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| author | Justin S <3630356+codeandkey@users.noreply.github.com> | 2019-11-27 20:57:15 -0600 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-11-27 20:57:15 -0600 |
| commit | 1b24dfb8bafe86fbff47a9751b199e2707e3c23e (patch) | |
| tree | 3ae0d2b4e2080459501a116ddc324b0ab4f38b66 | |
| 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>
186 files changed, 3320 insertions, 1326 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index 556049e22c..c0cc7875db 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -9,12 +9,15 @@ from spack import * class RA4(RPackage): """Automated Affymetrix Array Analysis Umbrella Package.""" - homepage = "https://www.bioconductor.org/packages/a4/" + homepage = "https://bioconductor.org/packages/a4" git = "https://git.bioconductor.org/packages/a4.git" + version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712') + version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d') + version('1.28.0', commit='e81a8c15e1062ed9433e2d4d333f0484bc0e8bfb') + version('1.26.0', commit='e6af2cba5b684f81cc6e44dbc432916f75a2f774') version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4base', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-a4classif', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index 53d80c567c..0cf3429b67 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -7,14 +7,17 @@ from spack import * class RA4base(RPackage): - """Automated Affymetrix Array Analysis.""" + """Automated Affymetrix Array Analysis Base Package.""" - homepage = "https://www.bioconductor.org/packages/a4Base/" + homepage = "https://bioconductor.org/packages/a4Base" git = "https://git.bioconductor.org/packages/a4Base.git" + version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7') + version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229') + version('1.28.0', commit='3918a9ebafa065027c29620ee4d83789cb02f932') + version('1.26.0', commit='9b8ee4a8be90f5035a4b105ecebb8bb5b50cd0d9') version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annaffy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py index 6117d3bb7c..efe6a579aa 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -9,12 +9,15 @@ from spack import * class RA4classif(RPackage): """Automated Affymetrix Array Analysis Classification Package.""" - homepage = "https://www.bioconductor.org/packages/a4Classif/" + homepage = "https://bioconductor.org/packages/a4Classif" git = "https://git.bioconductor.org/packages/a4Classif.git" + version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88') + version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3') + version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7') + version('1.26.0', commit='bc4018c3c441e1840bb3e2959c07611489439a50') version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4core', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-mlinterfaces', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py index e5a78fec2f..e874f45628 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -9,11 +9,14 @@ from spack import * class RA4core(RPackage): """Automated Affymetrix Array Analysis Core Package.""" - homepage = "https://www.bioconductor.org/packages/a4Core/" + homepage = "https://bioconductor.org/packages/a4Core" git = "https://git.bioconductor.org/packages/a4Core.git" + version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce') + version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141') + version('1.28.0', commit='39b6ee29bc2f2fdc5733438c14dc02f8abc6460b') + version('1.26.0', commit='e7be935f20b486165a2b27dbbf9e99ba07151bcd') version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-glmnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index 78db0cc963..9ec59b8d0f 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -9,10 +9,13 @@ from spack import * class RA4preproc(RPackage): """Automated Affymetrix Array Analysis Preprocessing Package.""" - homepage = "https://www.bioconductor.org/packages/a4Preproc/" + homepage = "https://bioconductor.org/packages/a4Preproc" git = "https://git.bioconductor.org/packages/a4Preproc.git" + version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558') + version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978') + version('1.28.0', commit='435d66727f1187020d034a1beaf4cd8bd4f76981') + version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea') version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py index bf6c5264b7..7da009e1e6 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -9,11 +9,14 @@ from spack import * class RA4reporting(RPackage): """Automated Affymetrix Array Analysis Reporting Package.""" - homepage = "https://www.bioconductor.org/packages/a4Reporting" + homepage = "https://bioconductor.org/packages/a4Reporting" git = "https://git.bioconductor.org/packages/a4Reporting.git" + version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792') + version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390') + version('1.28.0', commit='0fe72f48374353c39479a45e5516d0709f8c9ef7') + version('1.26.0', commit='cce201502e2d3b28fd2823b66d9f81b034dc7eaa') version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annaffy', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py index 2f4f6f1ebc..e1995f649b 100644 --- a/var/spack/repos/builtin/packages/r-abadata/package.py +++ b/var/spack/repos/builtin/packages/r-abadata/package.py @@ -7,16 +7,24 @@ from spack import * class RAbadata(RPackage): - """Provides the data for the gene expression enrichment analysis - conducted in the package 'ABAEnrichment'. The package includes three - datasets which are derived from the Allen Brain Atlas: (1) Gene - expression data from Human Brain (adults) averaged across donors, - (2) Gene expression data from the Developing Human Brain pooled into - five age categories and averaged across donors and (3) a developmental - effect score based on the Developing Human Brain expression data. - All datasets are restricted to protein coding genes.""" + """Averaged gene expression in human brain regions from Allen Brain Atlas. - homepage = "https://bioconductor.org/packages/ABAData/" - url = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.14.0.tar.gz" + Provides the data for the gene expression enrichment analysis conducted + in the package 'ABAEnrichment'. The package includes three datasets + which are derived from the Allen Brain Atlas: (1) Gene expression data + from Human Brain (adults) averaged across donors, (2) Gene expression + data from the Developing Human Brain pooled into five age categories and + averaged across donors and (3) a developmental effect score based on the + Developing Human Brain expression data. All datasets are restricted to + protein coding genes.""" - version('1.14.0', sha256='d203d968044c292cdfab57a4d6bf52dfb60470bd78b4c9bd88892577ac42b2b7') + homepage = "https://bioconductor.org/packages/ABAData" + git = "https://git.bioconductor.org/packages/ABAData.git" + + version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd') + version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d') + version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a') + version('1.8.0', commit='181a4af1af349064eb432255970e925ae2564e1a') + version('1.6.0', commit='517c18a3d1809dde0291eeb47dd2545c7cfcdabe') + + depends_on('r@3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py index 8c0708ed81..fd2261670a 100644 --- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py +++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py @@ -7,28 +7,37 @@ from spack import * class RAbaenrichment(RPackage): - """The package ABAEnrichment is designed to test for enrichment - of user defined candidate genes in the set of expressed genes in - different human brain regions. The core function 'aba_enrich' - integrates the expression of the candidate gene set (averaged - across donors) and the structural information of the brain using - an ontology, both provided by the Allen Brain Atlas project. - 'aba_enrich' interfaces the ontology enrichment software FUNC to - perform the statistical analyses. Additional functions provided - in this package like 'get_expression' and 'plot_expression' - facilitate exploring the expression data. From version 1.3.5 - onwards genomic regions can be provided as input, too; and from - version 1.5.9 onwards the function 'get_annotated_genes' offers - an easy way to obtain annotations of genes to enriched or - user-defined brain regions.""" - - homepage = "https://bioconductor.org/packages/ABAEnrichment/" + """Gene expression enrichment in human brain regions. + + The package ABAEnrichment is designed to test for enrichment of user + defined candidate genes in the set of expressed genes in different human + brain regions. The core function 'aba_enrich' integrates the expression + of the candidate gene set (averaged across donors) and the structural + information of the brain using an ontology, both provided by the Allen + Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment + software FUNC to perform the statistical analyses. Additional functions + provided in this package like 'get_expression' and 'plot_expression' + facilitate exploring the expression data, and besides the standard + candidate vs. background gene set enrichment, also three additional + tests are implemented, e.g. for cases when genes are ranked instead of + divided into candidate and background.""" + + homepage = "https://bioconductor.org/packages/ABAEnrichment" git = "https://git.bioconductor.org/packages/ABAEnrichment.git" + version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23') + version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7') + version('1.10.0', commit='15f33ccb694a91d2d2067c937682c4bc952def6c') + version('1.8.0', commit='cb8155ee9a04fb55b2a2e8c23df7c0be15bb2624') version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1') - depends_on('r@3.4.0:3.4.9', when='@1.6.0') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-gtools', type=('build', 'run')) - depends_on('r-abadata', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-gplots@2.14.2:', type=('build', 'run')) + depends_on('r-gtools@3.5.0:', type=('build', 'run')) + depends_on('r-abadata@0.99.2:', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run')) + depends_on('r-data-table@1.10.4:', when='@1.8.0:', type=('build', 'run')) + + depends_on('r-gofuncr@1.1.2:', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py index 7e418ddf3d..57a1acb7fd 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -7,16 +7,23 @@ from spack import * class RAbsseq(RPackage): - """Inferring differential expression genes by absolute counts - difference between two groups, utilizing Negative binomial - distribution and moderating fold-change according to heterogeneity - of dispersion across expression level.""" + """ABSSeq: a new RNA-Seq analysis method based on modelling absolute + expression differences. - homepage = "https://www.bioconductor.org/packages/ABSSeq/" + Inferring differential expression genes by absolute counts difference + between two groups, utilizing Negative binomial distribution and + moderating fold-change according to heterogeneity of dispersion across + expression level.""" + + homepage = "https://bioconductor.org/packages/ABSSeq" git = "https://git.bioconductor.org/packages/ABSSeq.git" + version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce') + version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a') + version('1.34.1', commit='0c3a2514ef644c6e0de3714bc91959a302c9e006') + version('1.32.3', commit='189d81c3d70f957bf50780f76a6ddcee499b4784') version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a') - depends_on('r@3.4.0:3.4.9', when='@1.22.8') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 4b49104897..e44a2c2e4d 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -7,21 +7,27 @@ from spack import * class RAcde(RPackage): - """This package provides a multivariate inferential analysis method - for detecting differentially expressed genes in gene expression data. - It uses artificial components, close to the data's principal - components but with an exact interpretation in terms of differential - genetic expression, to identify differentially expressed genes while - controlling the false discovery rate (FDR). The methods on this - package are described in the vignette or in the article - 'Multivariate Method for Inferential Identification of - Differentially Expressed Genes in Gene Expression Experiments' by - J. P. Acosta, L. Lopez-Kleine and S. Restrepo - (2015, pending publication).""" + """Artificial Components Detection of Differentially Expressed Genes. - homepage = "https://www.bioconductor.org/packages/acde/" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/acde_1.14.0.tar.gz" + This package provides a multivariate inferential analysis method for + detecting differentially expressed genes in gene expression data. It + uses artificial components, close to the data's principal components but + with an exact interpretation in terms of differential genetic + expression, to identify differentially expressed genes while controlling + the false discovery rate (FDR). The methods on this package are + described in the vignette or in the article 'Multivariate Method for + Inferential Identification of Differentially Expressed Genes in Gene + Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo + (2015, pending publication).""" - version('1.14.0', sha256='e8d9ad688610d4b72cab729141dc46fce580c97128d929885336bb138345b788') + homepage = "https://bioconductor.org/packages/acde" + git = "https://git.bioconductor.org/packages/acde.git" - depends_on('r-boot', type=('build', 'run')) + version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417') + version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4') + version('1.10.0', commit='2c303dec45f3c70bf333a6eacae568a08d5ca010') + version('1.8.0', commit='f7fc3e1dce958445f920d3b28b56abde70bfb9de') + version('1.6.0', commit='244c81f435a077bf7895ea565fa6695e8b079f67') + + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-boot@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index 88b6fa3742..593b63860e 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -7,17 +7,23 @@ from spack import * class RAcgh(RPackage): - """Functions for reading aCGH data from image analysis output files - and clone information files, creation of aCGH S3 objects for storing - these data. Basic methods for accessing/replacing, subsetting, - printing and plotting aCGH objects.""" + """Classes and functions for Array Comparative Genomic Hybridization data.. - homepage = "https://www.bioconductor.org/packages/aCGH/" + Functions for reading aCGH data from image analysis output files and + clone information files, creation of aCGH S3 objects for storing these + data. Basic methods for accessing/replacing, subsetting, printing and + plotting aCGH objects.""" + + homepage = "https://bioconductor.org/packages/aCGH" git = "https://git.bioconductor.org/packages/aCGH.git" + version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f') + version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21') + version('1.58.0', commit='2decc79a21bff5a14d708cdc654e351515b20d3e') + version('1.56.0', commit='f3531ec99fc181044bdcb6a01c9976029efb6235') version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693') - depends_on('r@3.4.0:3.4.9', when='@1.54.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index 19ecf0fc99..513bbd6491 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -7,21 +7,27 @@ from spack import * class RAcme(RPackage): - """ACME (Algorithms for Calculating Microarray Enrichment) is a set - of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, - or other experiments that result in regions of the genome showing - "enrichment". It does not rely on a specific array technology - (although the array should be a "tiling" array), is very general - (can be applied in experiments resulting in regions of enrichment), - and is very insensitive to array noise or normalization methods. - It is also very fast and can be applied on whole-genome tiling array - experiments quite easily with enough memory.""" + """Algorithms for Calculating Microarray Enrichment (ACME). - homepage = "https://www.bioconductor.org/packages/ACME/" + ACME (Algorithms for Calculating Microarray Enrichment) is a set of + tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or + other experiments that result in regions of the genome showing + "enrichment". It does not rely on a specific array technology (although + the array should be a "tiling" array), is very general (can be applied + in experiments resulting in regions of enrichment), and is very + insensitive to array noise or normalization methods. It is also very + fast and can be applied on whole-genome tiling array experiments quite + easily with enough memory.""" + + homepage = "https://bioconductor.org/packages/ACME" git = "https://git.bioconductor.org/packages/ACME.git" + version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a') + version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b') + version('2.36.0', commit='39e056435b9775d35e7f7fc5446c2c3cafe15670') + version('2.34.0', commit='1f53d43e420e245423fdf2711d0dcb345f829469') version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407') - depends_on('r@3.4.0:3.4.9', when='@2.32.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index f70aa7996c..beffcadb8c 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -7,20 +7,26 @@ from spack import * class RAdsplit(RPackage): - """This package implements clustering of microarray gene expression - profiles according to functional annotations. For each term genes - are annotated to, splits into two subclasses are computed and a - significance of the supporting gene set is determined.""" + """Annotation-Driven Clustering. - homepage = "https://www.bioconductor.org/packages/adSplit/" + This package implements clustering of microarray gene expression + profiles according to functional annotations. For each term genes are + annotated to, splits into two subclasses are computed and a significance + of the supporting gene set is determined.""" + + homepage = "https://bioconductor.org/packages/adSplit" git = "https://git.bioconductor.org/packages/adSplit.git" + version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652') + version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19') + version('1.50.0', commit='a02e2c994e78ececd5a248575109c5ed36c969db') + version('1.48.0', commit='57dfcd93b9232cf53f05c34179ecb759bb7aff46') version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c') - depends_on('r@3.4.0:3.4.9', when='@1.46.0') + depends_on('r@2.1.0:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-kegg-db', type=('build', 'run')) - depends_on('r-multtest', type=('build', 'run')) + depends_on('r-biobase@1.5.12:', type=('build', 'run')) + depends_on('r-cluster@1.9.1:', type=('build', 'run')) + depends_on('r-go-db@1.8.1:', type=('build', 'run')) + depends_on('r-kegg-db@1.8.1:', type=('build', 'run')) + depends_on('r-multtest@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index c998207b74..d909ce1c7a 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -7,18 +7,24 @@ from spack import * class RAffxparser(RPackage): - """Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). - It provides methods for fast and memory efficient parsing of - Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- - and binary-based files are supported. Currently, there are methods - for reading chip definition file (CDF) and a cell intensity file (CEL). - These files can be read either in full or in part. For example, - probe signals from a few probesets can be extracted very quickly - from a set of CEL files into a convenient list structure.""" + """Affymetrix File Parsing SDK. - homepage = "https://www.bioconductor.org/packages/affxparser/" + Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It + provides methods for fast and memory efficient parsing of Affymetrix + files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based + files are supported. Currently, there are methods for reading chip + definition file (CDF) and a cell intensity file (CEL). These files can + be read either in full or in part. For example, probe signals from a few + probesets can be extracted very quickly from a set of CEL files into a + convenient list structure.""" + + homepage = "https://bioconductor.org/packages/affxparser" git = "https://git.bioconductor.org/packages/affxparser.git" + version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056') + version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f') + version('1.52.0', commit='8e0c4b89ee1cb4ff95f58a5dd947249dc718bc58') + version('1.50.0', commit='01ef641727eadc2cc17b5dbb0b1432364436e3d5') version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py index af454aefd7..51269c1a6e 100644 --- a/var/spack/repos/builtin/packages/r-affy/package.py +++ b/var/spack/repos/builtin/packages/r-affy/package.py @@ -7,19 +7,27 @@ from spack import * class RAffy(RPackage): - """The package contains functions for exploratory oligonucleotide array + """Methods for Affymetrix Oligonucleotide Arrays. + + The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.""" - homepage = "https://bioconductor.org/packages/affy/" + homepage = "https://bioconductor.org/packages/affy" git = "https://git.bioconductor.org/packages/affy.git" + version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605') + version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206') + version('1.58.0', commit='4698231f45f225228f56c0708cd477ad450b4ee6') + version('1.56.0', commit='d36a7b8f05b1ef60162d94e75037d45c48f88871') version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.12:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) + depends_on('r-affyio@1.13.3:', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0') + + depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py index 58d14736a6..4625411e96 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -7,13 +7,19 @@ from spack import * class RAffycomp(RPackage): - """The package contains functions that can be used to compare - expression measures for Affymetrix Oligonucleotide Arrays.""" + """Graphics Toolbox for Assessment of Affymetrix Expression Measures. - homepage = "https://www.bioconductor.org/packages/affycomp/" + The package contains functions that can be used to compare expression + measures for Affymetrix Oligonucleotide Arrays.""" + + homepage = "https://bioconductor.org/packages/affycomp" git = "https://git.bioconductor.org/packages/affycomp.git" + version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c') + version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef') + version('1.56.0', commit='b0994da338be19396e647c680059fd35341b50a2') + version('1.54.0', commit='65281c1ca37147c2a54ad3722a8d5ff0ffa5acc5') version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-biobase@2.3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py index 163c3a5468..1c07feb5b7 100644 --- a/var/spack/repos/builtin/packages/r-affycompatible/package.py +++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py @@ -7,19 +7,25 @@ from spack import * class RAffycompatible(RPackage): - """This package provides an interface to Affymetrix chip annotation - and sample attribute files. The package allows an easy way for users - to download and manage local data bases of Affynmetrix NetAffx - annotation files. The package also provides access to GeneChip - Operating System (GCOS) and GeneChip Command Console - (AGCC)-compatible sample annotation files.""" + """Affymetrix GeneChip software compatibility. - homepage = "https://www.bioconductor.org/packages/AffyCompatible/" + This package provides an interface to Affymetrix chip annotation and + sample attribute files. The package allows an easy way for users to + download and manage local data bases of Affynmetrix NetAffx annotation + files. The package also provides access to GeneChip Operating System + (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation + files.""" + + homepage = "https://bioconductor.org/packages/AffyCompatible" git = "https://git.bioconductor.org/packages/AffyCompatible.git" + version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476') + version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8') + version('1.40.0', commit='44838bdb5e8c26afbd898c49ed327ddd1a1d0301') + version('1.38.0', commit='d47ee3a3a3d3bce11121e80fe02ee216b9199b12') version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3') - depends_on('r@3.4.0:3.4.9', when=('@1.36.0')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-xml@2.8-1:', type=('build', 'run')) + depends_on('r-rcurl@0.8-1:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index 10e35b6cd7..254ac53532 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -7,15 +7,21 @@ from spack import * class RAffycontam(RPackage): - """structured corruption of cel file data to demonstrate QA - effectiveness.""" + """structured corruption of affymetrix cel file data. - homepage = "https://www.bioconductor.org/packages/affyContam/" + structured corruption of cel file data to demonstrate QA + effectiveness""" + + homepage = "https://bioconductor.org/packages/affyContam" git = "https://git.bioconductor.org/packages/affyContam.git" + version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe') + version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614') + version('1.38.0', commit='84651e8eade61619afefc83bb290047da101a5bc') + version('1.36.0', commit='aeb684a7d3f6fa9243f3946d214de53649fa4fd6') version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40') - depends_on('r@3.4.0:3.4.9', when=('@1.34.0')) + depends_on('r@2.7.