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copyright: update license headers for 2013-2019 copyright.
2018-12-31 22:04:23 -08:00
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-07 13:52:23 -07:00
# Spack Project Developers. See the top-level COPYRIGHT file for details.
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-07 13:52:23 -07:00
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
from spack import *
class RBiovizbase(RPackage):
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
"""Basic graphic utilities for visualization of genomic data..
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
The biovizBase package is designed to provide a set of utilities, color
schemes and conventions for genomic data. It serves as the base for
various high-level packages for biological data visualization. This
saves development effort and encourages consistency."""
homepage = "https://bioconductor.org/packages/biovizBase"
Add top-level attributes for git R (Bioconductor) packages
2018-07-23 21:56:48 -05:00
git = "https://git.bioconductor.org/packages/biovizBase.git"
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82')
version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063')
version('1.26.0', commit='640742f48384f01d117b70dc5c64737e97ae9b4b')
Add top-level attributes for git R (Bioconductor) packages
2018-07-23 21:56:48 -05:00
version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
depends_on('r@2.10:', type=('build', 'run'))
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
depends_on('r-scales', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-dichromat', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges@1.99.28:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.5.14:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
depends_on('r-summarizedexperiment', type=('build', 'run'))
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
depends_on('r-biostrings@2.33.11:', type=('build', 'run'))
depends_on('r-rsamtools@1.17.28:', type=('build', 'run'))
depends_on('r-genomicalignments@1.1.16:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.21.19:', type=('build', 'run'))
r-biovizbase: Create new package. (#6042)
2017-10-30 23:38:10 -05:00
depends_on('r-annotationdbi', type=('build', 'run'))
Replace git-based Bioconductor R packages (#12005) * 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>
2019-11-27 20:57:15 -06:00
depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
depends_on('r-annotationfilter@0.99.8:', type=('build', 'run'))
depends_on('r-rlang', when='@1.28.2:', type=('build', 'run'))
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