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2020-07-16gnu: Use HTTPS for mdc-berlin.de home pages....* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq) (pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-07-16gnu: Use HTTPS for biojava.org home pages....* gnu/packages/bioinformatics.scm (java-biojava-core) (java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0) (java-biojava-alignment-4.0)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-07-16gnu: r-rhdf5lib: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1. Ricardo Wurmus
2020-07-16gnu: r-qtl2: Update to 0.22-11....* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11. Ricardo Wurmus
2020-07-16gnu: r-genomicfeatures: Update to 1.40.1....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1. Ricardo Wurmus
2020-07-16gnu: r-summarizedexperiment: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2. Ricardo Wurmus
2020-07-16gnu: r-delayedmatrixstats: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1. Ricardo Wurmus
2020-07-16gnu: r-rhdf5: Update to 2.32.2....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2. Ricardo Wurmus
2020-07-12gnu: Remove ".git" from "https://github/…/….git"....Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix swh) would sometimes return #f for these because the ".git" URLs are redirects to the non-".git" URLs. Consequently, 'guix lint -c archival' would keep saying "scheduled Software Heritage archival"; likewise, the fallback download code would fail. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm, gnu/packages/android.scm, gnu/packages/animation.scm, gnu/packages/arcan.scm, gnu/packages/assembly.scm, gnu/packages/audio.scm, gnu/packages/authentication.scm, gnu/packages/avr.scm, gnu/packages/axoloti.scm, gnu/packages/backup.scm, gnu/packages/bash.scm, gnu/packages/benchmark.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/boost.scm, gnu/packages/build-tools.scm, gnu/packages/c.scm, gnu/packages/calendar.scm, gnu/packages/cdrom.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/chez.scm, gnu/packages/clojure.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/compton.scm, gnu/packages/coq.scm, gnu/packages/cpp.scm, gnu/packages/cran.scm, gnu/packages/crypto.scm, gnu/packages/curl.scm, gnu/packages/databases.scm, gnu/packages/datastructures.scm, gnu/packages/debug.scm, gnu/packages/disk.scm, gnu/packages/distributed.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/dns.scm, gnu/packages/docker.scm, gnu/packages/education.scm, gnu/packages/efi.scm, gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/embedded.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/erlang.scm, gnu/packages/fabric-management.scm, gnu/packages/file-systems.scm, gnu/packages/finance.scm, gnu/packages/firmware.scm, gnu/packages/flashing-tools.scm, gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/fpga.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/genealogy.scm, gnu/packages/genimage.scm, gnu/packages/geo.scm, gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/gnome-xyz.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/golang.scm, gnu/packages/gpodder.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/groff.scm, gnu/packages/groovy.scm, gnu/packages/gtk.scm, gnu/packages/guile-xyz.scm, gnu/packages/guile.scm, gnu/packages/hardware.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-xyz.scm, gnu/packages/hexedit.scm, gnu/packages/i2p.scm, gnu/packages/ibus.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/ipfs.scm, gnu/packages/java-graphics.scm, gnu/packages/java-maths.scm, gnu/packages/java.scm, gnu/packages/javascript.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/jupyter.scm, gnu/packages/kodi.scm, gnu/packages/language.scm, gnu/packages/lego.scm, gnu/packages/less.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm, gnu/packages/lirc.scm, gnu/packages/lisp-xyz.scm, gnu/packages/llvm.scm, gnu/packages/logging.scm, gnu/packages/lolcode.scm, gnu/packages/lua.scm, gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/maths.scm, gnu/packages/maven.scm, gnu/packages/mes.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/node-xyz.scm, gnu/packages/ocaml.scm, gnu/packages/ocr.scm, gnu/packages/onc-rpc.scm, gnu/packages/opencl.scm, gnu/packages/opencog.scm, gnu/packages/pantheon.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/perl6.scm, gnu/packages/phabricator.scm, gnu/packages/popt.scm, gnu/packages/printers.scm, gnu/packages/prolog.scm, gnu/packages/protobuf.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/qt.scm, gnu/packages/radio.scm, gnu/packages/rails.scm, gnu/packages/rdf.scm, gnu/packages/rednotebook.scm, gnu/packages/rpc.scm, gnu/packages/rsync.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/screen.scm, gnu/packages/security-token.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/shellutils.scm, gnu/packages/simh.scm, gnu/packages/sml.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/stenography.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/synergy.scm, gnu/packages/telephony.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tmux.scm, gnu/packages/tor.scm, gnu/packages/toys.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/virtualization.scm, gnu/packages/vlang.scm, gnu/packages/vnc.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wireservice.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, tests/lint.scm: Remove trailing ".git" from 'git-reference' URL. Ludovic Courtès
