ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-15 03:15:09 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
64200 commits 1 branch 0 tags 448 MiB
Commit graph

2440 commits

Author SHA1 Message Date
Jakub Kądziołka
56f12a65a0
gnu: r-rhdf5lib: Fix libsz substitution. 
This is a follow-up to commit b7f051db14 -
in the new version, some of the format strings being replaced gained
quotes. This commit fixes build of dependents of r-rhdf5lib, such as
r-hdf5array.

* gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
 2020-07-19 15:54:48 +02:00
Tobias Geerinckx-Rice
fe39c70195
gnu: 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.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice
c980589260
gnu: 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.
 2020-07-16 20:12:06 +02:00
Ricardo Wurmus
b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
82eafe32a2
gnu: r-qtl2: Update to 0.22-11. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
b80f141f86
gnu: r-delayedmatrixstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus
15597255e6
gnu: r-rhdf5: Update to 2.32.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
 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
bd978be3ae
gnu: r-annotationdbi: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
 2020-07-02 12:45:53 +02:00
Ricardo Wurmus
3d5334c390
gnu: blast+: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1.
 2020-06-30 18:49:11 +02:00
Efraim Flashner
5e5bcba295
gnu: r-qtl2: Update synopsis, description. 
* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's
synopsis.
[description]: Same.
 2020-06-28 10:18:47 +03:00
Efraim Flashner
54bb476670
gnu: r-qtl2: Update to 0.22-8. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8.
[source]: Download from cran.
 2020-06-28 10:15:21 +03:00
Ricardo Wurmus
fb4804d03d
gnu: r-scater: Update to 1.16.2. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.
 2020-06-28 05:46:19 +02:00
Ricardo Wurmus
e66f81cf63
gnu: r-biocviews: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.
 2020-06-28 05:46:19 +02:00
Ricardo Wurmus
fa7871af77
gnu: r-dexseq: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.
 2020-06-28 05:46:19 +02:00
Efraim Flashner
de0f36f0aa
gnu: miniasm: Make sure all phases return #t. 
* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom
'install phase return #t.
 2020-06-23 16:04:51 +03:00
Efraim Flashner
896f18210b
gnu: miniasm: Don't use unstable tarball. 
* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using
git-fetch.
 2020-06-23 16:04:04 +03:00
Pierre Langlois
6e31d6f3c4
gnu: 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>
 2020-06-22 15:44:16 +02:00
Pierre Langlois
20b545f768
gnu: 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>
 2020-06-22 15:44:08 +02:00
Pierre Langlois
3a79adab41
gnu: 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>
 2020-06-22 15:43:59 +02:00
Ricardo Wurmus
ebcebc59ab
gnu: r-hdf5array: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
b07e53bb09
gnu: r-rhdf5: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
f65d5e84de
gnu: r-biomart: Update to 2.44.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
55401384dc
gnu: r-genomeinfodb: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
acba72b914
gnu: 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".
 2020-06-22 09:07:51 +02:00
Ricardo Wurmus
8b00728144
gnu: r-limma: Update to 3.44.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
 2020-06-15 12:00:21 +02:00
Ricardo Wurmus
9ae4bd0b77
gnu: r-mzr: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:20:02 +02:00
Ricardo Wurmus
a3b55161c7
gnu: r-delayedmatrixstats: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus
47c7670c43
gnu: 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.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus
7039b53945
gnu: 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.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
9e7acf2f14
gnu: r-singlecellexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
16dd6bacaa
gnu: r-beachmat: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
87d5444d9f
gnu: 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.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
cf907680e8
gnu: r-hdf5array: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
46f188d1df
gnu: r-hitc: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
6be25cc2db
gnu: r-fithic: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
a811751f49
gnu: r-sushi: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
ddef43a29d
gnu: 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.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
522da60b29
gnu: 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.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
a97897bc3d
gnu: r-gqtlstats: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
6caad43c18
gnu: r-ldblock: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
87772ab4dd
gnu: r-erma: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
aab0e28fc1
gnu: r-snpstats: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
42d8cd9f97
gnu: r-gqtlbase: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
7038aeb210
gnu: r-ggbio: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
07518c3a34
gnu: r-biovizbase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
7c26687871
gnu: r-organismdbi: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
39da6fbc40
gnu: r-ensembldb: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:45 +02:00