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Author SHA1 Message Date
Ricardo Wurmus bfa23ec526
gnu: r-cytoml: Update to 2.4.0. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0.
[arguments]: Remove.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus 764e2dba20
gnu: r-flowworkspace: Update to 4.4.0. 
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0.
[arguments]: Remove.
[propagated-inputs]: Add r-delayedarray and r-s4vectors.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus b9751b629c
gnu: r-ncdfflow: Update to 2.38.0. 
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0.
[arguments]: Remove.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus 5c37a048bb
gnu: r-cytolib: Update to 2.4.0. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0.
[arguments]: Remove.
[native-inputs]: Remove pkg-config.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus 782d27f77d
gnu: r-rhdf5: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0.
[arguments]: Remove.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus 87d06a725f
gnu: r-mzr: Update to 2.26.0. 
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0.
[arguments]: Remove obsolute substitution.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus 5d13aab6ca
gnu: r-msnid: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0.
[arguments]: Set HOME variable.
 2021-06-05 09:12:40 +02:00
Ricardo Wurmus d0a7dc0cb6
gnu: r-bioccheck: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0.
[arguments]: Remove.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 1b0338d76b
gnu: r-rhdf5lib: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.0.
[source]: Update deletions.
[arguments]: Update substitutions.
[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 53ec97713a
gnu: Add r-metapod. 
* gnu/packages/bioconductor.scm (r-metapod): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 8caab75883
gnu: Add r-ggtree. 
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus ab4a91b252
gnu: Add r-treeio. 
* gnu/packages/bioconductor.scm (r-treeio): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus fd4fa40ac4
gnu: Add r-scaledmatrix. 
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus efefb2be3a
gnu: Add r-trajectoryutils. 
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus ce99b4da63
gnu: Add r-restfulr. 
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus ab66c9a2cd
gnu: Add r-arrow. 
* gnu/packages/cran.scm (r-arrow): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus b71f21339f
gnu: Add r-ggpointdensity. 
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 41ea9bed97
gnu: Add r-ggnewscale. 
* gnu/packages/cran.scm (r-ggnewscale): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus d5c08f11e1
gnu: Add r-aplot. 
* gnu/packages/cran.scm (r-aplot): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus c343c3bc1f
guix: Update to Bioconductor 3.13. 
* guix/build-system/r.scm (bioconductor-uri): Update version.
* guix/import/cran.scm (%bioconductor-version): Update.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
 2021-06-05 09:12:39 +02:00
Roel Janssen 7382aa00b8
gnu: python-scanpy: Update to 1.7.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
 2021-06-04 23:51:35 +02:00
Roel Janssen e639da604f
gnu: python-anndata: Update to 0.7.6. 
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
 2021-06-04 23:51:24 +02:00
Brendan Tildesley 29745d23b8
gnu: Use define-public in (gnu packages xiph). 
* gnu/pakages/xiph.scm: Replace all manual package #:exports with
define-public.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 15:08:35 +02:00
Marius Bakke bb934ab79d
gnu: python-pydantic: Update to 1.8.2. 
* gnu/packages/python-xyz.scm (python-pydantic): Update to 1.8.2.
[arguments]: Disable some new tests.
[native-inputs]: Add PYTHON-PYTEST-MOCK.
[propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS.
 2021-06-04 14:57:39 +02:00
Guillaume Le Vaillant 1ea00cceef
gnu: wfview: Update to 1.0. 
* gnu/packages/radio.scm (wfview): Update to 1.0.
 2021-06-04 13:50:52 +02:00
Maxime Devos f50a88c1fa
gnu: smalltalk: Find glibc even when cross-compiling. 
glibc is named "cross-libc" instead of "libc" when cross-compiling. Smalltalk
still fails to cross-compile though.

* gnu/packages/smalltalk.scm
  (smalltalk)[arguments]{phases}<#:fix-libc>: Also search for
  "cross-libc" instead of only "libc" in 'inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:40:02 +02:00
Maxime Devos 961a8f1302
gnu: smalltalk: Move 'zip' from 'inputs' to 'native-inputs'. 
The 'zip' package is not in the references of 'smalltalk'.
As such, it probably should be a native input, not a regular
input. This can be confirmed by trying to cross-compile
the 'smalltalk' package, without this commit. The configure
script will ask to install InfoZIP.

* gnu/packages/smalltalk.scm
  (smalltalk)[inputs]{zip}: Move to ...
  (smalltalk)[native-inputs]{zip} ... here.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:58 +02:00
Maxime Devos 4a600ada5a
gnu: ding: Use 'inputs' in build phases instead of '%build-inputs'. 
In build phases, the former is preferred.

* gnu/packages/dictionaries.scm
  (ding)[arguments]<#:phases>{install}: Use 'inputs' argument instead
  of '%build-inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:54 +02:00
Maxime Devos 156b8f9cd2
gnu: qemacs: Use 'native-inputs' instead of '%build-inputs'. 
In build phases, the former (or 'inputs', as appropriate) is preferred.

