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* gnu: r-scater: Update to 1.14.5.Ricardo Wurmus2019-12-15
| | | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.5. [propagated-inputs]: Remove r-dplyr.
* gnu: r-scran: Update to 1.14.5.Ricardo Wurmus2019-12-15
| | | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.5. [propagated-inputs]: Remove r-dynamictreecut.
* gnu: r-delayedmatrixstats: Update to 1.8.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.8.0.
* gnu: r-mzid: Update to 1.24.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.24.0.
* gnu: r-vsn: Update to 3.54.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.54.0.
* gnu: r-annotationfilter: Update to 1.10.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.10.0.
* gnu: r-chipseq: Update to 1.36.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.36.0.
* gnu: r-copywriter: Update to 2.18.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.18.0.
* gnu: r-affy: Update to 1.64.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-affy): Update to 1.64.0.
* gnu: r-affyio: Update to 1.56.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0.
* gnu: r-methylkit: Update to 1.12.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0.
* gnu: r-sva: Update to 3.34.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0.
* gnu: r-protgenerics: Update to 1.18.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.18.0.
* gnu: r-mzr: Update to 2.20.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0.
* gnu: Add r-qtl2.Efraim Flashner2019-12-10
| | | | * gnu/packages/bioinformatics.scm (r-qtl2): New variable.
* gnu: Really move lisp libraries to lisp-xyz, uglify-js to javascript and ↵Pierre Neidhardt2019-12-05
| | | | | | | | | | | | | | | | | stumpwm to wm. * gnu/local.mk: Include lisp-xyz.scm. * gnu/packages/lisp-xyz.scm: New file. * gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to javascript.scm and stumpwm to wm.scm. * gnu/packages/javascript.scm: Add uglify-js. * gnu/packages/wm.scm: Add stumpwm. * gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm. * gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm. * gnu/packages/web.scm: Find uglify-js in javascript.scm. * gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm. * guix/build-system/minify.scm (default-uglify-js): Find uglify-js in javascript module instead of lisp.
* Revert "gnu: Properly move lisp libraries to lisp-xyz, uglify-js to ↵Tobias Geerinckx-Rice2019-12-05
| | | | | | | javascript and stumpwm to wm." This reverts commit ac1ee30f4f7f9d0ae2a655676b0e8b9eb90a35dd, which still breaks ‘guix pull’.
* gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and ↵Pierre Neidhardt2019-12-05
| | | | | | | | | | | | | | | | | stumpwm to wm. * gnu/local.mk: Include lisp-xyz.scm. * gnu/packages/lisp-xyz.scm: New file. * gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to javascript.scm and stumpwm to wm.scm. * gnu/packages/javascript.scm: Add uglify-js. * gnu/packages/wm.scm: Add stumpwm. * gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm. * gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm. * gnu/packages/web.scm: Find uglify-js in javascript.scm. * gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm. * guix/build-system/minify.scm (default-uglify-js): Find uglify-js in javascript module instead of lisp.
* Merge branch 'staging'Marius Bakke2019-12-04
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| * Merge branch 'master' into stagingMarius Bakke2019-11-28
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| * \ Merge branch 'master' into stagingMarius Bakke2019-11-21
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| * \ \ Merge branch 'master' into stagingMarius Bakke2019-11-15
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| * \ \ \ Merge branch 'master' into stagingMarius Bakke2019-10-21
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| * \ \ \ \ Merge branch 'master' into stagingMarius Bakke2019-10-18
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| * | | | | | gnu: mariadb: Split into out, lib and dev.Julien Lepiller2019-10-12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/databases.scm (mariadb): Split into out, lib and dev. (perl-dbd-mysql, python-mysqlclient): Adjust dependencies. * gnu/packages/bioinformatics.scm (kentutils): Adjust dependencies. * gnu/packages/cran.scm (r-rmysql): Adjust dependencies. * gnu/packages/emacs-xyz.scm (emacs-emacsql): Adjust dependencies. * gnu/packages/kodi.scm (kodi): Adjust dependencies. * gnu/packages/qt.scm (qt, qtbase): Adjust dependencies. * gnu/packages/ruby.scm (ruby-mysql2): Adjust dependencies.
* | | | | | | gnu: python-scipy: Move to (gnu packages python-science).Ricardo Wurmus2019-12-02
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from here... * gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here. * gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm, gnu/packages/statistics.scm: Adjust module imports.
* | | | | | | Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and ↵Ricardo Wurmus2019-11-28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | stumpwm to wm." This reverts commit abf43a67d5929bf279edce3e790ef1348dda32a5 as it broke "guix pull".
* | | | | | | gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.Pierre Neidhardt2019-11-28
| |_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/local.mk: Include lisp-xyz.scm. * gnu/packages/lisp-xyz.scm: New file. * gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to javascript.scm and stumpwm to wm.scm. * gnu/packages/javascript.scm: Add uglify-js. * gnu/packages/wm.scm: Add stumpwm. * gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm. * gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm. * gnu/packages/web.scm: Find uglify-js in javascript.scm. * gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* | | | | | gnu: libdivsufsort: Move to datastructures.scm.Efraim Flashner2019-11-25
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (libdivsufsort): Move to ... * gnu/packages/datastructures.scm: ... here.
* | | | | | gnu: bioperl-minimal: Don't use unstable tarball.Efraim Flashner2019-11-25
| |_|_|_|/ |/| | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download using git-fetch.
* | | | | gnu: ngless: Update to 1.0.1.Timothy Sample2019-11-20
| |_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1. [arguments]: Add a 'create-Versions.hs' phase that patches the Makefile and invokes 'make' to generate a required file. [inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and 'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib', 'ghc-diagrams-svg', and 'ghc-tar-conduit'.
* | | | gnu: r-gprofiler: Update to 0.7.0.Ricardo Wurmus2019-11-14
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
* | | | gnu: Add 'file-name' where appropriate.Efraim Flashner2019-11-10
| |_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/admin.scm (detox, neofetch), gnu/packages/algebra.scm (python-fpylll), gnu/packages/bioinformatics.scm (tbsp, genrich), gnu/packages/crypto.scm (hpenc), gnu/packages/digest.scm (xxhash), gnu/packages/emacs-xyz.scm (emacs-tiny, emacs-ergoemacs-mode, emacs-make-it-so, emacs-poet-theme, emacs-deft, emacs-scribble-mode, emacs-helm-mu, emacs-unidecode, emacs-diff-hl, emacs-helm-exwm, emacs-gif-screencast, emacs-exec-path-from-shell), gnu/packages/engineering.scm (gpx), gnu/packages/freedesktop.scm (waylandpp), gnu/packages/golang.scm (go-github-com-sirupsen-logrus, go-github-com-shirou-gopsutil), gnu/packages/guile-xyz.scm (guile-studio, guile-picture-language, jupyter-guile-kernel), gnu/packages/image-viewers.scm (qview), gnu/packages/java-maths.scm (java-jblas), gnu/packages/llvm.scm (libclc), gnu/packages/logging.scm (spdlog), gnu/packages/ocaml.scm (ocaml-cstruct, ocaml-zarith), gnu/packages/terminals.scm (libtsm), gnu/packages/tigervnc.scm (tigervnc-client), gnu/packages/xdisorg.scm (xcalib, xbanish) [source]: Add file-name.
* | | gnu: Remove more GCC < 7 workarounds.Marius Bakke2019-10-20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | | gnu: r-rhdf5lib: Update to 1.6.3.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3.
* | | gnu: r-hdf5array: Update to 1.12.3.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3.
* | | gnu: r-gwascat: Update to 2.16.1.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1.
* | | gnu: r-ldblock: Update to 1.14.3.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3.
* | | gnu: r-ensembldb: Update to 2.8.1.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1.
* | | gnu: r-keggrest: Update to 1.24.1.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1.
* | | gnu: r-rhdf5: Update to 2.28.1.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1.
* | | gnu: r-rhtslib: Update to 1.16.3.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3.
* | | gnu: r-rsamtools: Update to 2.0.3.Ricardo Wurmus2019-10-18
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3.
* | | gnu: bowtie1: Update to 1.2.3.Ricardo Wurmus2019-10-18
| |/ |/| | | | | * gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3.
* | gnu: Add methyldackel.Ricardo Wurmus2019-10-14
| | | | | | | | * gnu/packages/bioinformatics.scm (methyldackel): New variable.
* | gnu: Add r-velocyto.Ricardo Wurmus2019-10-14
|/ | | | * gnu/packages/bioinformatics.scm (r-velocyto): New variable.
* Merge branch 'master' into core-updatesLudovic Courtès2019-10-07
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| * gnu: r-seurat: Update to 3.1.1.Ricardo Wurmus2019-10-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.1. [propagated-inputs]: Add r-httr.
| * gnu: r-rsamtools: Update to 2.0.2.Ricardo Wurmus2019-10-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
| * gnu: r-biomart: Update to 2.40.5.Ricardo Wurmus2019-10-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
generated by cgit v1.2.3 (git 2.49.0) at 2025-08-07 09:17:01 +0000