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2021-06-05gnu: r-affycoretools: Update to 1.64.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.64.0.
2021-06-05gnu: r-affycontam: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.50.0.
2021-06-05gnu: r-affycompatible: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.52.0.
2021-06-05gnu: r-affycomp: Update to 1.68.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.68.0.
2021-06-05gnu: r-affy: Update to 1.70.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affy): Update to 1.70.0.
2021-06-05gnu: r-iranges: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.26.0.
2021-06-05gnu: r-ideoviz: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.28.0.
2021-06-05gnu: r-bluster: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bluster): Update to 1.2.1. [propagated-inputs]: Add r-cluster.
2021-06-05gnu: r-delayedarray: Update to 0.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.18.0.
2021-06-05gnu: r-deepsnv: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0. [inputs]: Remove zlib. [native-inputs]: Add r-knitr.
2021-06-05gnu: r-decipher: Update to 2.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0. [propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector.
2021-06-05gnu: r-cummerbund: Update to 2.34.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0.
2021-06-05gnu: r-coverageview: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0.
2021-06-05gnu: r-biocgenerics: Update to 0.38.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0.
2021-06-05gnu: r-biocversion: Update to 3.13.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1.
2021-06-05gnu: r-aneufinder: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0.
2021-06-05gnu: r-hdf5array: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0. [arguments]: Remove. [propagated-inputs]: Add r-rhdf5filters.
2021-06-05gnu: r-cytoml: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0. [arguments]: Remove.
2021-06-05gnu: r-flowworkspace: Update to 4.4.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0. [arguments]: Remove. [propagated-inputs]: Add r-delayedarray and r-s4vectors.
2021-06-05gnu: r-ncdfflow: Update to 2.38.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0. [arguments]: Remove.
2021-06-05gnu: r-cytolib: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0. [arguments]: Remove. [native-inputs]: Remove pkg-config.
2021-06-05gnu: r-rhdf5: Update to 2.36.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0. [arguments]: Remove.
2021-06-05gnu: r-mzr: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0. [arguments]: Remove obsolute substitution.
2021-06-05gnu: r-msnid: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0. [arguments]: Set HOME variable.
2021-06-05gnu: r-bioccheck: Update to 1.28.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0. [arguments]: Remove.
2021-06-05gnu: r-rhdf5lib: Update to 1.14.0.Ricardo Wurmus
* 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.
2021-06-05gnu: Add r-metapod.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-metapod): New variable.
2021-06-05gnu: Add r-ggtree.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
2021-06-05gnu: Add r-treeio.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio): New variable.
2021-06-05gnu: Add r-scaledmatrix.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
2021-06-05gnu: Add r-trajectoryutils.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
2021-06-05gnu: Add r-restfulr.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
2021-06-05gnu: Add r-arrow.Ricardo Wurmus
* gnu/packages/cran.scm (r-arrow): New variable.
2021-06-05gnu: Add r-ggpointdensity.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
2021-06-05gnu: Add r-ggnewscale.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggnewscale): New variable.
2021-06-05gnu: Add r-aplot.Ricardo Wurmus
* gnu/packages/cran.scm (r-aplot): New variable.
2021-06-05gnu: pigx-rnaseq: Update to 0.0.13.Ricardo Wurmus
* 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.
2021-06-04gnu: python-scanpy: Update to 1.7.2.Roel Janssen
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04gnu: python-anndata: Update to 0.7.6.Roel Janssen
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
2021-06-04gnu: Use define-public in (gnu packages xiph).Brendan Tildesley
* gnu/pakages/xiph.scm: Replace all manual package #:exports with define-public. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-06-04gnu: python-pydantic: Update to 1.8.2.Marius Bakke
* 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.
2021-06-04gnu: wfview: Update to 1.0.Guillaume Le Vaillant
* gnu/packages/radio.scm (wfview): Update to 1.0.
2021-06-04gnu: smalltalk: Find glibc even when cross-compiling.Maxime Devos
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>
2021-06-04gnu: smalltalk: Move 'zip' from 'inputs' to 'native-inputs'.Maxime Devos
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>
2021-06-04gnu: ding: Use 'inputs' in build phases instead of '%build-inputs'.Maxime Devos
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>
2021-06-04gnu: qemacs: Use 'native-inputs' instead of '%build-inputs'.Maxime Devos
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>
2021-06-04gnu: neovim: Use 'inputs' in phases instead of '%build-inputs'.Maxime Devos
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>
2021-06-04gnu: smalltalk: Use 'inputs' in phases instead of '%build-inputs'.Maxime Devos
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>
2021-06-04gnu: ci: Use 'inputs' in build phases instead of '%build-inputs'.Maxime Devos
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>
2021-06-04gnu: Add pigx-sars-cov2-ww.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
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