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-affydata', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py index b7aad34a95..eba33cd6ca 100644 --- a/var/spack/repos/builtin/packages/r-affycoretools/package.py +++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py @@ -7,15 +7,21 @@ from spack import * class RAffycoretools(RPackage): - """Various wrapper functions that have been written to streamline - the more common analyses that a core Biostatistician might see.""" + """Functions useful for those doing repetitive analyses with Affymetrix + GeneChips. - homepage = "https://www.bioconductor.org/packages/affycoretools/" + Various wrapper functions that have been written to streamline the more + common analyses that a core Biostatistician might see.""" + + homepage = "https://bioconductor.org/packages/affycoretools" git = "https://git.bioconductor.org/packages/affycoretools.git" + version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898') + version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845') + version('1.52.2', commit='2f98c74fad238b94c1e453b972524ab7b573b0de') + version('1.50.6', commit='4be92bcb55d7bace2a110865b7530dcfac14e76e') version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) @@ -33,3 +39,5 @@ class RAffycoretools(RPackage): depends_on('r-edger', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) + + depends_on('r-dbi', when='@1.50.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py index c5bcc2c329..bcf4caf4cc 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -7,14 +7,20 @@ from spack import * class RAffydata(RPackage): - """Example datasets of a slightly large size. They represent 'real - world examples', unlike the artificial examples included in the - package affy.""" + """Affymetrix Data for Demonstration Purpose. - homepage = "https://www.bioconductor.org/packages/affydata/" - url = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.32.0.tar.gz" + Example datasets of a slightly large size. They represent 'real world + examples', unlike the artificial examples included in the package + affy.""" - version('1.32.0', sha256='059e05a2b8908720801d684d5617d5d5e45db7a5999c5659a22daf87658538d1') + homepage = "https://bioconductor.org/packages/affydata" + git = "https://git.bioconductor.org/packages/affydata.git" - depends_on('r@3.4.0:3.4.9', when=('@1.24.0')) - depends_on('r-affy', type=('build', 'run')) + version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd') + version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea') + version('1.28.0', commit='a106a5514c352bf0bbc624ded58a93886d4ce96f') + version('1.26.0', commit='eb0a44a39990b361f9fb1094837ffafb320f39a9') + version('1.24.0', commit='663991606507572f083232e2b393d901270291d4') + + depends_on('r@2.4.0:', type=('build', 'run')) + depends_on('r-affy@1.23.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py index f281ebecb9..b49240495d 100644 --- a/var/spack/repos/builtin/packages/r-affyexpress/package.py +++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py @@ -7,15 +7,21 @@ from spack import * class RAffyexpress(RPackage): - """The purpose of this package is to provide a comprehensive and - easy-to-use tool for quality assessment and to identify differentially - expressed genes in the Affymetrix gene expression data.""" + """Affymetrix Quality Assessment and Analysis Tool. - homepage = "https://www.bioconductor.org/packages/AffyExpress/" + The purpose of this package is to provide a comprehensive and easy-to- + use tool for quality assessment and to identify differentially expressed + genes in the Affymetrix gene expression data.""" + + homepage = "https://bioconductor.org/packages/AffyExpress" git = "https://git.bioconductor.org/packages/AffyExpress.git" + version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96') + version('1.48.0', commit='dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92') + version('1.46.0', commit='2add4a4436e21aa20f1ededbfd5f1365a3d28c85') + version('1.44.0', commit='7517bc8b363ceb107d5dca66dd74f94edefde52a') version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371') - depends_on('r@3.4.0:3.4.9', when='@1.42.0') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-affy@1.23.4:', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py index a32532a55f..3f83a05312 100644 --- a/var/spack/repos/builtin/packages/r-affyilm/package.py +++ b/var/spack/repos/builtin/packages/r-affyilm/package.py @@ -7,19 +7,24 @@ from spack import * class RAffyilm(RPackage): - """affyILM is a preprocessing tool which estimates gene - expression levels for Affymetrix Gene Chips. Input from - physical chemistry is employed to first background subtract - intensities before calculating concentrations on behalf - of the Langmuir model.""" + """Linear Model of background subtraction and the Langmuir isotherm. - homepage = "https://www.bioconductor.org/packages/affyILM/" + affyILM is a preprocessing tool which estimates gene expression levels + for Affymetrix Gene Chips. Input from physical chemistry is employed to + first background subtract intensities before calculating concentrations + on behalf of the Langmuir model.""" + + homepage = "https://bioconductor.org/packages/affyILM" git = "https://git.bioconductor.org/packages/affyILM.git" + version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132') + version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564') + version('1.32.0', commit='860f2ddada80435d309ba334eff3fab503817755') + version('1.30.0', commit='c07d91ae52a2a48f0a5f212c3ecf3243741bee13') version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de') - depends_on('r@3.4.0:3.4.9', when='@1.28.0') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r-affxparser', type=('build', 'run')) + depends_on('r-affxparser@1.16.0:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py index 4ef1265271..f9a0802378 100644 --- a/var/spack/repos/builtin/packages/r-affyio/package.py +++ b/var/spack/repos/builtin/packages/r-affyio/package.py @@ -7,14 +7,20 @@ from spack import * class RAffyio(RPackage): - """Routines for parsing Affymetrix data files based upon file format + """Tools for parsing Affymetrix data files. + + Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.""" - homepage = "https://bioconductor.org/packages/affyio/" + homepage = "https://bioconductor.org/packages/affyio" git = "https://git.bioconductor.org/packages/affyio.git" + version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f') + version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963') + version('1.50.0', commit='911ea4f8e4cdf7b649b87ef7ed1a5f5b111ef38a') + version('1.48.0', commit='01727a4492c3a0d50453fc91892e04bf5f7fcadb') version('1.46.0', commit='977597f2772e08273d86579486f452170566c880') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.46.0') diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py index 703859244f..3bd2b13da2 100644 --- a/var/spack/repos/builtin/packages/r-affypdnn/package.py +++ b/var/spack/repos/builtin/packages/r-affypdnn/package.py @@ -7,13 +7,19 @@ from spack import * class RAffypdnn(RPackage): - """The package contains functions to perform the PDNN method - described by Li Zhang et al.""" + """Probe Dependent Nearest Neighbours (PDNN) for the affy package. - homepage = "https://www.bioconductor.org/packages/affypdnn/" + The package contains functions to perform the PDNN method described by + Li Zhang et al.""" + + homepage = "https://bioconductor.org/packages/affypdnn" git = "https://git.bioconductor.org/packages/affypdnn.git" + version('1.58.0', commit='83d8b6b0d9606845bd77dbf7164dd5b160f32ccf') + version('1.56.0', commit='5fd9c5265fb895a1f646cf72e8d5169669d979f2') + version('1.54.0', commit='ea971b1b9cc443695a6614bef92e8e116ee87d55') + version('1.52.0', commit='17d74c593ce4f0dfd43f13a5016e482c1399d21e') version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a') - depends_on('r@3.4.0:3.4.9', when='@1.50.0') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-affy@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py index 036aa6dcf3..d3a94634de 100644 --- a/var/spack/repos/builtin/packages/r-affyplm/package.py +++ b/var/spack/repos/builtin/packages/r-affyplm/package.py @@ -7,21 +7,27 @@ from spack import * class RAffyplm(RPackage): - """A package that extends and improves the functionality of - the base affy package. Routines that make heavy use of compiled - code for speed. Central focus is on implementation of methods - for fitting probe-level models and tools using these models. - PLM based quality assessment tools.""" + """Methods for fitting probe-level models. - homepage = "https://www.bioconductor.org/packages/affyPLM/" + A package that extends and improves the functionality of the base affy + package. Routines that make heavy use of compiled code for speed. + Central focus is on implementation of methods for fitting probe-level + models and tools using these models. PLM based quality assessment + tools.""" + + homepage = "https://bioconductor.org/packages/affyPLM" git = "https://git.bioconductor.org/packages/affyPLM.git" + version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d') + version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8') + version('1.56.0', commit='13dfc558281af9a177d4d592c34cf7ace629af0e') + version('1.54.0', commit='09cf5f6e01dd2d0aae3e9ddab27301f04bfd645c') version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43') - depends_on('r@3.4.0:3.4.9', when='@1.52.1') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + depends_on('r-affy@1.11.0:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-preprocesscore@1.5.1:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py index 1092c436f4..4e6b053e51 100644 --- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py +++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py @@ -7,17 +7,22 @@ from spack import * class RAffyqcreport(RPackage): - """This package creates a QC report for an AffyBatch object. - The report is intended to allow the user to quickly assess the - quality of a set of arrays in an AffyBatch object.""" + """QC Report Generation for affyBatch objects. - homepage = "https://www.bioconductor.org/packages/affyQCReport/" + This package creates a QC report for an AffyBatch object. The report is + intended to allow the user to quickly assess the quality of a set of + arrays in an AffyBatch object.""" + + homepage = "https://bioconductor.org/packages/affyQCReport" git = "https://git.bioconductor.org/packages/affyQCReport.git" + version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4') + version('1.60.0', commit='d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa') + version('1.58.0', commit='14be93a1e7a6d1a64c38ed2f53e0c52a389b2a1b') + version('1.56.0', commit='5c824045c7364155eafc2dd5bb342374aa1ca072') version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1') - depends_on('r@3.4.0:3.4.9', when='@1.54.0') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biobase@1.13.16:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-affyplm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py index bfbbdad428..eafc202fe9 100644 --- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py +++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py @@ -7,17 +7,23 @@ from spack import * class RAffyrnadegradation(RPackage): - """The package helps with the assessment and correction of - RNA degradation effects in Affymetrix 3' expression arrays. - The parameter d gives a robust and accurate measure of RNA - integrity. The correction removes the probe positional bias, - and thus improves comparability of samples that are affected - by RNA degradation.""" + """Analyze and correct probe positional bias in microarray data due to RNA + degradation. - homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/" + The package helps with the assessment and correction of RNA degradation + effects in Affymetrix 3' expression arrays. The parameter d gives a + robust and accurate measure of RNA integrity. The correction removes the + probe positional bias, and thus improves comparability of samples that + are affected by RNA degradation.""" + + homepage = "https://bioconductor.org/packages/AffyRNADegradation" git = "https://git.bioconductor.org/packages/AffyRNADegradation.git" + version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1') + version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24') + version('1.26.0', commit='6ab03ad624701464280bf7dfe345d200e846298a') + version('1.24.0', commit='1f85f3da4720cef94623828713eb84d8accbcf8a') version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3') - depends_on('r@3.4.0:3.4.9', when='@1.22.0') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py index c9bf147975..0754a8e66e 100644 --- a/var/spack/repos/builtin/packages/r-agdex/package.py +++ b/var/spack/repos/builtin/packages/r-agdex/package.py @@ -7,14 +7,20 @@ from spack import * class RAgdex(RPackage): - """A tool to evaluate agreement of differential expression - for cross-species genomics.""" + """Agreement of Differential Expression Analysis. - homepage = "http://bioconductor.org/packages/AGDEX/" + A tool to evaluate agreement of differential expression for cross- + species genomics""" + + homepage = "https://bioconductor.org/packages/AGDEX" git = "https://git.bioconductor.org/packages/AGDEX.git" + version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf') + version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b') + version('1.28.0', commit='7d78ee424485018b73cd019ceaed7a2ed53adf3f') + version('1.26.0', commit='260bc641111770176707d4d43e67b5877bf5eb82') version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-gseabase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py index 971c2c4b84..e1feadffcd 100644 --- a/var/spack/repos/builtin/packages/r-agilp/package.py +++ b/var/spack/repos/builtin/packages/r-agilp/package.py @@ -7,11 +7,17 @@ from spack import * class RAgilp(RPackage): - """Agilent expression array processing package.""" + """Agilent expression array processing package. - homepage = "http://bioconductor.org/packages/agilp/" + More about what it does (maybe more than one line)""" + + homepage = "https://bioconductor.org/packages/agilp" git = "https://git.bioconductor.org/packages/agilp.git" + version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47') + version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61') + version('3.12.0', commit='a86dea1b03b2b56c2c8317d4b10903fb8948ffcb') + version('3.10.0', commit='cffec1004704a0c5119a50e3ad474897978981be') version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53') - depends_on('r@3.4.0:3.4.9', when='@3.8.0') + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py index 8c905a69dc..421205830f 100644 --- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py +++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py @@ -7,16 +7,21 @@ from spack import * class RAgimicrorna(RPackage): - """Processing and Analysis of Agilent microRNA data.""" + """Processing and Differential Expression Analysis of Agilent microRNA + chips.""" - homepage = "https://www.bioconductor.org/packages/AgiMicroRna/" + homepage = "https://bioconductor.org/packages/AgiMicroRna" git = "https://git.bioconductor.org/packages/AgiMicroRna.git" + version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a') + version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8') + version('2.30.0', commit='99b5a8284cfe3e93c3ae85a2436e87101b9599dd') + version('2.28.0', commit='62c4a12f1168c7aa1ab46d2c97090ef71478328e') version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053') - depends_on('r@3.4.0:3.4.9', when='@2.26.0') - depends_on('r-affycoretools', type=('build', 'run')) - depends_on('r-preprocesscore', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-affy@1.22:', type=('build', 'run')) + depends_on('r-preprocesscore', type=('build', 'run')) + depends_on('r-affycoretools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py index baf7f878b6..38eba694b5 100644 --- a/var/spack/repos/builtin/packages/r-aims/package.py +++ b/var/spack/repos/builtin/packages/r-aims/package.py @@ -7,17 +7,23 @@ from spack import * class RAims(RPackage): - """This package contains the AIMS implementation. It contains - necessary functions to assign the five intrinsic molecular - subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, - Normal-like). Assignments could be done on individual samples - as well as on dataset of gene expression data.""" + """AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype. - homepage = "http://bioconductor.org/packages/AIMS/" + This package contains the AIMS implementation. It contains necessary + functions to assign the five intrinsic molecular subtypes (Luminal A, + Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be + done on individual samples as well as on dataset of gene expression + data.""" + + homepage = "https://bioconductor.org/packages/AIMS" git = "https://git.bioconductor.org/packages/AIMS.git" + version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84') + version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f') + version('1.12.0', commit='d7eaa723d19a6aca37df244fd0b3d5426ed0a626') + version('1.10.0', commit='972945980b39168502a02ac3aa396f9b99fb3d71') version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py index 856f7b50ae..0fc9a5c279 100644 --- a/var/spack/repos/builtin/packages/r-aldex2/package.py +++ b/var/spack/repos/builtin/packages/r-aldex2/package.py @@ -7,26 +7,33 @@ from spack import * class RAldex2(RPackage): - """A differential abundance analysis for the comparison of - two or more conditions. For example, single-organism and - meta-RNA-seq high-throughput sequencing assays, or of - selected and unselected values from in-vitro sequence selections. - Uses a Dirichlet-multinomial model to infer abundance from counts, - that has been optimized for three or more experimental replicates. - Infers sampling variation and calculates the expected false - discovery rate given the biological and sampling variation - using the Wilcox rank test or Welches t-test (aldex.ttest) or - the glm and Kruskal Wallis tests (aldex.glm). Reports both P - and fdr values calculated by the Benjamini Hochberg correction.""" - - homepage = "http://bioconductor.org/packages/ALDEx2/" + """Analysis Of Differential Abundance Taking Sample Variation Into Account. + + A differential abundance analysis for the comparison of two or more + conditions. Useful for analyzing data from standard RNA-seq or meta-RNA- + seq assays as well as selected and unselected values from in-vitro + sequence selections. Uses a Dirichlet-multinomial model to infer + abundance from counts, optimized for three or more experimental + replicates. The method infers biological and sampling variation to + calculate the expected false discovery rate, given the variation, based + on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a + Kruskal-Wallis test (via aldex.kw), a generalized linear model (via + aldex.glm), or a correlation test (via aldex.corr). All tests report + p-values and Benjamini-Hochberg corrected p-values.""" + + homepage = "https://bioconductor.org/packages/ALDEx2" git = "https://git.bioconductor.org/packages/ALDEx2.git" + version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f') + version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8') + version('1.12.0', commit='9efde428d22a0be1fe7b6655d45ddce8fcded180') + version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a') version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) + + depends_on('r-multtest', when='@1.