| Age | Commit message (Expand) | Author |
|---|
| 2020-06-22 | 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>
| Pierre Langlois |
| 2020-06-22 | 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>
| Pierre Langlois |
| 2020-06-22 | 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>
| Pierre Langlois |
| 2020-06-22 | gnu: r-hdf5array: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
| Ricardo Wurmus |
| 2020-06-22 | gnu: r-rhdf5: Update to 2.32.1....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1.
| Ricardo Wurmus |
| 2020-06-22 | gnu: r-biomart: Update to 2.44.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
| Ricardo Wurmus |
| 2020-06-22 | gnu: r-genomeinfodb: Update to 1.24.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2.
| Ricardo Wurmus |
| 2020-06-22 | 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".
| Ricardo Wurmus |
| 2020-06-15 | gnu: r-limma: Update to 3.44.3....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | 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.
| Ricardo Wurmus |
| 2020-06-13 | 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.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | 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.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-hdf5array: Update to 1.16.0....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-hitc: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: r-sushi: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
| Ricardo Wurmus |
| 2020-06-13 | 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.
| Ricardo Wurmus |
| 2020-06-13 | 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.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: r-snpstats: Update to 1.38.0....* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: r-biovizbase: Update to 1.36.0....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-organismdbi: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: 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 |
| 2020-06-13 | gnu: r-dirichletmultinomial: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-complexheatmap: Update to 2.4.2....* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.2.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-genomicfiles: Update to 1.24.0....* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.24.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-gage: Update to 2.37.0....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.37.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-keggrest: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.28.0.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-fastseg: Update to 1.34.0....* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.34.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-annotationhub: Update to 2.20.0....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.0.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-interactivedisplaybase: Update to 1.26.3....* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.26.3.
[propagated-inputs]: Add r-dt.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-edaseq: Update to 2.22.0....* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.22.0.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-deseq: Update to 1.39.0....* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.39.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-aroma-light: Update to 3.18.0....* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.18.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-msnid: Update to 1.22.0....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.22.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-msnbase: Update to 2.14.2....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.14.2.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-pcamethods: Update to 1.80.0....* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.80.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-mzid: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.26.0.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-vsn: Update to 3.56.0....* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.56.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-affy: Update to 1.66.0....* gnu/packages/bioinformatics.scm (r-affy): Update to 1.66.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-affyio: Update to 1.58.0....* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.58.0.
| Ricardo Wurmus |
| 2020-06-13 | gnu: r-protgenerics: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.20.0.
| Ricardo Wurmus |
