1b24dfb8ba
* Replace git-based Bioconductor R packages The current collection of bioconductor packages tend to have scattered dependencies and missing versions. This commit replaces git-based packages with tool-generated Spack package recipes with correct dependencies and descriptions in place. * Fix some broken package names, add periods to title docstrings * r-clue: new package at 0.3-57 * r-genomeinfodbdata: add 1.2.1 * r-gofuncr: new package at 1.4.0 * r-pfam-db: add 3.8.2 * Add missed package r-genelendatabase * update r-goseq package * update r-glimma package * update r-rots package * r-org-hs-eg-db: add 3.8.2 * r-vgam: fix incorrect R version * r-rnaseqmap: new package at 2.42.0 * r-rhdf5lib: new package at 1.6.0 * r-scrime: new package at 1.3.5 * r-delayedmatrixstats: new package at 1.6.0 * r-hdf5array: new package at 1.12.1 * r-biocfilecache: new package at 1.8.0 * r-ctc: add new versions, dependencies * r-genemeta: new package at 1.56.0 * r-scrime: fix flake8 * r-ensembldb: add missing dependencies * Added missing dependencies to packages with certain DESCRIPTIONS * r-mapplots: new package at 1.5.1 * r-beachmat: new package at 2.0.0 * r-beeswarm: new package at 0.2.3 * r-biocneighbors: new package at 1.2.0 * r-biocsingular: new package at 1.0.0 * r-ecp: new package at 3.1.1 * r-enrichplot: new package at 1.4.0 * r-europepmc: new package at 0.3 * r-ggbeeswarm: new package at 0.6.0 * r-ggplotify: new package at 0.0.3 * r-ggraph: new package at 1.0.2 * r-gridgraphics: new package at 0.4-1 * r-rcppannoy: new package at 0.0.12 * r-rcpphnsw: new package at 0.1.0 * r-rsvd: new package at 1.0.1 * r-scater: new package at 1.12.2 * r-singlecellexperiment: new package at 1.6.0 * r-tximport: new package at 1.12.3 * r-upsetr: new package at 1.4.0 * r-vioplot: new package at 0.3.2 * r-readr: add 1.3.1 * r-matrixstats: add 0.54.0 * r-ecp: flake8 fix * r-biocmanager: new package at 1.30.4 * update bioconductor packages requiring BiocManager, new versions * r-lambda-r: add 1.2.3 * r-vegan: add 2.5-5 * r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF * r-chemometrics: flake8 fixes * r-vgam: flake8 fixes * CRAN packages: use cloud.r-project.org * Use DESCRIPTION for R version constraints over bioconductor releases * Update missed packages ABAData, acde, affydata * Update remaining missed packages * bio: Drop 'when' clause from first checksummed versions * bio: improve package description generation logic * r-genomeinfodbdata: use explicit sha256 sums * r-pfam-db: update dependencies, add 3.10.0 * update r-org-hs-eg-db * r-dirichletmultinomial: re-add gsl * r-polyclip: new package at 1.10-0 * r-farver: new package at 1.1.0 * r-tweenr: new package at 1.0.1 * r-ggforce: new package at 0.3.1 * r-ggforce: remove redundant dep * r-ggraph: add missing deps * r-rcpphnsw: remove redundant depends_on * r-reportingtools: re-add r-r-utils dep * r-rhdf5: add gmake dep * r-rhtslib: add system dependencies * r-rsamtools: add gmake dep * r-farver: remove redundant dep * r-tweenr: remove redundant dep * r-variantannotation: add gmake dep * r-rgraphviz: add graphviz dep * r-vsn: correct r-hexbin constraint * r-scater: fix obsolete deps * r-variantannotation: fix gmake dep type * r-scater: tighten R version constraints * r-rsamtools: fix gmake dep type * r-rhtslib: fix gmake dep type * r-rhtslib: use xz over lzma * r-rhdf5: fix gmake dep type * r-farver: replace with newer recipe for 2.0.1 * r-mzr: remove old dependency * r-reportingtools: remove builtin dependency * r-mzr: add gmake dep * r-rhtslib: make system libraries link deps * r-genomeinfodbdata: fix R version constraints * r-geoquery: remove old deps from new versions * r-genomicfeatures: tighten r-rmysql dep * r-ensembldb: tighten r-annotationhub dep * r-complexheatmap: fix r-dendextend dep * r-cner: fix utils dep name * r-clusterprofiler: fix r-gosemsim version req * r-biostrings: fix r-iranges version reqs * r-rhdf5lib: add gmake dep * r-oligoclasses: fix r-biocinstaller dep range * r-organismdbi: fix r-biocinstaller dep range * r-hdf5array: add gmake dep * r-gtrellis: tighten r-circlize version req * r-gostats: fix r-graph version req * r-glimma: fix old dependency ranges * r-biostrings: syntax fix * r-organismdbi: syntax fix * r-dose: fix r-igraph dep * r-dose: fix r-scales, r-rvcheck deps * r-affy: fix r-biocinstaller dep * r-ampliqueso: fix homepage * r-aneufinder: fix r-biocgenerics dep * r-beachmat: fix changed deps * r-biocneighbors: fix old R constraint * r-biocmanager: rewrite recipe for 1.30.10 * Update var/spack/repos/builtin/packages/r-biocinstaller/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/r-oligoclasses/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
43 lines
1.9 KiB
Python
43 lines
1.9 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class RClusterprofiler(RPackage):
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"""statistical analysis and visualization of functional profiles for genes
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and gene clusters.
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This package implements methods to analyze and visualize functional
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profiles (GO and KEGG) of gene and gene clusters."""
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homepage = "https://bioconductor.org/packages/clusterProfiler"
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git = "https://git.bioconductor.org/packages/clusterProfiler.git"
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version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
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version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c')
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version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36')
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version('3.6.0', commit='ff15e3dba69b93bc872d5f5d07821cd9ae20d829')
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version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
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depends_on('r@3.3.1:', type=('build', 'run'))
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depends_on('r-dose@3.1.3:', type=('build', 'run'))
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depends_on('r-annotationdbi', type=('build', 'run'))
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depends_on('r-ggplot2', type=('build', 'run'))
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depends_on('r-go-db', type=('build', 'run'))
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depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run'))
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depends_on('r-gosemsim', type=('build', 'run'))
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depends_on('r-magrittr', type=('build', 'run'))
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depends_on('r-plyr', type=('build', 'run'))
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depends_on('r-qvalue', type=('build', 'run'))
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depends_on('r-rvcheck', type=('build', 'run'))
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depends_on('r-tidyr', type=('build', 'run'))
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depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run'))
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depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
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depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run'))
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depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run'))
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