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py index cb55456cb9..ee928e15b3 100644 --- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py +++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py @@ -7,24 +7,30 @@ from spack import * class RAllelicimbalance(RPackage): - """Provides a framework for allelic specific expression - investigation using RNA-seq data.""" + """Investigates Allele Specific Expression. - homepage = "http://bioconductor.org/packages/AllelicImbalance/" + Provides a framework for allelic specific expression investigation using + RNA-seq data.""" + + homepage = "https://bioconductor.org/packages/AllelicImbalance" git = "https://git.bioconductor.org/packages/AllelicImbalance.git" + version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a') + version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3') + version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea') + version('1.16.0', commit='85f652ae8a0dd15535819b6e934065182df5544a') version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c') - depends_on('r@3.4.0:3.4.9', when='@1.14.0') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run')) depends_on('r-genomicalignments', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-bsgenome', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-genomicfeatures', type=('build', 'run')) @@ -35,3 +41,15 @@ class RAllelicimbalance(RPackage): depends_on('r-seqinr', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run')) + + depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py index c169833a45..3aa1aec7d3 100644 --- a/var/spack/repos/builtin/packages/r-alpine/package.py +++ b/var/spack/repos/builtin/packages/r-alpine/package.py @@ -7,15 +7,21 @@ from spack import * class RAlpine(RPackage): - """Fragment sequence bias modeling and correction for RNA-seq - transcript abundance estimation.""" + """alpine. - homepage = "http://bioconductor.org/packages/alpine/" + Fragment sequence bias modeling and correction for RNA-seq transcript + abundance estimation.""" + + homepage = "https://bioconductor.org/packages/alpine" git = "https://git.bioconductor.org/packages/alpine.git" + version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c') + version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4') + version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274') + version('1.4.0', commit='c85beb208fd6bfc0a61a483a98498b589640f946') version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb') - depends_on('r@3.4.0:3.4.9', when='@1.2.0') + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py index 00a21e60ca..507fa456c3 100644 --- a/var/spack/repos/builtin/packages/r-alsace/package.py +++ b/var/spack/repos/builtin/packages/r-alsace/package.py @@ -7,18 +7,24 @@ from spack import * class RAlsace(RPackage): - """Alternating Least Squares (or Multivariate Curve Resolution) - for analytical chemical data, in particular hyphenated data where - the first direction is a retention time axis, and the second a - spectral axis. Package builds on the basic als function from the - ALS package and adds functionality for high-throughput analysis, - including definition of time windows, clustering of profiles, - retention time correction, etcetera.""" + """ALS for the Automatic Chemical Exploration of mixtures. - homepage = "https://www.bioconductor.org/packages/alsace/" + Alternating Least Squares (or Multivariate Curve Resolution) for + analytical chemical data, in particular hyphenated data where the first + direction is a retention time axis, and the second a spectral axis. + Package builds on the basic als function from the ALS package and adds + functionality for high-throughput analysis, including definition of time + windows, clustering of profiles, retention time correction, etcetera.""" + + homepage = "https://bioconductor.org/packages/alsace" git = "https://git.bioconductor.org/packages/alsace.git" + version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389') + version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191') + version('1.16.0', commit='5a51a19aeccbba0123222201cb7a228559f29653') + version('1.14.0', commit='aebb13b00eb850f9569391c4c92183b55b70ae89') version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-als', type=('build', 'run')) - depends_on('r-ptw', type=('build', 'run')) + depends_on('r-ptw@1.0.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py index b774502a26..b1d95c731b 100644 --- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py +++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py @@ -7,17 +7,23 @@ from spack import * class RAltcdfenvs(RPackage): - """Convenience data structures and functions to handle cdfenvs.""" + """alternative CDF environments (aka probeset mappings). - homepage = "https://www.bioconductor.org/packages/altcdfenvs/" + Convenience data structures and functions to handle cdfenvs""" + + homepage = "https://bioconductor.org/packages/altcdfenvs" git = "https://git.bioconductor.org/packages/altcdfenvs.git" + version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b') + version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133') + version('2.42.0', commit='00ec6461877a063d938494b8ed0cd273a3b20b85') + version('2.40.0', commit='517a208f49f168bdd3cde40ed216282c417237d7') version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291') - depends_on('r@3.4.0:3.4.9', when='@2.38.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.7:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-biobase@2.15.1:', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-makecdfenv', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py index 64009d8bd5..929ec04ce1 100644 --- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py +++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py @@ -7,26 +7,32 @@ from spack import * class RAmpliqueso(RPackage): - """The package provides tools and reports for the analysis of - amplicon sequencing panels, such as AmpliSeq.""" + """Analysis of amplicon enrichment panels. - homepage = "https://www.bioconductor.org/packages/ampliQueso/" + The package provides tools and reports for the analysis of amplicon + sequencing panels, such as AmpliSeq""" + + homepage = "https://bioconductor.org/packages/3.8/bioc/html/ampliQueso.html" git = "https://git.bioconductor.org/packages/ampliQueso.git" + version('1.21.0', commit='ed99c5194a452ee299a93e981da2224e4dab5bdd') + version('1.20.0', commit='ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8') + version('1.18.0', commit='c27fa51094135ef8da52cd2b34a27ec6454abd8e') + version('1.16.0', commit='25d2543ff9dedef4f966f999c95cdf87185d3bb3') version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b') - depends_on('r@3.4.0:3.4.9', when='@1.14.0') - depends_on('r-samr', type=('build', 'run')) - depends_on('r-deseq', type=('build', 'run')) - depends_on('r-edger', type=('build', 'run')) - depends_on('r-xtable', type=('build', 'run')) - depends_on('r-statmod', type=('build', 'run')) - depends_on('r-genefilter', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-doparallel', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-rgl', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-rnaseqmap@2.17.1:', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rnaseqmap', type=('build', 'run')) + depends_on('r-rgl', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gplots', type=('build', 'run')) + depends_on('r-doparallel', type=('build', 'run')) + depends_on('r-foreach', type=('build', 'run')) + depends_on('r-variantannotation', type=('build', 'run')) + depends_on('r-genefilter', type=('build', 'run')) + depends_on('r-statmod', type=('build', 'run')) + depends_on('r-xtable', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-deseq', type=('build', 'run')) + depends_on('r-samr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py index 8e71cc5a8e..257b9d2570 100644 --- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py +++ b/var/spack/repos/builtin/packages/r-analysispageserver/package.py @@ -7,15 +7,21 @@ from spack import * class RAnalysispageserver(RPackage): - """AnalysisPageServer is a modular system that enables sharing - of customizable R analyses via the web.""" + """A framework for sharing interactive data and plots from R through the + web. - homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/" + AnalysisPageServer is a modular system that enables sharing of + customizable R analyses via the web.""" + + homepage = "https://bioconductor.org/packages/AnalysisPageServer" git = "https://git.bioconductor.org/packages/AnalysisPageServer.git" + version('1.18.1', commit='08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630') + version('1.16.0', commit='67b063523f80e2af1d26262367ff50f34e195174') + version('1.14.0', commit='620c0ea1e129ddd1a0866e2c9d7c3fcf06a8baf4') + version('1.12.0', commit='146501974ef1938ee1ec4eb293ea7eeca331a0dc') version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50') - depends_on('r@3.4.0:3.4.9', when='@1.10.0') depends_on('r-log4r', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py index a8b13ab853..f188cae3f5 100644 --- a/var/spack/repos/builtin/packages/r-anaquin/package.py +++ b/var/spack/repos/builtin/packages/r-anaquin/package.py @@ -7,22 +7,28 @@ from spack import * class RAnaquin(RPackage): - """The project is intended to support the use of sequins - (synthetic sequencing spike-in controls) owned and made available - by the Garvan Institute of Medical Research. The goal is to - provide a standard open source library for quantitative analysis, - modelling and visualization of spike-in controls.""" + """Statistical analysis of sequins. - homepage = "https://www.bioconductor.org/packages/Anaquin/" + The project is intended to support the use of sequins (synthetic + sequencing spike-in controls) owned and made available by the Garvan + Institute of Medical Research. The goal is to provide a standard open + source library for quantitative analysis, modelling and visualization of + spike-in controls.""" + + homepage = "https://bioconductor.org/packages/Anaquin" git = "https://git.bioconductor.org/packages/Anaquin.git" + version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601') + version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6') + version('2.4.0', commit='0d6ae80ff622151a782e4774ca274f06024a71d2') + version('2.2.0', commit='739f4ed2b73c43f934fd65a993ecb48242a5d5da') version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119') - depends_on('r@3.4.0:3.4.9', when='@1.2.0') - depends_on('r-deseq2', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-locfit', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-rocr', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-knitr', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-locfit', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-deseq2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py index 9dc0384bf9..f623d35256 100644 --- a/var/spack/repos/builtin/packages/r-aneufinder/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py @@ -7,21 +7,28 @@ from spack import * class RAneufinder(RPackage): - """This package implements functions for CNV calling, plotting, - export and analysis from whole-genome single cell sequencing data.""" + """Analysis of Copy Number Variation in Single-Cell-Sequencing Data. - homepage = "https://www.bioconductor.org/packages/AneuFinder/" + AneuFinder implements functions for copy-number detection, breakpoint + detection, and karyotype and heterogeneity analysis in single-cell whole + genome sequencing and strand-seq data.""" + + homepage = "https://bioconductor.org/packages/AneuFinder" git = "https://git.bioconductor.org/packages/AneuFinder.git" + version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e') + version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd') + version('1.8.0', commit='36a729d244add5aafbe21c37a1baaea6a50354d3') + version('1.6.0', commit='0cfbdd1951fb4df5622e002260cfa86294d65d1d') version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e') - depends_on('r@3.4.0:3.4.9', when='@1.4.0') + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-cowplot', type=('build', 'run')) depends_on('r-aneufinderdata', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics', when='@1.4.0:1.6.0', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) @@ -33,6 +40,10 @@ class RAneufinder(RPackage): depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-ggdendro', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-reordercluster', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) - depends_on('r-ggrepel', type=('build', 'run')) + + depends_on('r-ecp', when='@1.8.0:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py index 4cee62c83c..c8773d6d1f 100644 --- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py @@ -7,12 +7,18 @@ from spack import * class RAneufinderdata(RPackage): - """Whole-genome single cell sequencing data for demonstration - purposes in the AneuFinder package.""" + """WGSCS Data for Demonstration Purposes. - homepage = "https://www.bioconductor.org/packages/AneuFinderData/" + Whole-genome single cell sequencing data for demonstration purposes in + the AneuFinder package.""" + + homepage = "https://bioconductor.org/packages/AneuFinderData" git = "https://git.bioconductor.org/packages/AneuFinderData.git" + version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1') + version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035') + version('1.8.0', commit='4f00f8d5f2e968fea667a7feafc0a4607d6e0c6e') + version('1.6.0', commit='8fe5b221619aab75fe84c9094708d240dd1e6730') version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40') - depends_on('r@3.4.0:3.4.9', when='@1.4.0') + depends_on('r@3.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index ba0481bda2..07f62db7ea 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -3,24 +3,29 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# -# from spack import * class RAnnaffy(RPackage): - """Functions for handling data from Bioconductor Affymetrix - annotation data packages. Produces compact HTML and text - reports including experimental data and URL links to many - online databases. Allows searching biological metadata - using various criteria.""" + """Annotation tools for Affymetrix biological metadata. + + Functions for handling data from Bioconductor Affymetrix annotation data + packages. Produces compact HTML and text reports including experimental + data and URL links to many online databases. Allows searching biological + metadata using various criteria.""" - homepage = "https://www.bioconductor.org/packages/annaffy/" + homepage = "https://bioconductor.org/packages/annaffy" git = "https://git.bioconductor.org/packages/annaffy.git" + version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233') + version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484') + version('1.52.0', commit='ef84030163045f702941c8d5a59fbd4a09f30e2c') + version('1.50.0', commit='a822e20f3e961a8afa5eb23536343115a33fb259') version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.5.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-go-db', type=('build', 'run')) depends_on('r-kegg-db', type=('build', 'run')) + depends_on('r-annotationdbi@0.1.15:', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index 5fc2ba5c2d..c0dd6f3fc4 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -7,17 +7,24 @@ from spack import * class RAnnotate(RPackage): - """Using R enviroments for annotation.""" + """Annotation for microarrays. - homepage = "https://www.bioconductor.org/packages/annotate/" + Using R enviroments for annotation.""" + + homepage = "https://bioconductor.org/packages/annotate" git = "https://git.bioconductor.org/packages/annotate.git" + version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd') + version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16') version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc') + version('1.56.2', commit='95ec3b004f5356bd78b2a60cbf7f93e0d48cf346') version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.5:', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-rcurl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py index 8c917104ef..d19912d9c6 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -7,19 +7,28 @@ from spack import * class RAnnotationdbi(RPackage): - """Provides user interface and database connection code for - annotation data packages using SQLite data storage.""" + """Manipulation of SQLite-based annotations in Bioconductor. - homepage = "https://www.bioconductor.org/packages/AnnotationDbi/" + Implements a user-friendly interface for querying SQLite-based + annotation data packages.""" + + homepage = "https://bioconductor.org/packages/AnnotationDbi" git = "https://git.bioconductor.org/packages/AnnotationDbi.git" + version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9') + version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac') version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3') + version('1.40.0', commit='e34dff07e10402eecbf95604a512bc1fc4edb127') version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36') - depends_on('r@3.4.0:3.4.9', when='@1.38.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.42.1', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-biobase@1.17.0:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py index 5e76c4f6a5..8788e1f38e 100644 --- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py +++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py @@ -7,16 +7,21 @@ from spack import * class RAnnotationfilter(RPackage): - """This package provides class and other infrastructure to implement - filters for manipulating Bioconductor annotation resources. The - filters will be used by ensembldb, Organism.dplyr, and other - packages.""" + """Facilities for Filtering Bioconductor Annotation Resources. - homepage = "https://bioconductor.org/packages/AnnotationFilter/" + This package provides class and other infrastructure to implement + filters for manipulating Bioconductor annotation resources. The filters + will be used by ensembldb, Organism.dplyr, and other packages.""" + + homepage = "https://bioconductor.org/packages/AnnotationFilter" git = "https://git.bioconductor.org/packages/AnnotationFilter.git" + version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed') + version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3') + version('1.4.0', commit='acbd3309f478843a7899bd9773af5f19f986b829') + version('1.2.0', commit='744b82915d7b85031de462d9d0a2bf9fdfd0e29d') version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9') + depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.0.0') diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py index fbf7d266ff..385d520b08 100644 --- a/var/spack/repos/builtin/packages/r-annotationforge/package.py +++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py @@ -7,19 +7,24 @@ from spack import * class RAnnotationforge(RPackage): - """Provides code for generating Annotation packages and - their databases. Packages produced are intended to be used - with AnnotationDbi.""" + """Tools for building SQLite-based annotation data packages. - homepage = "https://www.bioconductor.org/packages/AnnotationForge/" + Provides code for generating Annotation packages and their databases. + Packages produced are intended to be used with AnnotationDbi.""" + + homepage = "https://bioconductor.org/packages/AnnotationForge" git = "https://git.bioconductor.org/packages/AnnotationForge.git" + version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e') + version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d') + version('1.22.2', commit='8eafb1690c1c02f6291ccbb38ac633d54b8217f8') + version('1.20.0', commit='7b440f1570cb90acce8fe2fa8d3b5ac34f638882') version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1') - depends_on('r@3.4.0:3.4.9', when='@1.18.2') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-biobase@1.17.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.14:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py index 0465d3c126..1dbf83c759 100644 --- a/var/spack/repos/builtin/packages/r-annotationhub/package.py +++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py @@ -7,25 +7,39 @@ from spack import * class RAnnotationhub(RPackage): - """This package provides a client for the Bioconductor AnnotationHub web + """Client to access AnnotationHub resources. + + This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from - standard locations (e.g., UCSC, Ensembl) can be discovered. The - resource includes metadata about each resource, e.g., a textual - description, tags, and date of modification. The client creates and - manages a local cache of files retrieved by the user, helping with - quick and reproducible access.""" + standard locations (e.g., UCSC, Ensembl) can be discovered. The resource + includes metadata about each resource, e.g., a textual description, + tags, and date of modification. The client creates and manages a local + cache of files retrieved by the user, helping with quick and + reproducible access.""" - homepage = "https://bioconductor.org/packages/AnnotationHub/" + homepage = "https://bioconductor.org/packages/AnnotationHub" git = "https://git.bioconductor.org/packages/AnnotationHub.git" + version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed') + version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12') + version('2.12.1', commit='471407bd9cdc612e01deb071c91bd9e5f1ea5e55') + version('2.10.1', commit='b7cb668de9b9625ac2beb3dcde1fa39e289eec29') version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c') + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-annotationdbi@1.31.19:', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-interactivedisplaybase', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.8.3') + + depends_on('r-curl', when='@2.10.1:', type=('build', 'run')) + + depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run')) + + depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run')) + depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run')) + depends_on('r-dplyr', when='@2.16.