2020-07-02gnu: r-annotationdbi: Update to 1.50.1....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1. Ricardo Wurmus
2020-06-30gnu: blast+: Update to 2.10.1....* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1. Ricardo Wurmus
2020-06-28gnu: r-qtl2: Update synopsis, description....* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's synopsis. [description]: Same. Efraim Flashner
2020-06-28gnu: r-qtl2: Update to 0.22-8....* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8. [source]: Download from cran. Efraim Flashner
2020-06-28gnu: r-scater: Update to 1.16.2....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2. Ricardo Wurmus
2020-06-28gnu: r-biocviews: Update to 1.56.1....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1. Ricardo Wurmus
2020-06-28gnu: r-dexseq: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1. Ricardo Wurmus
2020-06-23gnu: miniasm: Make sure all phases return #t....* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom 'install phase return #t. Efraim Flashner
2020-06-23gnu: miniasm: Don't use unstable tarball....* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using git-fetch. Efraim Flashner
2020-06-22gnu: python-plotly: Update to 4.8.1....But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pierre Langlois
2020-06-22gnu: python-pandas: Update to 1.0.5....But also keep version 0.25.3 around for packages requiring an earlier versions, as well as version 0.24.2 for a version with python2. * gnu/packages/python-science.scm (python-pandas): Update to 1.0.5. [arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not delete tests that depend on "moto", they are skipped automatically. [propagated-inputs]: Add python-jinja2. [inputs]: Add xsel and xclip. [native-inputs]: Add xorg-server-for-tests so we can test clipboard support. (python-pandas-0.24): New variable. (python2-pandas): Inherit from python-pandas-0.25. * gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]: Switch to python-pandas-0.25. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pierre Langlois
2020-06-22gnu: deeptools: Deprecate in favor of python-deeptools....And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Pierre Langlois
2020-06-22gnu: r-hdf5array: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1. Ricardo Wurmus
2020-06-22gnu: r-rhdf5: Update to 2.32.1....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1. Ricardo Wurmus
2020-06-22gnu: r-biomart: Update to 2.44.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1. Ricardo Wurmus
2020-06-22gnu: r-genomeinfodb: Update to 1.24.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2. Ricardo Wurmus
2020-06-22gnu: express: Update to 1.5.3....* gnu/packages/bioinformatics.scm (express): Update to 1.5.3. [source]: Fetch from Github. [arguments]: Add phase "remove-update-check". Ricardo Wurmus
2020-06-15gnu: r-limma: Update to 3.44.3....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3. Ricardo Wurmus
2020-06-13gnu: r-mzr: Update to 2.22.0....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-delayedmatrixstats: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-scran: Update to 1.16.0....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.16.0. [propagated-inputs]: Add r-iranges. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-scater: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.1. [propagated-inputs]: Add r-rlang. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-singlecellexperiment: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-beachmat: Update to 2.4.0....* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-rhdf5lib: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.0. [source]: Update snippet. [arguments]: Replace ZLIB variables in Makevars. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-hdf5array: Update to 1.16.0....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0. Ricardo Wurmus
2020-06-13gnu: r-hitc: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0. Ricardo Wurmus
2020-06-13gnu: r-fithic: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-sushi: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0. Ricardo Wurmus
2020-06-13gnu: r-gwascat: Update to 2.20.1....* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.20.1. [propagated-inputs]: Remove r-homo-sapiens; add r-ggplot2. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-gviz: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.32.0. [propagated-inputs]: Add r-ensembldb. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-gqtlstats: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-ldblock: Update to 1.18.0....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-erma: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-snpstats: Update to 1.38.0....* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0. Ricardo Wurmus
2020-06-13gnu: r-gqtlbase: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-ggbio: Update to 1.36.0....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-biovizbase: Update to 1.36.0....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0. Ricardo Wurmus
2020-06-13gnu: r-organismdbi: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0. Ricardo Wurmus
2020-06-13gnu: r-ensembldb: Update to 2.12.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-13gnu: r-dirichletmultinomial: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0. Ricardo Wurmus
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