, ghc-bytes, ghc-bytestring-builder, ghc-bytestring-handle, ghc-bytestring-lexing, ghc-bzlib-conduit, ghc-c2hs, ghc-cairo, ghc-call-stack, ghc-call-stack-boot, ghc-case-insensitive, ghc-cereal, ghc-cereal-conduit, ghc-cgi, ghc-charset, ghc-chart, ghc-chart-cairo, ghc-chasingbottoms, ghc-cheapskate, ghc-chell, ghc-chell-quickcheck, ghc-chunked-data, ghc-clock, ghc-clock-bootstrap, ghc-cmark, ghc-cmark-gfm, ghc-cmdargs, ghc-code-page, ghc-colour, ghc-comonad, ghc-concatenative, ghc-concurrent-output, ghc-conduit, ghc-conduit-algorithms, ghc-conduit-combinators, ghc-conduit-extra, ghc-configurator, ghc-connection, ghc-constraints, ghc-contravariant, ghc-contravariant-extras, ghc-convertible, ghc-data-accessor, ghc-data-accessor-transformers, ghc-data-default, ghc-data-default-class, ghc-data-default-instances-base, ghc-data-default-instances-containers, ghc-data-default-instances-dlist, ghc-data-default-instances-old-locale, ghc-data-hash, ghc-data-ordlist, ghc-deepseq-generics, ghc-descriptive, ghc-diff, ghc-disk-free-space, ghc-distributive, ghc-dlist, ghc-doctemplates, ghc-doctest, ghc-double-conversion, ghc-easy-file, ghc-easyplot, ghc-echo, ghc-edisonapi, ghc-edisoncore, ghc-edit-distance, ghc-either, ghc-email-validate, ghc-enclosed-exceptions, ghc-equivalence, ghc-erf, ghc-errorcall-eq-instance, ghc-errors, ghc-esqueleto, ghc-exactprint, ghc-exceptions, ghc-executable-path, ghc-extensible-exceptions, ghc-extra, ghc-fail, ghc-fast-logger, ghc-feed, ghc-fgl, ghc-fgl-arbitrary, ghc-file-embed, ghc-filemanip, ghc-findbin, ghc-fingertree, ghc-fixed, ghc-foldl, ghc-foundation, ghc-free, ghc-fsnotify, ghc-generic-deriving, ghc-generics-sop, ghc-geniplate-mirror, ghc-genvalidity, ghc-genvalidity-property, ghc-gitrev, ghc-glob, ghc-gluraw, ghc-glut, ghc-gnuplot, ghc-graphviz, ghc-gtk2hs-buildtools, ghc-hackage-security, ghc-haddock, ghc-haddock-api, ghc-haddock-library, ghc-half, ghc-happy, ghc-hashable, ghc-hashable-bootstrap, ghc-hashable-time, ghc-hashtables, ghc-haskell-lexer, ghc-haskell-src, ghc-haskell-src-exts, ghc-haskell-src-exts-util, ghc-haskell-src-meta, ghc-hasktags, ghc-hex, ghc-highlighting-kate, ghc-hindent, ghc-hinotify, ghc-hmatrix, ghc-hmatrix-gsl, ghc-hmatrix-gsl-stats, ghc-hmatrix-special, ghc-hostname, ghc-hourglass, ghc-hpack, ghc-hs-bibutils, ghc-hslogger, ghc-hslua, ghc-hslua-module-text, ghc-http-api-data, ghc-ieee754, ghc-ifelse, ghc-indents, ghc-inline-c, ghc-inline-c-cpp, ghc-integer-logarithms, ghc-integer-logarithms-bootstrap, ghc-interpolate, ghc-intervalmap, ghc-invariant, ghc-iproute, ghc-iwlib, ghc-json, ghc-juicypixels, ghc-kan-extensions, ghc-language-c, ghc-language-haskell-extract, ghc-lens, ghc-libffi, ghc-libmpd, ghc-libxml, ghc-lifted-async, ghc-lifted-base, ghc-linear, ghc-logging-facade, ghc-logict, ghc-lzma, ghc-lzma-conduit, ghc-markdown-unlit, ghc-math-functions, ghc-megaparsec, ghc-memory, ghc-memotrie, ghc-microlens, ghc-microlens-ghc, ghc-microlens-mtl, ghc-microlens-platform, ghc-microlens-th, ghc-missingh, ghc-mmap, ghc-mmorph, ghc-mockery, ghc-monad-control, ghc-monad-logger, ghc-monad-loops, ghc-monad-par, ghc-monad-par-extras, ghc-monadplus, ghc-monadrandom, ghc-monads-tf, ghc-mono-traversable, ghc-murmur-hash, ghc-mwc-random, ghc-nats, ghc-nats-bootstrap, ghc-network, ghc-network-info, ghc-network-uri, ghc-newtype-generics, ghc-objectname, ghc-old-locale