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Author SHA1 Message Date
Ricardo Wurmus 3159fcf145
gnu: r-wgcna: Move to (gnu packages bioconductor).
This is a follow-up to commit 6e0ab26f31.

* gnu/packages/cran.scm (r-wgcna): Move from here...
* gnu/packages/bioconductor.scm (r-wgcna): ...to here.
2020-09-14 21:40:15 +02:00
zimoun 3292f6eda0
gnu: r-fithic: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-fithic): Move from here...
* gnu/packages/bioconductor.scm (r-fithic): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:40:15 +02:00
zimoun 7df42d3774
gnu: r-hitc: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-hitc): Move from here...
* gnu/packages/bioconductor.scm (r-hitc): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:40:15 +02:00
zimoun 63b75c01c2
gnu: r-hdf5array: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here...
* gnu/packages/bioconductor.scm (r-hdf5array): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:40:10 +02:00
zimoun c61268c1b7
gnu: r-rhdf5lib: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:33 +02:00
zimoun 8863c14cd8
gnu: r-beachmat: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-beachmat): Move from here...
* gnu/packages/bioconductor.scm (r-beachmat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:30 +02:00
zimoun 916a3e59ab
gnu: r-singlecellexperiment: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here...
* gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:27 +02:00
zimoun 6b1946b334
gnu: r-scater: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-scater): Move from here...
* gnu/packages/bioconductor.scm (r-scater): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:24 +02:00
zimoun 1193b77e60
gnu: r-scran: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:22 +02:00
zimoun 8c7c6db408
gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here...
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:19 +02:00
zimoun b3a998374c
gnu: r-rgraphviz: Move to (gnu packages bioconductor).
* gnu/packages/graph.scm (r-rgraphviz): Move from here...
* gnu/packages/bioconductor.scm (r-rgraphviz): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:16 +02:00
zimoun 6e0ab26f31
gnu: r-preprocesscore: Move to (gnu packages bioconductor).
* gnu/packages/statistics.scm (r-preprocesscore): Move from here...
* gnu/packages/bioconductor.scm (r-preprocesscore): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:12 +02:00
zimoun f4d920b9f7
gnu: r-fourcseq: Move to (gnu packages bioconductor).
* gnu/packages/cran.scm (r-fourcseq): Move from here...
* gnu/packages/bioconductor.scm (r-fourcseq): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14 21:39:00 +02:00
Ricardo Wurmus e1ce10e385
gnu: r-activedriverwgs: Update to 1.1.0.
* gnu/packages/bioconductor.scm (r-activedriverwgs): Update to 1.1.0.
[propagated-inputs]: Remove r-plyr.
[native-inputs]: Add r-knitr.
2020-09-14 19:07:44 +02:00
zimoun b17ace24ca
gnu: r-codedepends: Comment why it is in bioconductor.scm.
* gnu/packages/bioconductor.scm (r-codedepends): Add comment.
2020-09-11 21:46:51 +02:00
Peter Lo 7e88ee9f02
gnu: Add r-fhtest.
* gnu/packages/bioconductor.scm (r-fhtest): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:33:02 +02:00
Peter Lo 655c4bb25c
gnu: Add r-interval.
* gnu/packages/bioconductor.scm (r-interval): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:01:30 +02:00
Peter Lo 488001eb3f
gnu: Add r-icens.
* gnu/packages/bioconductor.scm (r-icens): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 19:13:58 +02:00
Ricardo Wurmus 40f378e18a
gnu: r-cicero: Update to 1.6.2.
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.6.2.
2020-09-04 22:01:40 +02:00
Ricardo Wurmus 6bc6a71119
gnu: r-mixomics: Update to 6.12.2.
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.12.2.
2020-09-04 22:01:40 +02:00
Ricardo Wurmus 60cc838403
gnu: r-atacseqqc: Update to 1.12.4.
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.12.4.
2020-09-04 22:01:40 +02:00
Ricardo Wurmus e1636671ec
gnu: r-gkmsvm: Update to 0.81.0.
* gnu/packages/bioconductor.scm (r-gkmsvm): Update to 0.81.0.
2020-09-04 22:01:40 +02:00
Ricardo Wurmus 0d2369be8b
gnu: r-chippeakanno: Update to 3.22.3.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.22.3.
2020-09-04 22:01:40 +02:00
Ricardo Wurmus b828c3ea90
gnu: r-biocset: Update to 1.2.2.
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.2.2.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus a27a402eba
gnu: r-experimenthub: Update to 1.14.2.
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.14.2.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 1bdc770dc6
gnu: r-variancepartition: Update to 1.18.3.
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.3.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 1bf630660b
gnu: r-rsubread: Update to 2.2.6.
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.6.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus a20538ab7e
gnu: r-rbowtie: Update to 1.28.1.
* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.28.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 4a504b80c2
gnu: r-biocfilecache: Update to 1.12.1.
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.12.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 82cb9a99f8
gnu: r-rbowtie2: Update to 1.10.1.
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.10.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus a8840a04d7
gnu: r-motifstack: Update to 1.32.1.
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.32.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 69f3b27822
gnu: r-clusterprofiler: Update to 3.16.1.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.16.1.
