| Age | Commit message (Expand) | Author |
|---|
| 2019-02-19 | gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01....This makes progress towards fixing <https://bugs.gnu.org/27462>.
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove
variables.
| Andreas Enge |
| 2019-02-17 | gnu: Remove unneeded uses of python{,2}-minimal....The "python-minimal" package exists mostly to resolve a dependency cycle. To
reduce duplication, packages should prefer the regular Python variants.
* gnu/packages/admin.scm (htop)[native-inputs]: Change PYTHON-MINIMAL-WRAPPER
to PYTHON-WRAPPER.
* gnu/packages/crypto.scm (botan)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Change
PYTHON-MINIMAL to PYTHON.
* gnu/packages/dictionaries.scm (apertium)[native-inputs]: Likewise.
* gnu/packages/databases.scm (mongodb)[native-inputs]: Change PYTHON2-MINIMAL
to PYTHON2.
* gnu/packages/games.scm (openttd-opensfx, openttd-openmsx)[native-inputs]:
Likewise.
* gnu/packages/gnome.scm (deja-dup)[native-inputs]: Likewise.
| Marius Bakke |
| 2019-02-15 | gnu: Add python-pyfit-sne....* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
| Ricardo Wurmus |
| 2019-02-12 | gnu: python-pybedtools: Update to 0.8.0 and fix build....From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 10 Feb 2019 23:39:25 -0500
Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build.
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0.
[phases]{disable-broken-tests}: Do not disable "test_issue_157" and
"test_to_dataframe" tests. Disable the "test_getting_example_beds".
{remove-cython-generated-files}: Add phase.
{generate-cython-extensions}: Add phase.
{check}: Move from python2-pybedtools to here. Add a scripts
subdirectory of the build directory to the PATH, so that the tests can call
them. Invoke pytest rather than nosetests.
[modules]: Move from python2-pybedtools to here.
[propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26.
[native-inputs]: Replace python-nose by python-pytest and add python-psutil.
| Maxim Cournoyer |
| 2019-02-12 | gnu: Add cnvkit....* gnu/packages/bioinformatics.scm (cnvkit): New variable.
| Ricardo Wurmus |
| 2019-02-08 | gnu: rcas-web: Update to 0.1.0....* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.1.0.
[inputs]: Replace guile2.2-redis with guile-redis.
| Ricardo Wurmus |
| 2019-02-06 | gnu: star: Update to 2.7.0b....* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b.
[arguments]: Add "add-missing-header" build phase.
| Ricardo Wurmus |
| 2019-01-30 | gnu: star: Update to 2.7.0a....* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a.
| Ricardo Wurmus |
| 2019-01-28 | gnu: r-genomicfeatures: Update to 1.34.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2.
| Ricardo Wurmus |
| 2019-01-28 | gnu: r-variantannotation: Update to 1.28.10....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10.
| Ricardo Wurmus |
| 2019-01-28 | gnu: r-qtl: Update to 1.44-9....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9.
| Ricardo Wurmus |
| 2019-01-28 | gnu: r-optparse: Update to 1.6.1....* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1.
| Ricardo Wurmus |
| 2019-01-28 | gnu: Move most packages from guile.scm to new module....* gnu/packages/guile.scm (artanis, guildhall, guile-aspell, guile-bash,
guile-8sync, guile-daemon, guile-dsv, guile-fibers, guile-syntax-highlight,
guile-sjson, guile-colorized, guile-pfds, guile-aa-tree, guile-simple-zmq,
jupyter-guile-kernel, guile-sparql, guile-debbugs, guile-email,
guile-debbugs-next, guile-newt, guile-mastodon, guile-parted, guile-xosd,
guile-dbi, guile-dbd-sqlite3, guile-config, guile-hall, guile-ics, guile-wisp,
guile-sly, g-wrap, guile-miniadapton, guile-reader, guile2.2-reader,
guile-ncurses, guile-ncurses/gpm, guile-lib, guile2.0-lib, guile2.2-lib,
guile-minikanren, guile2.0-minikanren, guile2.2-minikanren, guile-irregex,
guile2.0-irregex, guile2.2-irregex, haunt, guile2.0-haunt, guile2.2-haunt,
guile-redis, guile2.0-redis, guile2.2-redis, guile-commonmark,
guile2.0-commonmark, guile2.2-commonmark, mcron, mcron2): Move these variables
from here...
