a9083169c6
gnu: r-affycoretools: Update to 1.64.0.
...
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.64.0.
2021-06-05 09:12:41 +02:00
3abb0b6523
gnu: r-affycontam: Update to 1.50.0.
...
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.50.0.
2021-06-05 09:12:41 +02:00
bd17befeb1
gnu: r-affycompatible: Update to 1.52.0.
...
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.52.0.
2021-06-05 09:12:41 +02:00
b045bf2d6f
gnu: r-affycomp: Update to 1.68.0.
...
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.68.0.
2021-06-05 09:12:41 +02:00
af04e2cc12
gnu: r-affy: Update to 1.70.0.
...
* gnu/packages/bioconductor.scm (r-affy): Update to 1.70.0.
2021-06-05 09:12:41 +02:00
60b9546472
gnu: r-iranges: Update to 2.26.0.
...
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.26.0.
2021-06-05 09:12:41 +02:00
cfd4c05bd4
gnu: r-ideoviz: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.28.0.
2021-06-05 09:12:40 +02:00
4075ac7287
gnu: r-bluster: Update to 1.2.1.
...
* gnu/packages/bioconductor.scm (r-bluster): Update to 1.2.1.
[propagated-inputs]: Add r-cluster.
2021-06-05 09:12:40 +02:00
8eb0c715e3
gnu: r-delayedarray: Update to 0.18.0.
...
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.18.0.
2021-06-05 09:12:40 +02:00
f0f839c124
gnu: r-deepsnv: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0.
[inputs]: Remove zlib.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:40 +02:00
dec096f827
gnu: r-decipher: Update to 2.20.0.
...
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0.
[propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector.
2021-06-05 09:12:40 +02:00
116df58449
gnu: r-cummerbund: Update to 2.34.0.
...
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0.
2021-06-05 09:12:40 +02:00
e6c5d8ce2c
gnu: r-coverageview: Update to 1.30.0.
...
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0.
2021-06-05 09:12:40 +02:00
7bac473d06
gnu: r-biocgenerics: Update to 0.38.0.
...
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0.
2021-06-05 09:12:40 +02:00
b05761a5a9
gnu: r-biocversion: Update to 3.13.1.
...
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1.
2021-06-05 09:12:40 +02:00
405b386656
gnu: r-aneufinder: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0.
2021-06-05 09:12:40 +02:00
75817956c1
gnu: r-hdf5array: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0.
[arguments]: Remove.
[propagated-inputs]: Add r-rhdf5filters.
2021-06-05 09:12:40 +02:00
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
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
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
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
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
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
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
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
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
53ec97713a
gnu: Add r-metapod.
...
* gnu/packages/bioconductor.scm (r-metapod): New variable.
2021-06-05 09:12:39 +02:00
8caab75883
gnu: Add r-ggtree.
...
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
2021-06-05 09:12:39 +02:00
ab4a91b252
gnu: Add r-treeio.
...
* gnu/packages/bioconductor.scm (r-treeio): New variable.
2021-06-05 09:12:39 +02:00
fd4fa40ac4
gnu: Add r-scaledmatrix.
...
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
2021-06-05 09:12:39 +02:00
efefb2be3a
gnu: Add r-trajectoryutils.
...
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
2021-06-05 09:12:39 +02:00
ce99b4da63
gnu: Add r-restfulr.
...
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
2021-06-05 09:12:39 +02:00
ab66c9a2cd
gnu: Add r-arrow.
...
* gnu/packages/cran.scm (r-arrow): New variable.
2021-06-05 09:12:39 +02:00
b71f21339f
gnu: Add r-ggpointdensity.
...
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
2021-06-05 09:12:39 +02:00
41ea9bed97
gnu: Add r-ggnewscale.
...
* gnu/packages/cran.scm (r-ggnewscale): New variable.
2021-06-05 09:12:39 +02:00
d5c08f11e1
gnu: Add r-aplot.
...
* gnu/packages/cran.scm (r-aplot): New variable.
2021-06-05 09:12:39 +02:00
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
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
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
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
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
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
1ea00cceef
gnu: wfview: Update to 1.0.
...
* gnu/packages/radio.scm (wfview): Update to 1.0.
2021-06-04 13:50:52 +02:00
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
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
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
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
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
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
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
Ricardo Wurmus
Roel Janssen
Brendan Tildesley
Marius Bakke
Guillaume Le Vaillant
Maxime Devos