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py index c296426285..78992b44db 100644 --- a/var/spack/repos/builtin/packages/r-bamsignals/package.py +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -7,20 +7,30 @@ from spack import * class RBamsignals(RPackage): - """This package allows to efficiently obtain count vectors - from indexed bam files. It counts the number of reads in given - genomic ranges and it computes reads profiles and coverage - profiles. It also handles paired-end data.""" + """Extract read count signals from bam files. - homepage = "https://www.bioconductor.org/packages/bamsignals/" + This package allows to efficiently obtain count vectors from indexed bam + files. It counts the number of reads in given genomic ranges and it + computes reads profiles and coverage profiles. It also handles paired- + end data.""" + + homepage = "https://bioconductor.org/packages/bamsignals" git = "https://git.bioconductor.org/packages/bamsignals.git" + version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657') + version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d') + version('1.12.1', commit='06b6282df377cf9db58e8016be4ac8ddcc960939') + version('1.10.0', commit='7499312ce71e8680680eda10b49d7dff682fc776') version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.10.6:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-rhtslib', type=('build', 'run')) + + depends_on('r-rhtslib@1.12.1:', when='@1.12.1:', type=('build', 'run')) + + depends_on('r-rhtslib@1.13.1:', when='@1.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py new file mode 100644 index 0000000000..00aeba6f4b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-beachmat/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBeachmat(RPackage): + """Compiling Bioconductor to Handle Each Matrix Type. + + Provides a consistent C++ class interface for reading from and writing + data to a variety of commonly used matrix types. Ordinary matrices and + several sparse/dense Matrix classes are directly supported, third-party + S4 classes may be supported by external linkage, while all other + matrices are handled by DelayedArray block processing.""" + + homepage = "https://bioconductor.org/packages/beachmat" + git = "https://git.bioconductor.org/packages/beachmat.git" + + version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab') + version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a') + version('1.2.1', commit='ebae81772045a314e568c2f7d73ea3b27e7bf7d8') + version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-rcpp@0.12.14:', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-rhdf5', when='@1.0.2:1.4.0', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run')) + depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run')) + depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run')) + + depends_on('r-hdf5array@1.9.5:', when='@1.4.0', type=('build', 'run')) + depends_on('r-delayedarray@0.7.38:', when='@1.4.0', type=('build', 'run')) + depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-beeswarm/package.py b/var/spack/repos/builtin/packages/r-beeswarm/package.py new file mode 100644 index 0000000000..0e0a8597ed --- /dev/null +++ b/var/spack/repos/builtin/packages/r-beeswarm/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBeeswarm(RPackage): + """beeswarm: The Bee Swarm Plot, an Alternative to Stripchart""" + + homepage = "http://www.cbs.dtu.dk/~eklund/beeswarm/" + url = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm" + + version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843') diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py index 1ff0d25de5..baeb3de55e 100644 --- a/var/spack/repos/builtin/packages/r-biobase/package.py +++ b/var/spack/repos/builtin/packages/r-biobase/package.py @@ -3,21 +3,25 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -# from spack import * class RBiobase(RPackage): - """Functions that are needed by many other packages - or which replace R functions.""" + """Biobase: Base functions for Bioconductor. + + Functions that are needed by many other packages or which replace R + functions.""" - homepage = "https://www.bioconductor.org/packages/Biobase/" + homepage = "https://bioconductor.org/packages/Biobase" git = "https://git.bioconductor.org/packages/Biobase.git" + version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3') + version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d') version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5') version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424') version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075') - depends_on('r-biocgenerics@0.16.1:', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.36.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.40.0', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@2.42.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py new file mode 100644 index 0000000000..c31a255d61 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocfilecache(RPackage): + """Manage Files Across Sessions. + + This package creates a persistent on-disk cache of files that the user + can add, update, and retrieve. It is useful for managing resources (such + as custom Txdb objects) that are costly or difficult to create, web + resources, and data files used across sessions.""" + + homepage = "https://bioconductor.org/packages/BiocFileCache" + git = "https://git.bioconductor.org/packages/BiocFileCache.git" + + version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0') + version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba') + version('1.4.0', commit='a2c473d17f78899c7899b9638faea8c30735eb80') + version('1.2.3', commit='d78bf5b46c8a329f5ddef879fe51230444bc42f8') + version('1.0.1', commit='dbf4e8dd4d8d9f475066cd033481efe95c56df75') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-dbplyr@1.0.0:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) + depends_on('r-rappdirs', type=('build', 'run')) + depends_on('r-httr', type=('build', 'run')) + + depends_on('r-curl', when='@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py index 347bcc22bc..04f2ceecdd 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -7,16 +7,17 @@ from spack import * class RBiocgenerics(RPackage): - """S4 generic functions needed by many Bioconductor packages.""" + """S4 generic functions used in Bioconductor. - homepage = "https://www.bioconductor.org/packages/BiocGenerics/" + The package defines S4 generic functions used in Bioconductor.""" + + homepage = "https://bioconductor.org/packages/BiocGenerics" git = "https://git.bioconductor.org/packages/BiocGenerics.git" version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8') + version('0.28.0', commit='041fc496504f2ab1d4d863fffb23372db214394b') version('0.26.0', commit='5b2a6df639e48c3cd53789e0b174aec9dda6b67d') version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1') version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad') - depends_on('r@3.4.0:3.4.9', when='@0.22.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.26.0', type=('build', 'run')) - depends_on('r@3.6.0:', when='@0.30.0', type=('build', 'run')) + depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py index fe1e132691..ef78d9f819 100644 --- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py +++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py @@ -7,12 +7,20 @@ from spack import * class RBiocinstaller(RPackage): - """This package is used to install and update Bioconductor, CRAN, - and (some) github packages.""" + """Install/Update Bioconductor, CRAN, and github Packages. - homepage = "https://bioconductor.org/packages/BiocInstaller/" + This package is used to install and update Bioconductor, CRAN, and + (some) github packages.""" + + homepage = "https://bioconductor.org/packages/3.8/bioc/html/BiocInstaller.html" git = "https://git.bioconductor.org/packages/BiocInstaller.git" + version('1.33.1', commit='6193f31c18e7e64d91e0e15ed0ba6924eda1416f') + version('1.32.1', commit='4c2a39e1cae470af3a5cf1491715f272b70f4bb4') + version('1.30.0', commit='27bcb7a378cb5d8b5d23b7b840340463f7e090bc') + version('1.28.0', commit='7261763529a0a1f730cde8a1bbdbf454c3e25603') version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98') - depends_on('r@3.4.0:3.4.9', when='@1.26.1') + depends_on('r@3.4.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocmanager/package.py b/var/spack/repos/builtin/packages/r-biocmanager/package.py new file mode 100644 index 0000000000..d5f24dc3b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocmanager/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocmanager(RPackage): + """BiocManager: Access the Bioconductor Project Package Repository""" + + homepage = "https://cloud.r-project.org/package=BiocManager" + url = "https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BiocManager" + + version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e') diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py new file mode 100644 index 0000000000..82ed74150d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocneighbors(RPackage): + """Nearest Neighbor Detection for Bioconductor Packages. + + Implements exact and approximate methods for nearest neighbor detection, + in a framework that allows them to be easily switched within + Bioconductor packages or workflows. Exact searches can be performed + using the k-means for k-nearest neighbors algorithm or with vantage + point trees. Approximate searches can be performed using the Annoy or + HNSW libraries. Searching on either Euclidean or Manhattan distances is + supported. Parallelization is achieved for all methods by using + BiocParallel. Functions are also provided to search for all neighbors + within a given distance.""" + + homepage = "https://bioconductor.org/packages/BiocNeighbors" + git = "https://git.bioconductor.org/packages/BiocNeighbors.git" + + version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273') + version('1.0.0', commit='e252fc04b6d22097f2c5f74406e77d85e7060770') + + depends_on('r@3.5:', when='@1.0.0', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-rcppannoy', type=('build', 'run')) + + depends_on('r-biocgenerics', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py index cee7cffd53..d572d477ae 100644 --- a/var/spack/repos/builtin/packages/r-biocparallel/package.py +++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py @@ -7,18 +7,22 @@ from spack import * class RBiocparallel(RPackage): - """This package provides modified versions and novel implementation of + """Bioconductor facilities for parallel evaluation. + + This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.""" - homepage = "https://bioconductor.org/packages/BiocParallel/" + homepage = "https://bioconductor.org/packages/BiocParallel" git = "https://git.bioconductor.org/packages/BiocParallel.git" + version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e') + version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4') version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299') + version('1.12.0', commit='2143a9addceed0151a27b95c70aadd2add5cbace') version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d') depends_on('r-futile-logger', type=('build', 'run')) depends_on('r-snow', type=('build', 'run')) - depends_on('r-bh', type=('build', 'link', 'run'), when='@1.14.2:') - depends_on('r@3.4.0:3.4.9', when='@1.10.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.14.2', type=('build', 'run')) + + depends_on('r-bh', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py new file mode 100644 index 0000000000..80ded9c70f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RBiocsingular(RPackage): + """Singular Value Decomposition for Bioconductor Packages. + + Implements exact and approximate methods for singular value + decomposition and principal components analysis, in a framework that + allows them to be easily switched within Bioconductor packages or + workflows. Where possible, parallelization is achieved using the + BiocParallel framework.""" + + homepage = "https://bioconductor.org/packages/BiocSingular" + git = "https://git.bioconductor.org/packages/BiocSingular.git" + + version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833') + + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-irlba', type=('build', 'run')) + depends_on('r-rsvd', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-beachmat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py index d3d0435c6b..be6812681d 100644 --- a/var/spack/repos/builtin/packages/r-biocstyle/package.py +++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py @@ -7,16 +7,23 @@ from spack import * class RBiocstyle(RPackage): - """Provides standard formatting styles for Bioconductor PDF and HTML - documents. Package vignettes illustrate use and functionality.""" + """Standard styles for vignettes and other Bioconductor documents. - homepage = "https://www.bioconductor.org/packages/BiocStyle/" + Provides standard formatting styles for Bioconductor PDF and HTML + documents. Package vignettes illustrate use and functionality.""" + + homepage = "https://bioconductor.org/packages/BiocStyle" git = "https://git.bioconductor.org/packages/BiocStyle.git" + version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498') + version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70') + version('2.8.2', commit='3210c19ec1e5e0ed8d5a2d31da990aa47b42dbd8') + version('2.6.1', commit='5ff52cbb439a45575d0f58c4f7a83195a8b7337b') version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138') depends_on('r-bookdown', type=('build', 'run')) depends_on('r-knitr@1.12:', type=('build', 'run')) depends_on('r-rmarkdown@1.2:', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.4.1') + + depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py index 6e82f30218..c22736083b 100644 --- a/var/spack/repos/builtin/packages/r-biomart/package.py +++ b/var/spack/repos/builtin/packages/r-biomart/package.py @@ -7,22 +7,26 @@ from spack import * class RBiomart(RPackage): - """In recent years a wealth of biological data has become available in + """Interface to BioMart databases (i.e. Ensembl). + + In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite - (http://www.biomart.org). The package enables retrieval of large amounts - of data in a uniform way without the need to know the underlying - database schemas or write complex SQL queries. Examples of BioMart - databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and - dbSNP mapped to Ensembl. These major databases give biomaRt users direct - access to a diverse set of data and enable a wide range of powerful - online queries from gene annotation to database mining.""" - - homepage = "https://bioconductor.org/packages/biomaRt/" + (<http://www.biomart.org>). The package enables retrieval of large + amounts of data in a uniform way without the need to know the underlying + database schemas or write complex SQL queries. The most prominent + examples of BioMart databases are maintain by Ensembl, which provides + biomaRt users direct access to a diverse set of data and enables a wide + range of powerful online queries from gene annotation to database + mining.""" + + homepage = "https://bioconductor.org/packages/biomaRt" git = "https://git.bioconductor.org/packages/biomaRt.git" + version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68') + version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658') version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f') version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b') version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f') @@ -30,8 +34,7 @@ class RBiomart(RPackage): depends_on('r-xml', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-progress', type=('build', 'run'), when='@2.34.2:') - depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:') - depends_on('r-httr', type=('build', 'run'), when='@2.34.2:') - depends_on('r@3.4.0:3.4.9', when='@2.32.1:2.35.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.36.1', type=('build', 'run')) + + depends_on('r-progress', when='@2.34.2:', type=('build', 'run')) + depends_on('r-stringr', when='@2.34.2:', type=('build', 'run')) + depends_on('r-httr', when='@2.34.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py index 4a5382beae..e797b9aa5b 100644 --- a/var/spack/repos/builtin/packages/r-biomformat/package.py +++ b/var/spack/repos/builtin/packages/r-biomformat/package.py @@ -7,23 +7,29 @@ from spack import * class RBiomformat(RPackage): - """This is an R package for interfacing with the BIOM format. This - package includes basic tools for reading biom-format files, accessing - and subsetting data tables from a biom object (which is more complex - than a single table), as well as limited support for writing a - biom-object back to a biom-format file. The design of this API is - intended to match the python API and other tools included with the - biom-format project, but with a decidedly "R flavor" that should be - familiar to R users. This includes S4 classes and methods, as well - as extensions of common core functions/methods.""" + """An interface package for the BIOM file format. - homepage = "https://www.bioconductor.org/packages/biomformat/" + This is an R package for interfacing with the BIOM format. This package + includes basic tools for reading biom-format files, accessing and + subsetting data tables from a biom object (which is more complex than a + single table), as well as limited support for writing a biom-object back + to a biom-format file. The design of this API is intended to match the + python API and other tools included with the biom-format project, but + with a decidedly "R flavor" that should be familiar to R users. This + includes S4 classes and methods, as well as extensions of common core + functions/methods.""" + + homepage = "https://bioconductor.org/packages/biomformat" git = "https://git.bioconductor.org/packages/biomformat.git" + version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a') + version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09') + version('1.8.0', commit='acd207377b24e4d8310eaff06c16dcfe6c04509a') + version('1.6.0', commit='61fb8c7b34ad561c3c46cacc0dd1957be56da85e') version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a') - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-plyr@1.8:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) + depends_on('r-matrix@1.2:', type=('build', 'run')) depends_on('r-rhdf5', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.4.0') diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py index d57e9d8a44..6a04a28bc7 100644 --- a/var/spack/repos/builtin/packages/r-biostrings/package.py +++ b/var/spack/repos/builtin/packages/r-biostrings/package.py @@ -7,23 +7,34 @@ from spack import * class RBiostrings(RPackage): - """Memory efficient string containers, string matching algorithms, and - other utilities, for fast manipulation of large biological sequences - or sets of sequences.""" + """Efficient manipulation of biological strings. - homepage = "https://bioconductor.org/packages/Biostrings/" + Memory efficient string containers, string matching algorithms, and + other utilities, for fast manipulation of large biological sequences or + sets of sequences.""" + + homepage = "https://bioconductor.org/packages/Biostrings" git = "https://git.bioconductor.org/packages/Biostrings.git" + version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5') + version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2') version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b') + version('2.46.0', commit='3bf6978c155498b50607d1bb471d1687d185a0fa') version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.15.6:', when='@2.48.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@2.48.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', when='@2.44.2:2.46.0', type=('build', 'run')) + depends_on('r-xvector@0.11.6:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.25:', when='@2.48.0:', type=('build', 'run')) depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.8:', when='@2.48.0', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.44.2', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.48.0', type=('build', 'run')) + depends_on('r-xvector@0.19.8:', when='@2.48.0:', type=('build', 'run')) + + depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run')) + depends_on('r-xvector@0.21.4:', when='@2.50.2:', type=('build', 'run')) + depends_on('r-iranges', when='@2.50.2:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.13:', when='@2.52.0:', type=('build', 'run')) + depends_on('r-xvector@0.23.2:', when='@2.52.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py index f26e3325a8..7353aee800 100644 --- a/var/spack/repos/builtin/packages/r-biovizbase/package.py +++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py @@ -7,33 +7,40 @@ from spack import * class RBiovizbase(RPackage): - """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.""" + """Basic graphic utilities for visualization of genomic data.. - homepage = "http://bioconductor.org/packages/biovizBase/" + 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" git = "https://git.bioconductor.org/packages/biovizBase.git" + version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8') + version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82') + version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063') + version('1.26.0', commit='640742f48384f01d117b70dc5c64737e97ae9b4b') version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c') - depends_on('r@3.4.0:3.4.9', when='@1.24.0') + depends_on('r@2.10:', type=('build', 'run')) 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')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + 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')) depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + 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')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-ensembldb', type=('build', 'run')) - depends_on('r-annotationfilter', type=('build', 'run')) + 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')) diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py index 1578380eb7..1edef3ee35 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py @@ -7,25 +7,36 @@ from spack import * class RBsgenome(RPackage): - """Infrastructure shared by all the Biostrings-based genome data - packages.""" + """Software infrastructure for efficient representation of full genomes and + their SNPs.""" - homepage = "https://www.bioconductor.org/packages/BSgenome/" + homepage = "https://bioconductor.org/packages/BSgenome" git = "https://git.bioconductor.org/packages/BSgenome.git" + version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b') + version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9') + version('1.48.0', commit='092a1b90482ace329cbd8ca2a338e91449acb93e') version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5') version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0') + depends_on('r@2.8.