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author | Justin S <3630356+codeandkey@users.noreply.github.com> | 2019-11-27 20:57:15 -0600 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-11-27 20:57:15 -0600 |
commit | 1b24dfb8bafe86fbff47a9751b199e2707e3c23e (patch) | |
tree | 3ae0d2b4e2080459501a116ddc324b0ab4f38b66 /var/spack/repos/builtin/packages/r-rhdf5/package.py | |
parent | 0f46c3452f03a5098aedb8c546acd6dc8c2486cd (diff) | |
download | spack-1b24dfb8bafe86fbff47a9751b199e2707e3c23e.tar.gz spack-1b24dfb8bafe86fbff47a9751b199e2707e3c23e.tar.bz2 spack-1b24dfb8bafe86fbff47a9751b199e2707e3c23e.tar.xz spack-1b24dfb8bafe86fbff47a9751b199e2707e3c23e.zip |
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>
Diffstat (limited to 'var/spack/repos/builtin/packages/r-rhdf5/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/r-rhdf5/package.py | 32 |
1 files changed, 22 insertions, 10 deletions
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py index 0f86da44f3..2750110df9 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py @@ -7,18 +7,30 @@ from spack import * class RRhdf5(RPackage): - """This R/Bioconductor package provides an interface between HDF5 - and R. HDF5's main features are the ability to store and access very - large and/or complex datasets and a wide variety of metadata on mass - storage (disk) through a completely portable file format. The rhdf5 - package is thus suited for the exchange of large and/or complex - datasets between R and other software package, and for letting R - applications work on datasets that are larger than the available RAM.""" - - homepage = "https://www.bioconductor.org/packages/rhdf5/" + """R Interface to HDF5. + + This package provides an interface between HDF5 and R. HDF5's main + features are the ability to store and access very large and/or complex + datasets and a wide variety of metadata on mass storage (disk) through a + completely portable file format. The rhdf5 package is thus suited for + the exchange of large and/or complex datasets between R and other + software package, and for letting R applications work on datasets that + are larger than the available RAM.""" + + homepage = "https://bioconductor.org/packages/rhdf5" git = "https://git.bioconductor.org/packages/rhdf5.git" + version('2.28.1', commit='e230fa34d6f3e97dd4e6065115675baf5e8213bb') + version('2.26.2', commit='81e11258db493661a19cf83e142b690ecac4e6cf') + version('2.24.0', commit='e926e8ce4e77082781afb943324a1e6745385b48') + version('2.22.0', commit='4431bdc0a2bcbb8086ee08a0f2300129b808d1be') version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc') - depends_on('r@3.4.0:3.4.9', when='@2.20.0') depends_on('r-zlibbioc', type=('build', 'run')) + + depends_on('r-rhdf5lib', when='@2.24.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@2.26.2:', type=('build', 'run')) + depends_on('r-rhdf5lib@1.3.2:', when='@2.26.2:', type=('build', 'run')) + + depends_on('gmake', type='build') |