* gnu/packages/guile-xyz.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/installer.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/ci.scm,
gnu/packages/gtk.scm,
gnu/packages/guile.scm,
gnu/packages/mail.scm,
gnu/packages/package-management.scm,
gnu/packages/skribilo.scm,
gnu/packages/web.scm,
gnu/services/mcron.scm: Update module references.
| Ricardo Wurmus |
| 2019-01-25 | gnu: pepr: Use PYPI-URI....* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
| Ricardo Wurmus |
| 2019-01-25 | gnu: python2-warpedlmm: Use PYPI-URI....* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
| Ricardo Wurmus |
| 2019-01-15 | gnu: Move Python compression packages to new module....* gnu/packages/compression.scm (python-lzo, python2-lzo, python-lz4,
python2-lz4, python-lzstring, python2-lzstring, bitshuffle,
bitshuffle-for-snappy): Move variables from here...
* gnu/packages/python-compression.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/bioinformatics.scm,
gnu/packages/java-compression.scm,
gnu/packages/xorg.scm: Adjust module references.
| Ricardo Wurmus |
| 2019-01-15 | gnu: Separate Python core packages from the rest....* gnu/packages/python.scm: Move hundreds of package definitions from here...
* gnu/packages/python-xyz.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/audio.scm,
gnu/packages/backup.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/calendar.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/cluster.scm,
gnu/packages/compression.scm,
gnu/packages/connman.scm,
gnu/packages/crypto.scm,
gnu/packages/cups.scm,
gnu/packages/databases.scm,
gnu/packages/dav.scm,
gnu/packages/direct-connect.scm,
gnu/packages/disk.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/docker.scm,
gnu/packages/ebook.scm,
gnu/packages/elf.scm,
gnu/packages/emacs.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm,
gnu/packages/finance.scm,
gnu/packages/fltk.scm,
gnu/packages/fontutils.scm,
gnu/packages/freedesktop.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/geo.scm,
gnu/packages/gl.scm,
gnu/packages/glib.scm,
gnu/packages/gnome.scm,
gnu/packages/gnupg.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/gtk.scm,
gnu/packages/ham-radio.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/kde-frameworks.scm,
gnu/packages/key-mon.scm,
gnu/packages/libffi.scm,
gnu/packages/libreoffice.scm,
gnu/packages/libusb.scm,
gnu/packages/lirc.scm,
gnu/packages/logging.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/mate.scm,
gnu/packages/maths.scm,
gnu/packages/medical.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mp3.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/nutrition.scm,
gnu/packages/openldap.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/photo.scm,
gnu/packages/polkit.scm,
gnu/packages/protobuf.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/qt.scm,
gnu/packages/rdf.scm,
gnu/packages/ruby.scm,
gnu/packages/search.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/simulation.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/sync.scm,
gnu/packages/terminals.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/virtualization.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wicd.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xorg.scm: Update module references.
| Ricardo Wurmus |
| 2019-01-13 | gnu: r-biocgenerics: Move to bioconductor....* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
| Ricardo Wurmus |
| 2019-01-13 | gnu: r-annotate: Move to bioconductor....* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
| Ricardo Wurmus |
| 2019-01-13 | gnu: r-vegan: Move from bioinformatics to cran....* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-rtracklayer: Update to 1.42.1....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-scater: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-singlecellexperiment: Update to 1.4.1....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-rhdf5lib: Update to 1.4.2....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-hdf5array: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-qvalue: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-gviz: Update to 1.26.4....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-biovizbase: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-ensembldb: Update to 2.6.3....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-dirichletmultinomial: Update to 1.24.1....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-gage: Update to 2.32.1....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-annotationhub: Update to 2.14.2....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-edaseq: Update to 2.16.3....* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-deseq: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-msnid: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-msnbase: Update to 2.8.3....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-mzid: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-mzr: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-sva: Update to 3.30.1....* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-methylkit: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-copywriter: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-rhdf5: Update to 2.26.2....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-tximport: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-genomicalignments: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-biostrings: Update to 2.50.2....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-biocparallel: Update to 1.16.5....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-limma: Update to 3.38.3....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-variantannotation: Update to 1.28.8....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-edger: Update to 3.24.3....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
| Ricardo Wurmus |
| 2019-01-12 | gnu: r-biocviews: Update to 1.50.10....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
| Ricardo Wurmus |