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) depends_on('r-s4vectors@0.9.36:', type=('build', 'run')) - depends_on('r-iranges@2.1.33:', type=('build', 'run'), when='@1.44.2') - depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0') - depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'), when='@1.44.2') - depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0') - depends_on('r-genomicranges@1.27.6:', type=('build', 'run'), when='@1.44.2') - depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0') + depends_on('r-iranges@2.1.33:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) depends_on('r-biostrings@2.35.3:', type=('build', 'run')) depends_on('r-rtracklayer@1.25.8:', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.44.2:') + depends_on('r-rsamtools', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py index 797bf43f25..74d909f8b9 100644 --- a/var/spack/repos/builtin/packages/r-bumphunter/package.py +++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py @@ -7,15 +7,22 @@ from spack import * class RBumphunter(RPackage): - """Tools for finding bumps in genomic data""" + """Bump Hunter. - homepage = "http://bioconductor.org/packages/bumphunter/" + Tools for finding bumps in genomic data""" + + homepage = "https://bioconductor.org/packages/bumphunter" git = "https://git.bioconductor.org/packages/bumphunter.git" + version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa') + version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b') + version('1.22.0', commit='fb71b193f4ef7fa12d100441e6eb498765f7afde') + version('1.20.0', commit='c9d8e7ab0c19299988e5d7fa74970312e9a1eac0') version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a') - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@2.3.23:', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) @@ -27,4 +34,7 @@ class RBumphunter(RPackage): depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-genomicfeatures', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.0') + + depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py index 85f4455a6b..a79df91e07 100644 --- a/var/spack/repos/builtin/packages/r-category/package.py +++ b/var/spack/repos/builtin/packages/r-category/package.py @@ -7,14 +7,20 @@ from spack import * class RCategory(RPackage): - """A collection of tools for performing category analysis.""" + """Category Analysis. - homepage = "https://www.bioconductor.org/packages/Category/" + A collection of tools for performing category (gene set enrichment) + analysis.""" + + homepage = "https://bioconductor.org/packages/Category" git = "https://git.bioconductor.org/packages/Category.git" + version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9') + version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5') + version('2.46.0', commit='c8aeee4dee3fb120f25e0647dd06e895a3ffbc2a') + version('2.44.0', commit='eaba50c1a801ba7983e6ffdf41ab0fc9cfe5a626') version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd') - depends_on('r@3.4.0:3.4.9', when='@2.42.1') depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index 6ce8e29ecf..19bb113916 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -7,8 +7,9 @@ from spack import * class RChemometrics(RPackage): - """R companion to the book "Introduction to Multivariate Statistical Analysis - in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).""" + """R companion to the book "Introduction to Multivariate Statistical + Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser + (2009).""" homepage = "https://cloud.r-project.org/package=chemometrics" url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" diff --git a/var/spack/repos/builtin/packages/r-clue/package.py b/var/spack/repos/builtin/packages/r-clue/package.py new file mode 100644 index 0000000000..c8cf1c0278 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-clue/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RClue(RPackage): + """clue: Cluster Ensembles""" + + homepage = "https://cloud.r-project.org/package=clue" + url = "https://cloud.r-project.org/src/contrib/clue_0.3-57.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clue" + + version('0.3-57', sha256='6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py index 88a3b3107b..a1571f37f1 100644 --- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py +++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py @@ -7,22 +7,36 @@ from spack import * class RClusterprofiler(RPackage): - """This package implements methods to analyze and visualize functional - profiles (GO and KEGG) of gene and gene clusters.""" + """statistical analysis and visualization of functional profiles for genes + and gene clusters. - homepage = "https://www.bioconductor.org/packages/clusterProfiler/" + This package implements methods to analyze and visualize functional + profiles (GO and KEGG) of gene and gene clusters.""" + + homepage = "https://bioconductor.org/packages/clusterProfiler" git = "https://git.bioconductor.org/packages/clusterProfiler.git" + version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2') + version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c') + version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36') + version('3.6.0', commit='ff15e3dba69b93bc872d5f5d07821cd9ae20d829') version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7') - depends_on('r@3.4.0:3.4.9', when='@3.4.4') - depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-rvcheck', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-gosemsim', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.3.1:', type=('build', 'run')) + depends_on('r-dose@3.1.3:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-dose', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-go-db', type=('build', 'run')) + depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run')) + depends_on('r-gosemsim', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-rvcheck', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) + + depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index bc06676d85..c3c9bc83af 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -7,22 +7,29 @@ from spack import * class RCner(RPackage): - """"Large-scale identification and advanced visualization of sets of - conserved noncoding elements.""" + """CNE Detection and Visualization. - homepage = "https://bioconductor.org/packages/CNEr/" + Large-scale identification and advanced visualization of sets of + conserved noncoding elements.""" + + homepage = "https://bioconductor.org/packages/CNEr" git = "https://git.bioconductor.org/packages/CNEr.git" + version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5') + version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606') + version('1.16.1', commit='a2bec4b98d5938709f959a69c151f553ef357941') version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897') + version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017') + depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-biostrings@2.33.4:', type=('build', 'run')) - depends_on('r-dbi@0.7:', type=('build', 'run')) depends_on('r-rsqlite@0.11.4:', type=('build', 'run')) depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) depends_on('r-genomicranges@1.23.16:', type=('build', 'run')) depends_on('r-rtracklayer@1.25.5:', type=('build', 'run')) depends_on('r-xvector@0.5.4:', type=('build', 'run')) depends_on('r-genomicalignments@1.1.9:', type=('build', 'run')) + depends_on('r-dbi@0.6:', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) depends_on('r-iranges@2.5.27:', type=('build', 'run')) depends_on('r-readr@0.2.2:', type=('build', 'run')) @@ -32,6 +39,8 @@ class RCner(RPackage): depends_on('r-powerlaw@0.60.3:', type=('build', 'run')) depends_on('r-annotate@1.50.0:', type=('build', 'run')) depends_on('r-go-db@3.3.0:', type=('build', 'run')) - depends_on('r-keggrest@1.14.0:', type=('build', 'run')) depends_on('r-r-utils@2.3.0:', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.14.0') + depends_on('r-keggrest@1.14.0:', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run')) + depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py index 7cf86dfd66..a824995318 100644 --- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py @@ -7,20 +7,34 @@ from spack import * class RComplexheatmap(RPackage): - """Complex heatmaps are efficient to visualize associations between - different sources of data sets and reveal potential structures. Here - the ComplexHeatmap package provides a highly flexible way to arrange - multiple heatmaps and supports self-defined annotation graphics.""" + """Make Complex Heatmaps. - homepage = "https://bioconductor.org/packages/ComplexHeatmap/" + Complex heatmaps are efficient to visualize associations between + different sources of data sets and reveal potential patterns. Here the + ComplexHeatmap package provides a highly flexible way to arrange + multiple heatmaps and supports various annotation graphics.""" + + homepage = "https://bioconductor.org/packages/ComplexHeatmap" git = "https://git.bioconductor.org/packages/ComplexHeatmap.git" + version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4') + version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f') + version('1.18.1', commit='be0dd9d666a219c61335efe0dac50b2eed2a8825') + version('1.17.1', commit='f647c97e556d9e918a17be15883a0b72a91d688f') version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34') - depends_on('r-circlize', type=('build', 'run')) + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-circlize@0.3.4:', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-dendextend', type=('build', 'run')) - depends_on('r-globaloptions', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') + depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', type=('build', 'run')) + depends_on('r-globaloptions@0.0.10:', type=('build', 'run')) + + depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run')) + + depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', type=('build', 'run')) + + depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-clue', when='@2.0.0:', type=('build', 'run')) + depends_on('r-png', when='@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py index 8c8c170072..47b9c4a0ab 100644 --- a/var/spack/repos/builtin/packages/r-ctc/package.py +++ b/var/spack/repos/builtin/packages/r-ctc/package.py @@ -7,13 +7,18 @@ from spack import * class RCtc(RPackage): - """Tools for export and import classification trees and clusters - to other programs""" + """Cluster and Tree Conversion.. - homepage = "https://www.bioconductor.org/packages/release/bioc/html/ctc.html" + Tools for export and import classification trees and clusters to other + programs""" + + homepage = "https://bioconductor.org/packages/ctc" git = "https://git.bioconductor.org/packages/ctc.git" + version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb') + version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f') version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e') + version('1.52.0', commit='ffff8693cab5ebad610d139367f089418f1830a1') + version('1.50.0', commit='4ee7519c3e5172e140c2658b4cf5271d229acc7e') depends_on('r-amap', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.54.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py index 10652164c8..93c2915f9c 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -7,37 +7,42 @@ from spack import * class RDelayedarray(RPackage): - """Wrapping an array-like object (typically an on-disk object) in a - DelayedArray object allows one to perform common array operations on it - without loading the object in memory. In order to reduce memory usage - and optimize performance, operations on the object are either delayed - or executed using a block processing mechanism. Note that this also - works on in-memory array-like objects like DataFrame objects (typically - with Rle columns), Matrix objects, and ordinary arrays and data frames. + """A unified framework for working transparently with on-disk and in-memory + array-like datasets. + Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage - and optimize performance, operations on the object are either delayed - or executed using a block processing mechanism. Note that this also - works on in-memory array-like objects like DataFrame objects (typically - with Rle columns), Matrix objects, and ordinary arrays and data - frames.""" + and optimize performance, operations on the object are either delayed or + executed using a block processing mechanism. Note that this also works + on in-memory array-like objects like DataFrame objects (typically with + Rle columns), Matrix objects, and ordinary arrays and data frames.""" - homepage = "https://bioconductor.org/packages/DelayedArray/" + homepage = "https://bioconductor.org/packages/DelayedArray" git = "https://git.bioconductor.org/packages/DelayedArray.git" - version('0.6.5', commit='7d1cb6477cb024c38bf1ee0c9155e010249ed94e') + version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a') + version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f') + version('0.6.6', commit='bdb0ac0eee71edd40ccca4808f618fa77f595a64') version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1') version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4') - depends_on('r-biocparallel', when='@0.6.5:', type=('build', 'run')) + depends_on('r@3.4:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@0.6.5', type=('build', 'run')) - depends_on('r-s4vectors@0.14.3:', when='@0.2.7', type=('build', 'run')) - depends_on('r-s4vectors@0.15.3:', when='@0.4.1', type=('build', 'run')) - depends_on('r-s4vectors@0.17.43:', when='@0.6.5', type=('build', 'run')) + depends_on('r-s4vectors@0.14.3:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.2.7', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.6.5', type=('build', 'run')) + + depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run')) + depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', type=('build', 'run')) + depends_on('r-biocparallel', when='@0.6.6:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.19.15:', when='@0.8.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.7:', when='@0.10.0:', type=('build', 'run')) + depends_on('r-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run')) + depends_on('r-matrix', when='@0.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py new file mode 100644 index 0000000000..47253903ce --- /dev/null +++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDelayedmatrixstats(RPackage): + """Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects. + + A port of the 'matrixStats' API for use with DelayedMatrix objects from + the 'DelayedArray' package. High-performing functions operating on rows + and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / + rowRanks(), and col / rowSds(). Functions optimized per data type and + for subsetted calculations such that both memory usage and processing + time is minimized.""" + + homepage = "https://bioconductor.org/packages/DelayedMatrixStats" + git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git" + + version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d') + version('1.4.0', commit='eb5b390ef99651fe87a346848f807de95afe8971') + version('1.2.0', commit='de868e730be6280dfad41a280ab09f4d3083c9ac') + version('1.0.3', commit='e29a3444980ff727c5b12286884b06dfaebf5b5b') + + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-matrixstats@0.53.1:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + + depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-biocparallel', when='@1.4.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py index dc60c09f45..d7cdac0f7c 100644 --- a/var/spack/repos/builtin/packages/r-deseq/package.py +++ b/var/spack/repos/builtin/packages/r-deseq/package.py @@ -7,18 +7,24 @@ from spack import * class RDeseq(RPackage): - """Estimate variance-mean dependence in count data from - high-throughput sequencing assays and test for differential - expression based on a model using the negative binomial - distribution.""" + """Differential gene expression analysis based on the negative binomial + distribution. - homepage = "https://www.bioconductor.org/packages/DESeq/" + Estimate variance-mean dependence in count data from high-throughput + sequencing assays and test for differential expression based on a model + using the negative binomial distribution""" + + homepage = "https://bioconductor.org/packages/DESeq" git = "https://git.bioconductor.org/packages/DESeq.git" + version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e') + version('1.34.1', commit='e86f1b03a30bc02de4bfd4a0759af2f65cb48c62') + version('1.32.0', commit='e3d623b815b53d79eae7cdd09d097cc6098d28c9') + version('1.30.0', commit='90c93d991dd980d538c13b0361d3345f9546794e') version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.5:', type=('build', 'run')) + depends_on('r-biobase@2.21.7:', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index ac9f7257de..2690978df8 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -7,24 +7,27 @@ from spack import * class RDeseq2(RPackage): - """Estimate variance-mean dependence in count data from - high-throughput sequencing assays and test for differential - expression based on a model using the negative binomial - distribution.""" + """Differential gene expression analysis based on the negative binomial + distribution. - homepage = "https://www.bioconductor.org/packages/DESeq2/" + Estimate variance-mean dependence in count data from high-throughput + sequencing assays and test for differential expression based on a model + using the negative binomial distribution.""" + + homepage = "https://bioconductor.org/packages/DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" + version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf') + version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce') version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c') version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7') - version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5') + version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb') - depends_on("r-rcpparmadillo", type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.5:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) @@ -32,6 +35,5 @@ class RDeseq2(RPackage): depends_on('r-geneplotter', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcpparmadillo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py index 02e911d5d6..1ef0a4aea1 100644 --- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py +++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py @@ -7,19 +7,25 @@ from spack import * class RDirichletmultinomial(RPackage): - """Dirichlet-multinomial mixture models can be used to describe - variability in microbial metagenomic data. + """Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome + Data. - This package is an interface to code originally made available by - Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed - further in the man page for this package, ?DirichletMultinomial.""" + Dirichlet-multinomial mixture models can be used to describe variability + in microbial metagenomic data. This package is an interface to code + originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE + 7(2): 1-15, as discussed further in the man page for this package, + ?DirichletMultinomial.""" - homepage = "https://bioconductor.org/packages/DirichletMultinomial/" + homepage = "https://bioconductor.org/packages/DirichletMultinomial" git = "https://git.bioconductor.org/packages/DirichletMultinomial.git" + version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f') + version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35') + version('1.22.0', commit='5864f4298105d12f345f27df77ad13bae4061ca5') version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272') + version('1.18.0', commit='81ccc8d83b8ef84f5d3e877bc0a04233a0f63c51') depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) depends_on('gsl') - depends_on('r@3.4.0:') diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py index 85bbd55e3c..7a96d1c4fb 100644 --- a/var/spack/repos/builtin/packages/r-dnacopy/package.py +++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py @@ -7,11 +7,17 @@ from spack import * class RDnacopy(RPackage): - """Implements the circular binary segmentation (CBS) algorithm - to segment DNA copy number data and identify genomic regions - with abnormal copy number.""" + """DNA copy number data analysis. - homepage = "https://www.bioconductor.org/packages/DNAcopy/" + Implements the circular binary segmentation (CBS) algorithm to segment + DNA copy number data and identify genomic regions with abnormal copy + number.""" + + homepage = "https://bioconductor.org/packages/DNAcopy" git = "https://git.bioconductor.org/packages/DNAcopy.git" + version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23') + version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a') + version('1.54.0', commit='fe2657936afbce8ee03221461dff4265e3ded4c4') + version('1.52.0', commit='2632fbecec4cef3705b85676942a59188ae9bba4') version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8') diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py index 8313f4997e..a363d126a5 100644 --- a/var/spack/repos/builtin/packages/r-dose/package.py +++ b/var/spack/repos/builtin/packages/r-dose/package.py @@ -7,27 +7,37 @@ from spack import * class RDose(RPackage): - """This package implements five methods proposed by Resnik, Schlicker, - Jiang, Lin and Wang respectively for measuring semantic similarities - among DO terms and gene products. Enrichment analyses including - hypergeometric model and gene set enrichment analysis are also - implemented for discovering disease associations of high-throughput - biological data.""" - - homepage = "https://www.bioconductor.org/packages/DOSE/" + """Disease Ontology Semantic and Enrichment analysis. + + This package implements five methods proposed by Resnik, Schlicker, + Jiang, Lin and Wang respectively for measuring semantic similarities + among DO terms and gene products. Enrichment analyses including + hypergeometric model and gene set enrichment analysis are also + implemented for discovering disease associations of high-throughput + biological data.""" + + homepage = "https://bioconductor.org/packages/DOSE" git = "https://git.bioconductor.org/packages/DOSE.git" + version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3') + version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639') + version('3.6.1', commit='f2967f0482cea39222bfd15767d0f4a5994f241b') + version('3.4.0', commit='dabb70de1a0f91d1767601e871f2f1c16d29a612') version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b') - depends_on('r@3.4.0:3.4.9', when='@3.2.0') - depends_on('r-scales', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-qvalue', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-gosemsim', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-fgsea', type=('build', 'run')) - depends_on('r-do-db', type=('build', 'run')) - depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r@3.3.1:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-do-db', type=('build', 'run')) + depends_on('r-fgsea', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gosemsim@2.0.0:', type=('build', 'run')) + depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run')) + depends_on('r-qvalue', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-scales', when='@3.2.0:3.4.0', type=('build', 'run')) + + depends_on('r-rvcheck', when='@3.4.0', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ecp/package.py b/var/spack/repos/builtin/packages/r-ecp/package.py new file mode 100644 index 0000000000..44828d7f90 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ecp/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REcp(RPackage): + """ecp: Non-Parametric Multiple Change-Point Analysis of + MultivariateData""" + + homepage = "https://cloud.r-project.org/package=ecp" + url = "https://cloud.r-project.org/src/contrib/ecp_3.