[propagated-inputs]: Add r-rlang.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus fc1c3c6f9f
gnu: r-gosemsim: Update to 2.14.1.
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.14.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 0827e0be36
gnu: r-oligo: Update to 1.52.1.
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.52.1.
2020-08-20 21:25:33 +02:00
Ricardo Wurmus 1c43c6fa6b
gnu: r-oligoclasses: Update to 1.50.4.
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.50.4.
2020-08-20 21:25:29 +02:00
Ricardo Wurmus 8fe3ef5d5a
gnu: r-abseqr: Add pandoc-citeproc.
* gnu/packages/bioconductor.scm (r-abseqr)[inputs]: Add pandoc-citeproc.
2020-08-16 15:57:26 +02:00
Ricardo Wurmus 6fa5e4aaae
gnu: r-abseqr: Use pandoc instead of ghc-pandoc.
* gnu/packages/bioconductor.scm (r-abseqr)[inputs]: Replace ghc-pandoc with
pandoc.
2020-08-16 15:57:26 +02:00
Ricardo Wurmus 0a41d9be2e
gnu: r-nmf: Update to 0.23.0.
* gnu/packages/bioconductor.scm (r-nmf): Update to 0.23.0.
[native-inputs]: Add r-knitr.
2020-08-12 13:57:10 +02:00
Ricardo Wurmus 0b8c7e4bb5
gnu: Add r-m3c.
* gnu/packages/bioconductor.scm (r-m3c): New variable.
2020-08-11 11:27:06 +02:00
Tobias Geerinckx-Rice 702a101257
gnu: Use HTTPS for github.com (and subdomains) home pages.
* gnu/packages/bioconductor.scm (r-qvalue)[home-page]: Use HTTPS and
follow permanent redirection.
* gnu/packages/check.scm (python-codecov, python-nosexcover)
[home-page]: Likewise.
* gnu/packages/cran.scm (r-ffbase, r-ggrepel, r-valr)
[home-page]: Likewise.
* gnu/packages/crates-io.scm (rust-block-0.1, rust-dispatch-0.1)
(rust-objc-0.2, rust-objc-exception-0.1)
(rust-objc-foundation-0.1, rust-objc-id-0.1, rust-objc-test-utils-0.0)
(rust-onig-5.0, rust-onig-sys-69.2, rust-vergen-3.1)
[home-page]: Likewise.
* gnu/packages/finance.scm (ledger-agent, keepkey-agent)
[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-tasty-expected-failure)
[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-bsb-http-chunked, ghc-warp)
(ghc-warp-tls)[home-page]: Likewise.
* gnu/packages/haskell-xyz.scm (ghc-configurator, ghc-hasktags)
(ghc-linear, ghc-newtype-generics, ghc-retry, ghc-xdg-basedir)
(ghc-pretty-show)[home-page]: Likewise.
* gnu/packages/java.scm (java-javax-inject)[home-page]: Likewise.
* gnu/packages/libffi.scm (ruby-ffi)[home-page]: Likewise.
* gnu/packages/linux.scm (procenv)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-aiodns, python-flask-htpasswd)
(python-pycares)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-progressbar33, python-whatever)
(python-funcy)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-rubyzip, ruby-spinach, ruby-gherkin-ruby)
(ruby-code-statistics, ruby-colorize, ruby-wwtd)[home-page]: Likewise.
2020-07-16 20:12:06 +02:00
Ricardo Wurmus a9a912805a
gnu: r-activepathways: Update to 1.0.2.
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.0.2.
[propagated-inputs]: Remove r-metap.
2020-07-16 10:08:05 +02:00
Ricardo Wurmus 1a7d1c54d4
gnu: r-rsubread: Update to 2.2.4.
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.4.
2020-07-16 10:08:05 +02:00
Ricardo Wurmus 2d9c897dd0
gnu: r-variancepartition: Update to 1.18.2.
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.2.
2020-07-16 10:08:03 +02:00
Ludovic Courtès b0e7b6992f
gnu: 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.
2020-07-12 23:08:15 +02:00
Ricardo Wurmus 54e04fed9c
gnu: r-depecher: Update to 1.4.1.
* gnu/packages/bioconductor.scm (r-depecher): Update to 1.4.1.
2020-07-04 11:52:33 +02:00
Ricardo Wurmus c535717b6a
gnu: r-rsubread: Update to 2.2.3.
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.3.
2020-07-04 11:52:33 +02:00
Ricardo Wurmus c89afe7516
gnu: Add r-rgreat.
* gnu/packages/bioconductor.scm (r-rgreat): New variable.
2020-06-22 14:39:03 +02:00
Ricardo Wurmus f7d5721bc2
gnu: r-gdsfmt: Update to 1.24.1.
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.24.1.
2020-06-22 12:15:49 +02:00
Ricardo Wurmus 1893092d58
gnu: r-cicero: Update to 1.6.1.
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.6.1.
[propagated-inputs]: Add r-stringi.
2020-06-22 12:15:49 +02:00
Ricardo Wurmus ef58875705
gnu: r-cytoml: Update to 2.0.5.
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.0.5.
[propagated-inputs]: Add r-xml2.
2020-06-22 12:15:49 +02:00