* gnu/packages/text-editors.scm
  (qemacs)[arguments]<#:phases>{install-extra-documentation}: Use
  'native-inputs' argument instead of '%build-inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:49 +02:00
Maxime Devos 09be86744f
gnu: neovim: Use 'inputs' in phases instead of '%build-inputs'. 
In build phases, the former is preferred.

* gnu/packages/vim.scm
  (neovim)[arguments]<#:phases>{set-lua-path}: Use 'inputs'
  argument instead of '%build-inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:46 +02:00
Maxime Devos f5f78d0d02
gnu: smalltalk: Use 'inputs' in phases instead of '%build-inputs'. 
In build phases, the former is preferred.

* gnu/packages/smalltalk.scm
  (smalltalk)[arguments]<#:phases>{fix-libc}: Use 'inputs'
  argument instead of '%build-inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:42 +02:00
Maxime Devos 8190f5bb97
gnu: ci: Use 'inputs' in build phases instead of '%build-inputs'. 
In build phases, the former is preferred.

* gnu/packages/ci.scm
  (cuirass)[arguments]<#:phases>{wrap-program}: Use 'inputs'
  argument instead of '%build-inputs'.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:34:37 +02:00
Solene Rapenne a9afff4beb
doc: Mention virtualization module and add missing closing parenthesis. 
* doc/contributing.texi (Submitting Patches): Mention virtualization module
and add missing closing parenthesis.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-04 13:28:40 +02:00
Ricardo Wurmus d06ae05808
gnu: Add pigx-sars-cov2-ww. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
 2021-06-04 12:57:08 +02:00
Guillaume Le Vaillant 4f773bc22d
gnu: sbcl-nibbles: Update to 0.14-2.dad2524. 
* gnu/packages/lisp-xyz.scm (sbcl-nibbles): Update to 0.14-2.dad2524.
 2021-06-04 10:59:50 +02:00
Raghav Gururajan f1bfd9f194
gnu: remmina: Update to 1.4.18. 
* gnu/packages/vnc.scm (remmina)[version]: Update to 1.4.18.
 2021-06-03 23:46:04 -04:00
Raghav Gururajan 6148172c3e
gnu: gajim-omemo: Update to 2.7.14. 
* gnu/packages/messaging.scm (gajim-omemo)[version]: Update to 2.7.14.
 2021-06-03 23:35:12 -04:00
Leo Famulari 6b6b87f1c3
gnu: linux-libre 4.4: Update to 4.4.271. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.271.
(linux-libre-4.4-pristine-source): Update hash.
 2021-06-03 22:41:01 -04:00
Leo Famulari 6fa18e48a7
gnu: linux-libre 4.9: Update to 4.9.271. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.271.
(linux-libre-4.9-pristine-source): Update hash.
 2021-06-03 22:41:01 -04:00
Leo Famulari ba85dff344
gnu: linux-libre 4.14: Update to 4.14.235. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.235.
(linux-libre-4.14-pristine-source): Update hash.
 2021-06-03 22:41:01 -04:00
Leo Famulari 37ec3f3bec
gnu: linux-libre 4.19: Update to 4.19.193. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.193.
(linux-libre-4.19-pristine-source): Update hash.
 2021-06-03 22:41:01 -04:00
Leo Famulari a75aa36e0a
gnu: linux-libre 5.4: Update to 5.4.124. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.124.
(linux-libre-5.4-pristine-source): Update hash.
 2021-06-03 22:41:01 -04:00
Leo Famulari f23d5340c2
gnu: linux-libre 5.10: Update to 5.10.42. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.42.
(linux-libre-5.10-pristine-source): Update hash.
(deblob-scripts-5.10): Update hash.
 2021-06-03 22:41:00 -04:00
Leo Famulari 41d73dfba1
gnu: linux-libre: Update to 5.12.9. 
* gnu/packages/linux.scm (linux-libre-5.12-version): Update to 5.12.9.
(linux-libre-5.12-pristine-source): Update hash.
(deblob-scripts-5.12): Update hash.
 2021-06-03 22:40:51 -04:00
Xinglu Chen 7e16321560
licenses: Add BSD-1-Clause license. 
* licenses.scm (bsd-1): New variable.
 2021-06-03 21:53:05 +02:00
Leo Prikler bb414c9352
gnu: komikku: Update to 0.29.0. 
* gnu/packages/gnome.scm (komikku): Update to 0.29.0.
 2021-06-03 21:46:48 +02:00
Nicolas Goaziou 97b4a7e37c
gnu: emacs-calibredb: Update to 2.10.0. 
* gnu/packages/emacs-xyz.scm (emacs-calibredb): Update to 2.10.0.
 2021-06-03 21:13:23 +02:00
Eric Brown ecbfa20609
doc: Fix example iptables configuration. 
* doc/guix.texi (Networking Services): Allow established and related incoming
connections in example iptables configuration.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2021-06-04 00:11:47 +05:30
Guillaume Le Vaillant 9703a51048
gnu: Add rfcat. 
* gnu/packages/radio.scm (rfcat): New variable.
 2021-06-03 19:01:52 +02:00