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ecp" + + version('3.1.1', sha256='d2ab194e22e6ab0168222fbccfcf2e25c6cd51a73edc959086b0c6e0a7410268') + + depends_on('r@3.00:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py index b8c2036b56..d6ac1bc488 100644 --- a/var/spack/repos/builtin/packages/r-edger/package.py +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -7,22 +7,30 @@ from spack import * class REdger(RPackage): - """Differential expression analysis of RNA-seq expression profiles with + """Empirical Analysis of Digital Gene Expression Data in R. + + Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, - SAGE and CAGE.""" + Bisulfite-seq, SAGE and CAGE.""" - homepage = "https://bioconductor.org/packages/edgeR/" + homepage = "https://bioconductor.org/packages/edgeR" git = "https://git.bioconductor.org/packages/edgeR.git" - version('3.22.3', commit='e82e54afc9398ac54dc4caba0f7ae5c43e572203') + version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f') + version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d') + version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902') + version('3.20.9', commit='acbcbbee939f399673678653678cd9cb4917c4dc') version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495') + depends_on('r@2.15.0:', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'link', 'run')) - depends_on('r@3.5.0:3.5.9', when='@3.22.3') - depends_on('r@3.4.0:3.4.9', when='@3.18.1') + + depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run')) + depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run')) + + depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py new file mode 100644 index 0000000000..782b865595 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REnrichplot(RPackage): + """Visualization of Functional Enrichment Result. + + The 'enrichplot' package implements several visualization methods for + interpreting functional enrichment results obtained from ORA or GSEA + analysis. All the visualization methods are developed based on 'ggplot2' + graphics.""" + + homepage = "https://bioconductor.org/packages/enrichplot" + git = "https://git.bioconductor.org/packages/enrichplot.git" + + version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e') + version('1.2.0', commit='2eeaafb571d35a106eba8ae7df014f3201066e8b') + version('1.0.2', commit='ba7726fa0d4b581b7514dcbb04889cdbdd75ff29') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-cowplot', type=('build', 'run')) + depends_on('r-dose@3.5.1:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggraph', type=('build', 'run')) + depends_on('r-ggridges', type=('build', 'run')) + depends_on('r-gosemsim', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-upsetr', type=('build', 'run')) + + depends_on('r-europepmc', when='@1.2.0:', type=('build', 'run')) + depends_on('r-ggplotify', when='@1.2.0:', type=('build', 'run')) + depends_on('r-gridextra', when='@1.2.0:', type=('build', 'run')) + depends_on('r-purrr', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rcolorbrewer', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py index ec31c4a9e2..71311bd6a9 100644 --- a/var/spack/repos/builtin/packages/r-ensembldb/package.py +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -7,36 +7,54 @@ from spack import * class REnsembldb(RPackage): - """The package provides functions to create and use transcript centric + """Utilities to create and use Ensembl-based annotation databases. + + The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all - gene/transcript models and annotations from the database, the ensembldb - package provides also a filter framework allowing to retrieve - annotations for specific entries like genes encoded on a chromosome - region or transcript models of lincRNA genes.""" + gene/transcript models and annotations from the database, ensembldb + provides a filter framework allowing to retrieve annotations for + specific entries like genes encoded on a chromosome region or transcript + models of lincRNA genes. EnsDb databases built with ensembldb contain + also protein annotations and mappings between proteins and their + encoding transcripts. Finally, ensembldb provides functions to map + between genomic, transcript and protein coordinates.""" - homepage = "https://bioconductor.org/packages/ensembldb/" + homepage = "https://bioconductor.org/packages/ensembldb" git = "https://git.bioconductor.org/packages/ensembldb.git" + version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0') + version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c') + version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327') + version('2.2.2', commit='d71610e58aed88dbbe6a74e7a8ddfb7451398060') version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r-annotationfilter', type=('build', 'run')) - depends_on('r-rsqlite', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-genomicranges@1.23.21:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run')) + depends_on('r-annotationfilter@0.99.7:', type=('build', 'run')) + depends_on('r-rsqlite@1.1:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r-annotationdbi@1.31.19:', type=('build', 'run')) depends_on('r-rtracklayer', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-annotationhub', type=('build', 'run')) + depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', type=('build', 'run')) + + depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run')) + depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run')) + depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run')) + + depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-europepmc/package.py b/var/spack/repos/builtin/packages/r-europepmc/package.py new file mode 100644 index 0000000000..6cd644a759 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-europepmc/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REuropepmc(RPackage): + """europepmc: R Interface to the Europe PubMed Central RESTful Web + Service""" + + homepage = "http://github.com/ropensci/europepmc/" + url = "https://cloud.r-project.org/src/contrib/europepmc_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/europepmc" + + version('0.3', sha256='5044a253d223e2bb8502063cd03c0fe4db856467e497d650da7ccd8f75d0f8d9') + + depends_on('r@3.00:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-httr', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-progress', type=('build', 'run')) + depends_on('r-purrr', type=('build', 'run')) + depends_on('r-urltools', type=('build', 'run')) + depends_on('r-xml2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-farver/package.py b/var/spack/repos/builtin/packages/r-farver/package.py new file mode 100644 index 0000000000..855b679532 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-farver/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFarver(RPackage): + """farver: High Performance Colour Space Manipulation""" + + homepage = "https://github.com/thomasp85/farver" + url = "https://cloud.r-project.org/src/contrib/farver_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/farver" + + version('2.0.1', sha256='1642ca1519ef80616ab044ae7f6eaf464118356f2a7875e9d0e3df60ca84012b') diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py index 81bff39da6..04da77c0cd 100644 --- a/var/spack/repos/builtin/packages/r-fgsea/package.py +++ b/var/spack/repos/builtin/packages/r-fgsea/package.py @@ -7,20 +7,30 @@ from spack import * class RFgsea(RPackage): - """The package implements an algorithm for fast gene set enrichment - analysis. Using the fast algorithm allows to make more permutations - and get more fine grained p-values, which allows to use accurate - stantard approaches to multiple hypothesis correction.""" + """Fast Gene Set Enrichment Analysis. - homepage = "https://www.bioconductor.org/packages/fgsea/" + The package implements an algorithm for fast gene set enrichment + analysis. Using the fast algorithm allows to make more permutations and + get more fine grained p-values, which allows to use accurate stantard + approaches to multiple hypothesis correction.""" + + homepage = "https://bioconductor.org/packages/fgsea" git = "https://git.bioconductor.org/packages/fgsea.git" + version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3') + version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b') + version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d') + version('1.4.1', commit='73de5ff364e520ac99507a9ee5a61a0d23d3c44e') version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72') - depends_on('r@3.4.0:3.4.9', when='@1.2.1') - depends_on('r-fastmatch', type=('build', 'run')) - depends_on('r-gridextra', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-data-table', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-data-table', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-fastmatch', type=('build', 'run')) + + depends_on('r-matrix', when='@1.6.0:', type=('build', 'run')) + + depends_on('r-bh', when='@1.10.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py index 2a78008960..6a45cef8e9 100644 --- a/var/spack/repos/builtin/packages/r-gcrma/package.py +++ b/var/spack/repos/builtin/packages/r-gcrma/package.py @@ -7,17 +7,23 @@ from spack import * class RGcrma(RPackage): - """Background adjustment using sequence information""" + """Background Adjustment Using Sequence Information.""" - homepage = "https://bioconductor.org/packages/gcrma/" + homepage = "https://bioconductor.org/packages/gcrma" git = "https://git.bioconductor.org/packages/gcrma.git" + version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224') + version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc') + version('2.52.0', commit='d6e90b05432d2a8b0583d3fed001811ecdf49d7d') + version('2.50.0', commit='cbba460d131e1073059500b8d7b168a78f963992') version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4') - depends_on('r-affy', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-affy@1.23.2:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) + depends_on('r-affyio@1.13.3:', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biostrings@2.11.32:', type=('build', 'run')) depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.48.0') + + depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py index 960f98f1f4..b388b0d373 100644 --- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -7,22 +7,28 @@ from spack import * class RGdsfmt(RPackage): - """This package provides a high-level R interface to CoreArray Genomic - Data Structure (GDS) data files, which are portable across platforms - with hierarchical structure to store multiple scalable array-oriented - data sets with metadata information. It is suited for large-scale - datasets, especially for data which are much larger than the available - random-access memory. The gdsfmt package offers the efficient - operations specifically designed for integers of less than 8 bits, - since a diploid genotype, like single-nucleotide polymorphism (SNP), - usually occupies fewer bits than a byte. Data compression and - decompression are available with relatively efficient random access. - It is also allowed to read a GDS file in parallel with multiple R - processes supported by the package parallel.""" + """R Interface to CoreArray Genomic Data Structure (GDS) Files. - homepage = "http://bioconductor.org/packages/gdsfmt/" + This package provides a high-level R interface to CoreArray Genomic Data + Structure (GDS) data files, which are portable across platforms with + hierarchical structure to store multiple scalable array-oriented data + sets with metadata information. It is suited for large-scale datasets, + especially for data which are much larger than the available random- + access memory. The gdsfmt package offers the efficient operations + specifically designed for integers of less than 8 bits, since a diploid + genotype, like single-nucleotide polymorphism (SNP), usually occupies + fewer bits than a byte. Data compression and decompression are available + with relatively efficient random access. It is also allowed to read a + GDS file in parallel with multiple R processes supported by the package + parallel.""" + + homepage = "https://bioconductor.org/packages/gdsfmt" git = "https://git.bioconductor.org/packages/gdsfmt.git" + version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00') + version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9') + version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95') version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d') + version('1.12.0', commit='d705a95b0bea7be2a2b37e939f45017337ba0fb6') - depends_on('r@3.4.0:3.4.9', when='@1.14.1') + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index 73eebbd357..c94e3dee03 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -7,17 +7,20 @@ from spack import * class RGenefilter(RPackage): - """Some basic functions for filtering genes""" + """genefilter: methods for filtering genes from high-throughput + experiments.""" - homepage = "https://bioconductor.org/packages/genefilter/" + homepage = "https://bioconductor.org/packages/genefilter" git = "https://git.bioconductor.org/packages/genefilter.git" + version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf') + version('1.64.0', commit='82e91b7751bae997b9c898c219ea201fd02a8512') version('1.62.0', commit='eb119894f015c759f93f458af7733bdb770a22ad') + version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4') version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2') - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.9.42:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.58.1', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.62.0', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py index e569d285c2..17b7e76392 100644 --- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py +++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py @@ -7,14 +7,20 @@ from spack import * class RGenelendatabase(RPackage): - """Length of mRNA transcripts for a number of genomes and gene ID - formats, largely based on UCSC table browser""" + """Lengths of mRNA transcripts for a number of genomes. - homepage = "https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html" + Length of mRNA transcripts for a number of genomes and gene ID formats, + largely based on UCSC table browser""" + + homepage = "https://bioconductor.org/packages/geneLenDataBase" git = "https://git.bioconductor.org/packages/geneLenDataBase.git" + version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4') + version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07') version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198') + version('1.14.0', commit='b456b3ffb04eaf335893fdec2bb10f6795dd7e08') + version('1.12.0', commit='85d6536763c12850e6c01da9e2f9e0b9c07601fe') - depends_on('r@3.5.0:3.5.9', when='@1.16.0:', type=('build', 'run')) + depends_on('r@2.11.0:', type=('build', 'run')) depends_on('r-rtracklayer', type=('build', 'run')) depends_on('r-genomicfeatures@1.3.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py new file mode 100644 index 0000000000..75276b47f0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-genemeta/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGenemeta(RPackage): + """MetaAnalysis for High Throughput Experiments. + + A collection of meta-analysis tools for analysing high throughput + experimental data""" + + homepage = "https://bioconductor.org/packages/GeneMeta" + git = "https://git.bioconductor.org/packages/GeneMeta.git" + + version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d') + version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7') + version('1.52.0', commit='1f21759984a5852c42a19e89ee53ffd72053d49c') + version('1.50.0', commit='0f8603653285698ed451fcbf536a4b3f90015f92') + version('1.48.0', commit='68c65304d37f5a4722cf4c25afb23214c3a2f4c8') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) + depends_on('r-genefilter', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py index d1794933df..1c9362e515 100644 --- a/var/spack/repos/builtin/packages/r-geneplotter/package.py +++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py @@ -7,19 +7,21 @@ from spack import * class RGeneplotter(RPackage): - """Functions for plotting genomic data.""" + """Graphics related functions for Bioconductor.""" - homepage = "https://www.bioconductor.org/packages/geneplotter/" + homepage = "https://bioconductor.org/packages/geneplotter" git = "https://git.bioconductor.org/packages/geneplotter.git" + version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48') + version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad') version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde') + version('1.56.0', commit='881d25aece3dc00cc4280457ffecdc25e93bb1f1') version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py index b86edd6c00..ebe6e6e4e3 100644 --- a/var/spack/repos/builtin/packages/r-genie3/package.py +++ b/var/spack/repos/builtin/packages/r-genie3/package.py @@ -7,13 +7,17 @@ from spack import * class RGenie3(RPackage): - """This package implements the GENIE3 algorithm for inferring gene - regulatory networks from expression data.""" + """GEne Network Inference with Ensemble of trees. - homepage = "https://bioconductor.org/packages/GENIE3/" + This package implements the GENIE3 algorithm for inferring gene + regulatory networks from expression data.""" + + homepage = "https://bioconductor.org/packages/GENIE3" git = "https://git.bioconductor.org/packages/GENIE3.git" - version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93') + version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502') + version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08') + version('1.2.1', commit='1b56fe8184d521d1bb247f000efe9e2b540604c9') + version('1.0.0', commit='eb7c95ed12ea50d61e8fa20bc2b25ae9d74c302f') depends_on('r-reshape2', type=('build', 'run')) - depends_on('r@3.5.0:', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index bbf6bf0609..6f5fa9f8da 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -7,25 +7,29 @@ from spack import * class RGenomeinfodb(RPackage): - """Contains data and functions that define and allow translation between - different chromosome sequence naming conventions (e.g., "chr1" - versus "1"), including a function that attempts to place sequence - names in their natural, rather than lexicographic, order.""" + """Utilities for manipulating chromosome names, including modifying them to + follow a particular naming style. - homepage = "https://bioconductor.org/packages/GenomeInfoDb/" + Contains data and functions that define and allow translation between + different chromosome sequence naming conventions (e.g., "chr1" versus + "1"), including a function that attempts to place sequence names in + their natural, rather than lexicographic, order.""" + + homepage = "https://bioconductor.org/packages/GenomeInfoDb" git = "https://git.bioconductor.org/packages/GenomeInfoDb.git" + version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265') + version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f') version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa') version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6') version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.13.8:', when='@1.16.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.16.