| Age | Commit message (Expand) | Author |
|---|
| 2019-12-02 | gnu: python-scipy: Move to (gnu packages python-science)....* 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.
| Ricardo Wurmus |
| 2019-11-28 | Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stu......This reverts commit abf43a67d5929bf279edce3e790ef1348dda32a5 as it broke "guix pull".
| Ricardo Wurmus |
| 2019-11-28 | gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and 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.
| Pierre Neidhardt |
| 2019-11-25 | gnu: libdivsufsort: Move to datastructures.scm....* gnu/packages/bioinformatics.scm (libdivsufsort): Move to ...
* gnu/packages/datastructures.scm: ... here.
| Efraim Flashner |
| 2019-11-25 | gnu: bioperl-minimal: Don't use unstable tarball....* gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download
using git-fetch.
| Efraim Flashner |
| 2019-11-20 | gnu: ngless: Update to 1.0.1....* 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'.
| Timothy Sample |
| 2019-11-14 | gnu: r-gprofiler: Update to 0.7.0....* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.7.0.
| Ricardo Wurmus |
| 2019-11-10 | gnu: Add 'file-name' where appropriate....* 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.
| Efraim Flashner |
| 2019-10-20 | gnu: 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 |
| 2019-10-18 | gnu: r-rhdf5lib: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.3.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-hdf5array: Update to 1.12.3....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.3.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-gwascat: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.1.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-ldblock: Update to 1.14.3....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.3.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-ensembldb: Update to 2.8.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.1.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-keggrest: Update to 1.24.1....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.1.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-rhdf5: Update to 2.28.1....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.1.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-rhtslib: Update to 1.16.3....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.3.
| Ricardo Wurmus |
| 2019-10-18 | gnu: r-rsamtools: Update to 2.0.3....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.3.
| Ricardo Wurmus |
| 2019-10-18 | gnu: bowtie1: Update to 1.2.3....* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.2.3.
| Ricardo Wurmus |
| 2019-10-14 | gnu: Add methyldackel....* gnu/packages/bioinformatics.scm (methyldackel): New variable.
| Ricardo Wurmus |
| 2019-10-14 | gnu: Add r-velocyto....* gnu/packages/bioinformatics.scm (r-velocyto): New variable.
| Ricardo Wurmus |
| 2019-10-07 | Merge branch 'master' into core-updates | Ludovic Courtès |
| 2019-10-06 | gnu: 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 |
| 2019-10-06 | gnu: r-rsamtools: Update to 2.0.2....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.2.
| Ricardo Wurmus |
| 2019-10-06 | gnu: r-biomart: Update to 2.40.5....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.5.
| Ricardo Wurmus |
| 2019-10-06 | Merge branch 'master' into core-updates | Ricardo Wurmus |
| 2019-10-03 | gnu: rcas-web: Fix build with RCAS > 1.3.x....* gnu/packages/bioinformatics.scm (rcas-web)[arguments]: Add ‘find-RCAS’ phase.
| Tobias Geerinckx-Rice |
| 2019-10-01 | Merge branch 'master' into core-updates | Ludovic Courtès |
| 2019-09-28 | gnu: r-gviz: Update to 1.28.3....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.3.
| Ricardo Wurmus |
| 2019-09-28 | gnu: r-mzr: Update to 2.18.1....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.1.
| Ricardo Wurmus |
| 2019-09-28 | gnu: r-rhtslib: Update to 1.16.2....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.2.
| Ricardo Wurmus |
| 2019-09-28 | gnu: r-rsamtools: Update to 2.0.1....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.1.
| Ricardo Wurmus |
| 2019-09-28 | gnu: r-iranges: Update to 2.18.3....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.3.
| Ricardo Wurmus |
| 2019-09-17 | Merge branch 'master' into core-updates | Ludovic Courtès |
| 2019-09-14 | gnu: r-delayedmatrixstats: Update to 1.6.1....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.1.
| Ricardo Wurmus |
| 2019-09-14 | gnu: r-rhdf5lib: Update to 1.6.1....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.1.
| Ricardo Wurmus |
| 2019-09-14 | gnu: r-rtracklayer: Update to 1.44.4....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.4.
| Ricardo Wurmus |
| 2019-09-14 | gnu: r-genomicranges: Update to 1.36.1....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
| Ricardo Wurmus |
| 2019-09-14 | gnu: r-s4vectors: Update to 0.22.1....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
| Ricardo Wurmus |
| 2019-09-08 | gnu: r-gprofiler: Update to 0.6.8....* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.8.
| Ricardo Wurmus |
| 2019-09-08 | gnu: r-annotationhub: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.1.
| Ricardo Wurmus |
| 2019-09-08 | gnu: r-edger: Update to 3.26.8....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.8.
| Ricardo Wurmus |
| 2019-09-06 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2019-09-06 | gnu: Add samblaster....* gnu/packages/bioinformatics.scm (samblaster): New variable.
| Ricardo Wurmus |
| 2019-09-05 | gnu: libbigwig: Update to 0.4.4....* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4.
| Ricardo Wurmus |
| 2019-09-05 | gnu: 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 |
| 2019-09-05 | gnu: 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 |
| 2019-09-05 | gnu: 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 |
| 2019-09-02 | gnu: 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 |
| 2019-09-02 | gnu: 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 |