, ghc-old-time, ghc-opengl, ghc-openglraw, ghc-operational, ghc-options, ghc-optparse-applicative, ghc-pandoc, ghc-pandoc-citeproc, ghc-pandoc-types, ghc-parallel, ghc-parsec-numbers, ghc-parser-combinators, ghc-parsers, ghc-path, ghc-path-io, ghc-paths, ghc-patience, ghc-pcre-light, ghc-persistent, ghc-persistent-sqlite, ghc-persistent-template, ghc-polyparse, ghc-pqueue, ghc-prelude-extras, ghc-pretty-hex, ghc-pretty-show, ghc-primitive, ghc-profunctors, ghc-psqueues, ghc-random, ghc-raw-strings-qq, ghc-rebase, ghc-reducers, ghc-refact, ghc-reflection, ghc-regex, ghc-regex-applicative, ghc-regex-base, ghc-regex-compat, ghc-regex-compat-tdfa, ghc-regex-pcre-builtin, ghc-regex-posix, ghc-regex-tdfa, ghc-regex-tdfa-text, ghc-rerebase, ghc-resolv, ghc-resource-pool, ghc-resourcet, ghc-rfc5051, ghc-rio, ghc-safe, ghc-safe-exceptions, ghc-safeio, ghc-safesemaphore, ghc-sandi, ghc-scientific, ghc-scientific-bootstrap, ghc-sdl, ghc-sdl-image, ghc-sdl-mixer, ghc-securemem, ghc-semigroupoids, ghc-semigroups, ghc-semigroups-bootstrap, ghc-setenv, ghc-setlocale, ghc-shakespeare, ghc-shelly, ghc-silently, ghc-simple-reflect, ghc-simple-sendfile, ghc-skylighting-core, ghc-skylighting, ghc-smallcheck, ghc-socks, ghc-split, ghc-statevar, ghc-statistics, ghc-stm-chans, ghc-stm-conduit, ghc-stmonadtrans, ghc-storable-complex, ghc-streaming-commons, ghc-strict, ghc-stringbuilder, ghc-string-qq, ghc-stringsearch, ghc-stylish-haskell, ghc-syb, ghc-system-fileio, ghc-system-filepath, ghc-tagged, ghc-tar, ghc-temporary, ghc-temporary-rc, ghc-terminal-size, ghc-texmath, ghc-text-binary, ghc-tf-random, ghc-th-abstraction, ghc-th-expand-syns, ghc-th-lift, ghc-th-lift-instances, ghc-th-orphans, ghc-th-reify-many, ghc-time-locale-compat, ghc-tldr, ghc-transformers-base, ghc-transformers-compat, ghc-tree-diff, ghc-trifecta, ghc-tuple-th, ghc-typed-process, ghc-unbounded-delays, ghc-unexceptionalio, ghc-union-find, ghc-uniplate, ghc-unix-compat, ghc-unix-time, ghc-unliftio, ghc-unliftio-core, ghc-unordered-containers, ghc-unordered-containers-bootstrap, ghc-uri-bytestring, ghc-utf8-string, ghc-utility-ht, ghc-uuid, ghc-uuid-types, ghc-validation, ghc-validity, ghc-vault, ghc-vector, ghc-vector-algorithms, ghc-vector-binary-instances, ghc-vector-builder, ghc-vector-th-unbox, ghc-void, ghc-wave, ghc-wcwidth, ghc-wcwidth-bootstrap, ghc-weigh, ghc-wl-pprint, ghc-wl-pprint-annotated, ghc-wl-pprint-text, ghc-word8, ghc-x11, ghc-x11-xft, ghc-xdg-basedir, ghc-xml, ghc-xml-conduit, ghc-xml-types, ghc-yaml, ghc-zip-archive, ghc-zlib): Move variables from here... * gnu/packages/haskell-xyz.scm: ...to here. * gnu/packages/agda.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/cran.scm, gnu/packages/emacs-xyz.scm, gnu/packages/games.scm, gnu/packages/graphics.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-check.scm, gnu/packages/idris.scm, gnu/packages/statistics.scm, gnu/packages/wm.scm: Update module references. Co-authored-by: Timothy Sample <samplet@ngyro.com> Robert Vollmert
2019-08-22Merge branch 'master' into core-updatesMark H Weaver
2019-08-20gnu: edirect: Update to 12.1.20190819....* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190819. Efraim Flashner
2019-08-19gnu: r-gviz: Update to 1.28.1....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.1. Ricardo Wurmus
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