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.12:', when='@1.16.0', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@1.99.26:', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-genomeinfodbdata', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.12.3', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index ea436ffaef..cb07c47095 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -13,8 +13,11 @@ class RGenomeinfodbdata(RPackage): homepage = "https://bioconductor.org/packages/GenomeInfoDbData/" url = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" + version('1.2.1', sha256='75e6d683a29b8baeec66ba5194aa59a6aa69b04fae5a9c718a105c155fb41711', + url='https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz') version('1.1.0', sha256='6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c', url='https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz') version('0.99.0', sha256='457049804bbd70f218c1c84067a23e83bdecb7304a3e4d8b697fee0b16dc1888') - depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run')) + + depends_on('r@3.3:', when='@0.99.0:1.1.0', type=('build', 'run')) + depends_on('r@3.5:', when='@1.2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py index 3ffe5c5cf7..6d35d306d5 100644 --- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py +++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py @@ -7,35 +7,44 @@ from spack import * class RGenomicalignments(RPackage): - """Provides efficient containers for storing and manipulating short genomic - alignments (typically obtained by aligning short reads to a reference - genome). This includes read counting, computing the coverage, junction - detection, and working with the nucleotide content of the alignments.""" + """Representation and manipulation of short genomic alignments. - homepage = "https://bioconductor.org/packages/GenomicAlignments/" + Provides efficient containers for storing and manipulating short genomic + alignments (typically obtained by aligning short reads to a reference + genome). This includes read counting, computing the coverage, junction + detection, and working with the nucleotide content of the alignments.""" + + homepage = "https://bioconductor.org/packages/GenomicAlignments" git = "https://git.bioconductor.org/packages/GenomicAlignments.git" + version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd') + version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab') version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974') version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef') version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) - depends_on('r-s4vectors@0.17.28:', when='@1.16.0', type=('build', 'run')) - depends_on('r-iranges@2.5.36:', when='@1.12.2', type=('build', 'run')) - depends_on('r-iranges@2.11.16:', when='@1.14.2', type=('build', 'run')) - depends_on('r-iranges@2.13.25:', when='@1.16.0', type=('build', 'run')) - depends_on('r-genomeinfodb@1.11.5:', when='@1.12.2', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run')) - depends_on('r-genomicranges@1.27.19:', when='@1.12.2', type=('build', 'run')) - depends_on('r-genomicranges@1.29.14:', when='@1.14.2', type=('build', 'run')) - depends_on('r-genomicranges@1.31.19:', when='@1.16.0', type=('build', 'run')) + depends_on('r-iranges@2.5.36:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.19:', type=('build', 'run')) depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run')) - depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0', type=('build', 'run')) depends_on('r-biostrings@2.37.1:', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.16.0', type=('build', 'run')) depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) - depends_on('r-rsamtools@1.31.2:', when='@1.16.0', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.15.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py index 48015bbebd..693aebf13d 100644 --- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -7,7 +7,9 @@ from spack import * class RGenomicfeatures(RPackage): - """A set of tools and methods for making and manipulating transcript + """Conveniently import and query gene models. + + A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources @@ -16,35 +18,40 @@ class RGenomicfeatures(RPackage): exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.""" - homepage = "http://bioconductor.org/packages/GenomicFeatures/" + homepage = "https://bioconductor.org/packages/GenomicFeatures" git = "https://git.bioconductor.org/packages/GenomicFeatures.git" - version('1.32.2', commit='8487aedc8be85a99f0c3fc90cd62430b3fec3a03') + version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555') + version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387') + version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1') + version('1.30.3', commit='496bbf81beebd7c934b8d3dcea001e3e4a7d7dee') version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.29:', when='@1.32.2', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.23:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.4:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicranges@1.31.17:', when='@1.32.2', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-annotationdbi@1.41.4:', when='@1.32.2', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) + depends_on('r-iranges@2.9.19:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.15:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) - depends_on('r-rsqlite@2.0:', when='@1.28.5:', type=('build', 'run')) + depends_on('r-rsqlite@2.0:', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-rtracklayer@1.39.7:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biomart', type=('build', 'run')) - depends_on('r-biomart@2.17.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biobase@2.15.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.5', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run')) + depends_on('r-biostrings@2.23.3:', type=('build', 'run')) + depends_on('r-rtracklayer@1.29.24:', type=('build', 'run')) + depends_on('r-biomart@2.17.1:', type=('build', 'run')) + depends_on('r-biobase@2.15.1:', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-rmysql', when='@1.30.3', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py index 887d32f988..4a2312c1d6 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -7,35 +7,45 @@ from spack import * class RGenomicranges(RPackage): - """The ability to efficiently represent and manipulate genomic annotations + """Representation and manipulation of genomic intervals. + + The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are - defined in the GenomicAlignments and SummarizedExperiment packages + defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.""" - homepage = "https://bioconductor.org/packages/GenomicRanges/" + homepage = "https://bioconductor.org/packages/GenomicRanges" git = "https://git.bioconductor.org/packages/GenomicRanges.git" - version('1.32.6', commit='31426be0fd6b76f7858971dc45aaf6e6d1dbac4e') + version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a') + version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd') + version('1.32.7', commit='4c56dc836dbfd0d228dc810e8d401811cdbc267c') version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997') version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics@0.21.2:', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.3:', when='@1.32.6', type=('build', 'run')) depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) - depends_on('r-s4vectors@0.17.32:', when='@1.32.6', type=('build', 'run')) - depends_on('r-iranges@2.9.11:', when='@1.28.6', type=('build', 'run')) - depends_on('r-iranges@2.11.16:', when='@1.30.3', type=('build', 'run')) - depends_on('r-iranges@2.14.4:', when='@1.32.6', type=('build', 'run')) - depends_on('r-genomeinfodb@1.11.5:', when='@1.28.6', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.2:', when='@1.32.6', type=('build', 'run')) + depends_on('r-iranges@2.9.11:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.8:', when='@1.32.6', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.6', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.6', type=('build', 'run')) + + depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.3:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@1.34.0:', type=('build', 'run')) + + depends_on('r-iranges@2.17.1:', when='@1.36.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py index e2451534a4..261c4a4de6 100644 --- a/var/spack/repos/builtin/packages/r-geoquery/package.py +++ b/var/spack/repos/builtin/packages/r-geoquery/package.py @@ -7,18 +7,32 @@ from spack import * class RGeoquery(RPackage): - """The NCBI Gene Expression Omnibus (GEO) is a public repository of - microarray data. Given the rich and varied nature of this resource, - it is only natural to want to apply BioConductor tools to these data. + """Get data from NCBI Gene Expression Omnibus (GEO). + + The NCBI Gene Expression Omnibus (GEO) is a public repository of + microarray data. Given the rich and varied nature of this resource, it + is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.""" - homepage = "https://bioconductor.org/packages/GEOquery/" + homepage = "https://bioconductor.org/packages/GEOquery" git = "https://git.bioconductor.org/packages/GEOquery.git" + version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643') + version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97') + version('2.48.0', commit='6a8d1ca195b5c26fb717ae93beb1a8d9b7031c5e') + version('2.46.15', commit='a52b195ac640caae9679610d5b486b7cb828c0fd') version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb') depends_on('r-biobase', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-xml', when='@2.42.0', type=('build', 'run')) + depends_on('r-rcurl', when='@2.42.0', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.42.0') + + depends_on('r-readr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-xml2', when='@2.46.15:', type=('build', 'run')) + depends_on('r-dplyr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-tidyr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-magrittr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-limma', when='@2.46.15:', type=('build', 'run')) + + depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py new file mode 100644 index 0000000000..67c613c38d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggbeeswarm/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgbeeswarm(RPackage): + """ggbeeswarm: Categorical Scatter (Violin Point) Plots""" + + homepage = "https://github.com/eclarke/ggbeeswarm" + url = "https://cloud.r-project.org/src/contrib/ggbeeswarm_0.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggbeeswarm" + + version('0.6.0', sha256='bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333') + + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-beeswarm', type=('build', 'run')) + depends_on('r-ggplot2@2.0:', type=('build', 'run')) + depends_on('r-vipor', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py index b4918a8a1f..ed9529a4c4 100644 --- a/var/spack/repos/builtin/packages/r-ggbio/package.py +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -7,43 +7,59 @@ from spack import * class RGgbio(RPackage): - """The ggbio package extends and specializes the grammar of graphics for + """Visualization tools for genomic data. + + The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence - fragment length, edge-linked interval to data view, mismatch pileup, - and several splicing summaries.""" + fragment length, edge-linked interval to data view, mismatch pileup, and + several splicing summaries.""" - homepage = "http://bioconductor.org/packages/ggbio/" + homepage = "https://bioconductor.org/packages/ggbio" git = "https://git.bioconductor.org/packages/ggbio.git" + version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88') + version('1.30.0', commit='8b05258b089b06a743352e92058edda06c24cfb7') + version('1.28.5', commit='594521ca556ef7d97cf4882ecfa54d22c2a2faba') + version('1.26.1', commit='b4f4c898c92aa1082aa7574f1e5c2a0dae943fbc') version('1.24.1', commit='ef04c1bca1330f37152bcc21080cbde94849a094') + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-ggplot2@1.0.0:', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-gtable', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-biovizbase', type=('build', 'run')) + depends_on('r-biovizbase@1.23.3:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.10:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-genomicalignments', 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-bsgenome', type=('build', 'run')) - depends_on('r-variantannotation', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-variantannotation@1.11.4:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.16:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.17.13:', type=('build', 'run')) depends_on('r-organismdbi', type=('build', 'run')) depends_on('r-ggally', type=('build', 'run')) - depends_on('r-ensembldb', type=('build', 'run')) + depends_on('r-ensembldb@1.99.13:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annotationfilter', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.24.1') + + depends_on('r-iranges@2.11.16:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run')) + + depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run')) + depends_on('r-rlang', when='@1.28.5:', type=('build', 'run')) + + depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggforce/package.py b/var/spack/repos/builtin/packages/r-ggforce/package.py new file mode 100644 index 0000000000..1e934b3f27 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggforce/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgforce(RPackage): + """ggforce: Accelerating 'ggplot2'""" + + homepage = "https://ggforce.data-imaginist.com" + url = "https://cloud.r-project.org/src/contrib/ggforce_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggforce" + + version('0.3.1', sha256='a05271da9b226c12ae5fe6bc6eddb9ad7bfe19e1737e2bfcd6d7a89631332211') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-polyclip', type=('build', 'run')) + depends_on('r-rcpp@0.12.2:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-tidyselect', type=('build', 'run')) + depends_on('r-tweenr@0.1.5:', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggplotify/package.py b/var/spack/repos/builtin/packages/r-ggplotify/package.py new file mode 100644 index 0000000000..b41672be89 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggplotify/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgplotify(RPackage): + """ggplotify: Convert Plot to 'grob' or 'ggplot' Object""" + + homepage = "https://github.com/GuangchuangYu/ggplotify" + url = "https://cloud.r-project.org/src/contrib/ggplotify_0.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggplotify" + + version('0.0.3', sha256='7e7953a2933aa7127a0bac54375e3e0219a0744cfc3249c3d7b76065f7a51892') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gridgraphics', type=('build', 'run')) + depends_on('r-rvcheck', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggraph/package.py b/var/spack/repos/builtin/packages/r-ggraph/package.py new file mode 100644 index 0000000000..32f2b28fff --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggraph/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgraph(RPackage): + """ggraph: An Implementation of Grammar of Graphics for Graphs and + Networks""" + + homepage = "https://github.com/thomasp85/ggraph" + url = "https://cloud.r-project.org/src/contrib/ggraph_2.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggraph" + + version('2.0.0', sha256='4307efe85bfc6a0496797f6b86d6b174ba196538c51b1a6b6af55de0d4e04762') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.2', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-ggforce@0.3.1:', type=('build', 'run')) + depends_on('r-igraph@1.0.0:', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-tidygraph', type=('build', 'run')) + depends_on('r-graphlayouts@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py index 3e943d719c..e2a2aec250 100644 --- a/var/spack/repos/builtin/packages/r-glimma/package.py +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -7,18 +7,28 @@ from spack import * class RGlimma(RPackage): - """This package generates interactive visualisations for analysis of - RNA-sequencing data using output from limma, edgeR or DESeq2 packages - in an HTML page. The interactions are built on top of the popular - static representations of analysis results in order to provide - additional information.""" + """Interactive HTML graphics. - homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html" + This package generates interactive visualisations for analysis of RNA- + sequencing data using output from limma, edgeR or DESeq2 packages in an + HTML page. The interactions are built on top of the popular static + representations of analysis results in order to provide additional + information.""" + + homepage = "https://bioconductor.org/packages/Glimma" git = "https://git.bioconductor.org/packages/Glimma.git" - version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969') + version('1.12.0', commit='d02174239fe0b47983d6947ed42a1a53b24caecb') + version('1.10.1', commit='ffc7abc36190396598fadec5e9c653441e47be72') + version('1.8.2', commit='7696aca2c023f74d244b6c908a6e7ba52bfcb34b') + version('1.6.0', commit='57572996982806aa7ac155eedb97b03249979610') + version('1.4.0', commit='c613c5334ed7868f36d5716b97fdb6234fb291f8') - depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biobase', when='@1.4.0:1.6.0', type=('build', 'run')) depends_on('r-edger', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-scater', when='@1.4.0', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py new file mode 100644 index 0000000000..93319705e7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGofuncr(RPackage): + """Gene ontology enrichment using FUNC. + + GOfuncR performs a gene ontology enrichment analysis based on the + ontology enrichment software FUNC. GO-annotations are obtained from + OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph + is included in the package and updated regularly (27-Mar-2019). GOfuncR + provides the standard candidate vs. background enrichment analysis using + the hypergeometric test, as well as three additional tests: (i) the + Wilcoxon rank-sum test that is used when genes are ranked, (ii) a + binomial test that is used when genes are associated with two counts and + (iii) a Chi-square or Fisher's exact test that is used in cases when + genes are associated with four counts. To correct for multiple testing + and interdependency of the tests, family-wise error rates are computed + based on random permutations of the gene-associated variables. GOfuncR + also provides tools for exploring the ontology graph and the + annotations, and options to take gene-length or spatial clustering of + genes into account. It is also possible to provide custom gene + coordinates, annotations and ontologies.""" + + homepage = "https://bioconductor.org/packages/GOfuncR" + git = "https://git.bioconductor.org/packages/GOfuncR.git" + + version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709') + version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded') + version('1.0.0', commit='becd4ddde085c5477042adb856e7a4f40dbd648e') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-vioplot@0.2:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-mapplots@1.5:', type=('build', 'run')) + depends_on('r-gtools@3.5.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.28.4:', type=('build', 'run')) + depends_on('r-annotationdbi', type=('build', 'run')) + + depends_on('r-iranges', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py index 0077bb011e..58b10a5239 100644 --- a/var/spack/repos/builtin/packages/r-gosemsim/package.py +++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py @@ -7,20 +7,28 @@ from spack import * class RGosemsim(RPackage): - """The semantic comparisons of Gene Ontology (GO) annotations provide - quantitative ways to compute similarities between genes and gene - groups, and have became important basis for many bioinformatics - analysis approaches. GOSemSim is an R package for semantic similarity - computation among GO terms, sets of GO terms, gene products and gene - clusters. GOSemSim implemented five methods proposed by Resnik, - Schlicker, Jiang, Lin and Wang respectively.""" - - homepage = "https://www.bioconductor.org/packages/GOSemSim/" + """GO-terms Semantic Similarity Measures. + + The semantic comparisons of Gene Ontology (GO) annotations provide + quantitative ways to compute similarities between genes and gene groups, + and have became important basis for many bioinformatics analysis + approaches. GOSemSim is an R package for semantic similarity computation + among GO terms, sets of GO terms, gene products and gene clusters. + GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, + Lin and Wang respectively.""" + + homepage = "https://bioconductor.org/packages/GOSemSim" git = "https://git.bioconductor.org/packages/GOSemSim.git" + version('2.10.0', commit='5db1ecbf2f8d870430d6e587609327d05ba3ad7b') + version('2.8.0', commit='c8c985b2a814cc2365c7f05b2509205e1b6b7f58') + version('2.6.2', commit='2ffe78e89276e804306554965fc0799318ec56ed') + version('2.4.1', commit='0656e845860d14e054670ffc246a1c53f699299c') version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52') - depends_on('r@3.4.0:3.4.9', when='@2.2.0') + depends_on('r@3.3.2:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-go-db', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py index 0a4aabeaf4..800d9785c0 100644 --- a/var/spack/repos/builtin/packages/r-goseq/package.py +++ b/var/spack/repos/builtin/packages/r-goseq/package.py @@ -7,15 +7,21 @@ from spack import * class RGoseq(RPackage): - """Detects Gene Ontology and/or other user defined categories which are + """Gene Ontology analyser for RNA-seq and other length biased data. + + Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data""" - homepage = "https://bioconductor.org/packages/release/bioc/html/goseq.html" + homepage = "https://bioconductor.org/packages/goseq" git = "https://git.bioconductor.org/packages/goseq.git" + version('1.36.0', commit='26c9f7de18889afeee1b571ca1c4ab4d2877ab80') + version('1.34.1', commit='bad217b42cc34423698fbcf701d4e3591aac4474') version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36') + version('1.30.0', commit='fa8cafe0766ed0b6a97a4ed3374a709ed9d1daf1') + version('1.28.0', commit='ed0ce332a8972618d740d8a93711dff994657738') - depends_on('r@3.5.0:3.5.9', when='@1.32.0:', type=('build', 'run')) + depends_on('r@2.11.0:', type=('build', 'run')) depends_on('r-biasedurn', type=('build', 'run')) depends_on('r-genelendatabase@1.9.2:', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py index 1b61115882..80137e1a51 100644 --- a/var/spack/repos/builtin/packages/r-gostats/package.py +++ b/var/spack/repos/builtin/packages/r-gostats/package.py @@ -7,21 +7,31 @@ from spack import * class RGostats(RPackage): - """A set of tools for interacting with GO and microarray data. - A variety of basic manipulation tools for graphs, hypothesis - testing and other simple calculations.""" + """Tools for manipulating GO and microarrays. - homepage = "https://www.bioconductor.org/packages/GOstats/" + A set of tools for interacting with GO and microarray data. A variety of + basic manipulation tools for graphs, hypothesis testing and other simple + calculations.""" + + homepage = "https://bioconductor.org/packages/GOstats" git = "https://git.bioconductor.org/packages/GOstats.git" + version('2.50.0', commit='ee13f84341988d537a5485dcdcfb71f69e6e4930') + version('2.48.0', commit='5db7020f4bab725cd729b32bd1d5e819b31f2485') + version('2.46.0', commit='489d7a437488f77c3010f6212f3b81f4e240cd17') + version('2.44.0', commit='fc64ca2aa37c52656d396d6e46611f39d6efd48a') version('2.42.0', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e') - depends_on('r@3.4.1:3.4.9', when='@2.42.0') - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-category', type=('build', 'run')) - depends_on('r-go-db', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biobase@1.15.29:', type=('build', 'run')) + depends_on('r-category@2.3.26:', type=('build', 'run')) + depends_on('r-graph@1.15.15:', when='@2.42.0', type=('build', 'run')) + depends_on('r-annotationdbi@0.0.89:', type=('build', 'run')) + depends_on('r-go-db@1.13.0:', type=('build', 'run')) depends_on('r-rbgl', type=('build', 'run')) - depends_on('r-annotate', type=('build', 'run')) + depends_on('r-annotate@1.13.2:', type=('build', 'run')) depends_on('r-annotationforge', type=('build', 'run')) + + depends_on('r-category@2.43.2:', when='@2.44.0:', type=('build', 'run')) + depends_on('r-rgraphviz', when='@2.44.0:', type=('build', 'run')) + depends_on('r-graph', when='@2.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py index b962eb198e..e1dde24847 100644 --- a/var/spack/repos/builtin/packages/r-graph/package.py +++ b/var/spack/repos/builtin/packages/r-graph/package.py @@ -7,12 +7,18 @@ from spack import * class RGraph(RPackage): - """A package that implements some simple graph handling capabilities.""" + """graph: A package to handle graph data structures. - homepage = "https://www.bioconductor.org/packages/graph/" + A package that implements some simple graph handling capabilities.""" + + homepage = "https://bioconductor.org/packages/graph" git = "https://git.bioconductor.org/packages/graph.git" + version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3') + version('1.60.0', commit='e2aecb0a862f32091b16e0036f53367d3edf4c1d') + version('1.58.2', commit='6455d8e7a5a45dc733915942cb71005c1016b6a0') + version('1.56.0', commit='c4abe227dac525757679743e6fb4f49baa34acad') version('1.54.0', commit='2a8b08520096241620421078fc1098f4569c7301') - depends_on('r@2.10:', type=('build', 'run'), when='@1.54.0') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.11:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridgraphics/package.py b/var/spack/repos/builtin/packages/r-gridgraphics/package.py new file mode 100644 index 0000000000..a01f6e4b83 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridgraphics/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGridgraphics(RPackage): + """gridGraphics: Redraw Base Graphics Using 'grid' Graphics""" + + homepage = "https://github.com/pmur002/gridgraphics" + url = "https://cloud.r-project.org/src/contrib/gridGraphics_0.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gridGraphics" + + version('0.4-1', sha256='b770127b71664bbf67f8853a2666c071f2b9920743eddc9f3a58ecb948b923cf') diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index 946b97b9f7..2da111bd9c 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -7,18 +7,24 @@ from spack import * class RGseabase(RPackage): - """This package provides classes and methods to support Gene - Set Enrichment Analysis (GSEA).""" + """Gene set enrichment data structures and methods. - homepage = "https://www.bioconductor.org/packages/GSEABase/" + This package provides classes and methods to support Gene Set Enrichment + Analysis (GSEA).""" + + homepage = "https://bioconductor.org/packages/GSEABase" git = "https://git.bioconductor.org/packages/GSEABase.git" + version('1.46.0', commit='edce83a9256a0c03206c2bce7c90ada0d90f6622') + version('1.44.0', commit='7042ff64a98b05b9572231ee1b4f3ae4fc9c768e') + version('1.42.0', commit='5e40ce0fdd4dc0cff7601b169bbf6aa1430ae33e') + version('1.40.1', commit='3e5441708b80aab2c9642988bee709d5732831a6') version('1.38.2', commit='84c9f10c316163118ca990900a7a67555b96e75b') - depends_on('r@3.4.0:3.4.9', when='@1.38.2') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-annotate', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) + depends_on('r@2.6.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) + depends_on('r-annotate@1.45.3:', type=('build', 'run')) + depends_on('r-graph@1.37.2:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py index 93ccdcaebb..e5fe5ca983 100644 --- a/var/spack/repos/builtin/packages/r-gtrellis/package.py +++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py @@ -7,20 +7,28 @@ from spack import * class RGtrellis(RPackage): - """Genome level Trellis graph visualizes genomic data conditioned by + """Genome Level Trellis Layout. + + Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.""" - homepage = "https://bioconductor.org/packages/gtrellis/" + homepage = "https://bioconductor.org/packages/gtrellis" git = "https://git.bioconductor.org/packages/gtrellis.git" + version('1.16.1', commit='a9003ededc8f2a48c78d4545e2f214023c13a7da') + version('1.14.0', commit='93935fb34211d12b250e22291712e18a31b0208d') + version('1.12.1', commit='7f3941adddbbfa17f4cf474b703568678a38272d') + version('1.11.1', commit='ff47d99743fd697d5c724f7bb18131dfe76dee71') version('1.8.0', commit='f813b420a008c459f63a2a13e5e64c5507c4c472') + depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-circlize', type=('build', 'run')) + depends_on('r-circlize@0.3.3:', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.8.0') + + depends_on('r-circlize@0.4.8:', when='@1.16.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py index e079e4015f..d03c4d58ea 100644 --- a/var/spack/repos/builtin/packages/r-gviz/package.py +++ b/var/spack/repos/builtin/packages/r-gviz/package.py @@ -7,38 +7,43 @@ from spack import * class RGviz(RPackage): - """Genomic data analyses requires integrated visualization - of known genomic information and new experimental data. Gviz - uses the biomaRt and the rtracklayer packages to perform live - annotation queries to Ensembl and UCSC and translates this to - e.g. gene/transcript structures in viewports of the grid - graphics package. This results in genomic information plotted - together with your data.""" + """Plotting data and annotation information along genomic coordinates. - homepage = "http://bioconductor.org/packages/Gviz/" + Genomic data analyses requires integrated visualization of known genomic + information and new experimental data. Gviz uses the biomaRt and the + rtracklayer packages to perform live annotation queries to Ensembl and + UCSC and translates this to e.g. gene/transcript structures in viewports + of the grid graphics package. This results in genomic information + plotted together with your data.""" + + homepage = "https://bioconductor.org/packages/Gviz" git = "https://git.bioconductor.org/packages/Gviz.git" + version('1.28.3', commit='20b9825af144cfc888629c34aa980b5bbd65bf86') + version('1.26.5', commit='430310b9d2e098f9757a71d26a2f69871071f30c') + version('1.24.0', commit='3ee1eec97a56653c07c434a97f82cfe3c4281841') + version('1.22.3', commit='2238079d0a7017c474f010acb35d98ee7cc1c5d1') version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c') - depends_on('r@3.4.0:3.4.9', when='@1.20.0') - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-iranges@1.99.18:', type=('build', 'run')) + depends_on('r-genomicranges@1.17.20:', type=('build', 'run')) + depends_on('r-xvector@0.5.7:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.13:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-biomart', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r-bsgenome', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biovizbase', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-latticeextra', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-digest', type=('build', 'run')) + depends_on('r-biomart@2.11.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.5:', type=('build', 'run')) + depends_on('r-biobase@2.15.3:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.17.22:', type=('build', 'run')) + depends_on('r-bsgenome@1.33.1:', type=('build', 'run')) + depends_on('r-biostrings@2.33.11:', type=('build', 'run')) + depends_on('r-biovizbase@1.13.8:', type=('build', 'run')) + depends_on('r-rsamtools@1.17.28:', type=('build', 'run')) + depends_on('r-latticeextra@0.6-26:', type=('build', 'run')) + depends_on('r-matrixstats@0.8.14:', type=('build', 'run')) + depends_on('r-genomicalignments@1.1.16:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.11.3:', type=('build', 'run')) + depends_on('r-digest@0.6.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py new file mode 100644 index 0000000000..7f8904fda6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -0,0 +1,49 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RHdf5array(RPackage): + """HDF5 backend for DelayedArray objects. + + Implements the HDF5Array and TENxMatrix classes, 2 convenient and + memory-efficient array-like containers for on-disk representation of + HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. + dense) HDF5 representation. TENxMatrix is for datasets that use the + HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 + Million Brain Cell Dataset). Both containers being DelayedArray + extensions, they support all operations supported by DelayedArray + objects. These operations can be either delayed or block-processed.""" + + homepage = "https://bioconductor.org/packages/HDF5Array" + git = "https://git.bioconductor.org/packages/HDF5Array.git" + + version('1.12.3', commit='21c6077f3f789748a18f2e579110576c5522e975') + version('1.10.1', commit='0b8ae1dfb56e4203dd8e14781850370df46a5e2c') + version('1.8.1', commit='3c9aa23d117bf489b6341708dc80c943bd1af11a') + version('1.6.0', commit='95f2f8d3648143abe9dc77c76340c5edf4114c82') + version('1.4.8', commit='79ab96d123c8da8f8ead81f678fe714c0958ff45') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-delayedarray@0.2.4:', type=('build', 'run')) + depends_on('r-rhdf5', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + + depends_on('r-delayedarray@0.3.18:', when='@1.6.0:', type=('build', 'run')) + + depends_on('r-delayedarray@0.5.32:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.8.1:', type=('build', 'run')) + + depends_on('r-delayedarray@0.7.41:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-rhdf5@2.25.6:', when='@1.10.1:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.3:', when='@1.12.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.21.6:', when='@1.12.3:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.12.3:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py index 949ba5ad9b..112a33b4fd 100644 --- a/var/spack/repos/builtin/packages/r-hypergraph/package.py +++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py @@ -7,13 +7,19 @@ from spack import * class RHypergraph(RPackage): - """A package that implements some simple capabilities for - representing and manipulating hypergraphs.""" + """A package providing hypergraph data structures. - homepage = "https://www.bioconductor.org/packages/hypergraph/" + A package that implements some simple capabilities for representing and + manipulating hypergraphs.""" + + homepage = "https://bioconductor.org/packages/hypergraph" git = "https://git.bioconductor.org/packages/hypergraph.git" + version('1.56.0', commit='f8b977fe068f15ecea49d30e77a871a35afcb97b') + version('1.54.0', commit='cf134b9221e9b5f6329a6786a366f57426c49e7c') + version('1.52.0', commit='3e28d8e8ab4c3facb79857b4e4cfffd65e064aca') + version('1.50.0', commit='fb3d523caf1d5791ef6962dd3c1a142742025ad5') version('1.48.0', commit='a4c19ea0b5f15204f706a7bfdea5363706382820') - depends_on('r@3.4.0:3.4.9', when='@1.48.0') + depends_on('r@2.1.0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py index 2803acf903..6acdcda84f 100644 --- a/var/spack/repos/builtin/packages/r-illuminaio/package.py +++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py @@ -7,13 +7,17 @@ from spack import * class RIlluminaio(RPackage): - """Tools for parsing Illumina's microarray output files, including - IDAT.""" + """Parsing Illumina Microarray Output Files. - homepage = "http://bioconductor.org/packages/illuminaio/" + Tools for parsing Illumina's microarray output files, including IDAT.""" + + homepage = "https://bioconductor.org/packages/illuminaio" git = "https://git.bioconductor.org/packages/illuminaio.git" + version('0.26.0', commit='40c2f94df2ea64d745d25aadd2bfb33ac3e02f81') + version('0.24.0', commit='47953c77713c2da00a610f39308f86c5b44f6c59') + version('0.22.0', commit='dbd842340999569975ea593f47d70a729b3f68f2') + version('0.20.0', commit='d226628133b2396be9e7a6bf043f0309bd70c4ec') version('0.18.0', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda') depends_on('r-base64', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.18.0') diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py index 4ec6a450a6..b49102d70c 100644 --- a/var/spack/repos/builtin/packages/r-impute/package.py +++ b/var/spack/repos/builtin/packages/r-impute/package.py @@ -7,12 +7,17 @@ from spack import * class RImpute(RPackage): - """Imputation for microarray data (currently KNN only).""" + """impute: Imputation for microarray data. - homepage = "https://www.bioconductor.org/packages/impute/" + Imputation for microarray data (currently KNN only)""" + + homepage = "https://bioconductor.org/packages/impute" git = "https://git.bioconductor.org/packages/impute.git" + version('1.58.0', commit='dc17173df08d965a0d0aac9fa4ad519bd99d127e') + version('1.56.0', commit='6c037ed4dffabafceae684265f86f2a18751b559') + version('1.54.0', commit='efc61f5197e8c4baf4ae881fb556f0312beaabd8') + version('1.52.0', commit='7fa1b917a5dd60f2aaf52d9aae1fcd2c93511d63') version('1.50.1', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71') - version('1.56.0', branch='RELEASE_3_8') - depends_on('r@3.4.0:3.4.9', when='@1.50.1') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py index a6c65f8694..f234ddc550 100644 --- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py +++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py @@ -7,15 +7,22 @@ from spack import * class RInteractivedisplaybase(RPackage): - """The interactiveDisplayBase package contains the the basic methods - needed to generate interactive Shiny based display methods for - Bioconductor objects.""" + """Base package for enabling powerful shiny web displays of Bioconductor + objects. - homepage = "https://bioconductor.org/packages/interactiveDisplayBase/" + The interactiveDisplayBase package contains the the basic methods needed + to generate interactive Shiny based display methods for Bioconductor + objects.""" + + homepage = "https://bioconductor.org/packages/interactiveDisplayBase" git = "https://git.bioconductor.org/packages/interactiveDisplayBase.git" + version('1.22.0', commit='4ce3cde1dabc01375c153ad614d77a5e28b96916') + version('1.20.0', commit='f40912c8af7afbaaf68c003a6e148d81cbe84df6') + version('1.18.0', commit='d07ea72a595877f27bf054f664f23e8f0304def8') + version('1.16.0', commit='a86aa586b589497f5449d36c2ce67a6b6055026d') version('1.14.0', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index a4313a470b..ffdbe0756f 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -7,29 +7,34 @@ from spack import * class RIranges(RPackage): - """Provides efficient low-level and highly - reusable S4 classes for storing, - manipulating and aggregating over annotated ranges of - integers. Implements an - algebra of range operations, including efficient - algorithms for finding overlaps - and nearest neighbors. Defines efficient list-like - classes for storing, transforming - and aggregating large grouped data, - i.e., collections of atomic vectors and DataFrames.""" - - homepage = "https://www.bioconductor.org/packages/IRanges/" + """Foundation of integer range manipulation in Bioconductor. + + Provides efficient low-level and highly reusable S4 classes for storing, + manipulating and aggregating over annotated ranges of integers. + Implements an algebra of range operations, including efficient + algorithms for finding overlaps and nearest neighbors. Defines efficient + list-like classes for storing, transforming and aggregating large + grouped data, i.e., collections of atomic vectors and DataFrames.""" + + homepage = "https://bioconductor.org/packages/IRanges" git = "https://git.bioconductor.org/packages/IRanges.git" - version('2.14.10', commit='c76118a38e84c7c764141adbd66ee350d0882bc9') + version('2.18.3', commit='c98a7ba074e72f2e5ec98252dffe9d3392711972') + version('2.16.0', commit='26834c6868d7c279dd8ac1bb9daa16e6fef273c2') + version('2.14.12', commit='00af02756c14771a23df9efcf379409ab6eb3041') version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd') version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614') - depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@2.10.5') - depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0') - depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@2.14.10') - depends_on('r-s4vectors@0.13.17:', type=('build', 'run'), when='@2.10.5') - depends_on('r-s4vectors@0.15.5:', type=('build', 'run'), when='@2.12.0') - depends_on('r-s4vectors@0.18.2:', type=('build', 'run'), when='@2.14.10') - depends_on('r@3.4.0:3.4.9', when='@2.10.5', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.14.10', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.21.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.17:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@2.12.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.15.5:', when='@2.12.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.25.3:', when='@2.14.12:', type=('build', 'run')) + depends_on('r-s4vectors@0.18.2:', when='@2.14.12:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.11:', when='@2.16.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.9:', when='@2.18.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py index 15f6042d1e..aaa1197f8b 100644 --- a/var/spack/repos/builtin/packages/r-jaspar2018/package.py +++ b/var/spack/repos/builtin/packages/r-jaspar2018/package.py @@ -7,12 +7,15 @@ from spack import * class RJaspar2018(RPackage): - """Data package for JASPAR 2018. To search this databases, - please use the package TFBSTools (>= 1.15.6).""" + """Data package for JASPAR 2018. - homepage = "http://jaspar.genereg.net/" + Data package for JASPAR 2018. To search this databases, please use the + package TFBSTools (>= 1.15.6).""" + + homepage = "https://bioconductor.org/packages/JASPAR2018" git = "https://git.bioconductor.org/packages/JASPAR2018.git" + version('1.1.0', commit='cf8598d3c9054d85c43655cf82be17f74d800fa5') version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa') - depends_on('r@3.4.0:') + depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py index 3a75e2ef56..0aafb32153 100644 --- a/var/spack/repos/builtin/packages/r-kegggraph/package.py +++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py @@ -7,18 +7,26 @@ from spack import * class RKegggraph(RPackage): - """KEGGGraph is an interface between KEGG pathway and graph object as - well as a collection of tools to analyze, dissect and visualize these - graphs. It parses the regularly updated KGML (KEGG XML) files into graph - models maintaining all essential pathway attributes. The package offers - functionalities including parsing, graph operation, visualization and - etc.""" - - homepage = "https://www.bioconductor.org/packages/KEGGgraph/" + """KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor. + + KEGGGraph is an interface between KEGG pathway and graph object as well + as a collection of tools to analyze, dissect and visualize these graphs. + It parses the regularly updated KGML (KEGG XML) files into graph models + maintaining all essential pathway attributes. The package offers + functionalities including parsing, graph operation, visualization and + etc.""" + + homepage = "https://bioconductor.org/packages/KEGGgraph" git = "https://git.bioconductor.org/packages/KEGGgraph.git" + version('1.44.0', commit='2c24e8ec53fe34c72ea65f34e3c09905ab2e5c62') + version('1.42.0', commit='7d907e22a3ad7b4829a7cbaba5a8f8dc8013a609') + version('1.40.0', commit='6351a1637276f71697b01a994ebda0d3d1cf6d7a') + version('1.38.0', commit='72f102e2611e3966362cfaa43646a6e66dd2ba27') version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292') + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-xml@2.3-0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.38.1') + + depends_on('r-rcurl', when='@1.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py index 44f560c40d..17d522fd55 100644 --- a/var/spack/repos/builtin/packages/r-keggrest/package.py +++ b/var/spack/repos/builtin/packages/r-keggrest/package.py @@ -7,21 +7,21 @@ from spack import * class RKeggrest(RPackage): - """This package provides functions and routines useful in the analysis - of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In - particular, functions to perform a signature analysis with known - signatures (LCD = linear combination decomposition) and a signature - analysis on stratified mutational catalogue (SMC = stratify mutational - catalogue) are provided.""" + """Client-side REST access to KEGG. - homepage = "http://bioconductor.org/packages/KEGGREST" + A package that provides a client interface to the KEGG REST server. + Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG + (python package) by Aurelien Mazurie.""" + + homepage = "https://bioconductor.org/packages/KEGGREST" git = "https://git.bioconductor.org/packages/KEGGREST.git" - version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4') - version('1.2.0', commit='ed48de0def57a909894e237fa4731c4a052d8849') + version('1.24.1', commit='bbc3ef476e02147aad8e1f33178136cc797c1b3f') + version('1.22.0', commit='4374507376be811d29416d0cbbfd9115a50494d9') + version('1.20.2', commit='62b4519367841f3548536c117e7e2bfe3fa4bf72') + version('1.18.1', commit='580c126eabc3c52145967708f67a428ca46b23b2') + version('1.16.1', commit='ed48de0def57a909894e237fa4731c4a052d8849') depends_on('r-httr', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') - depends_on('r@3.4.3:3.4.9', when='@1.18.1') diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py index c4e7a04be3..85f4d56060 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -7,16 +7,20 @@ from spack import * class RLimma(RPackage): - """Data analysis, linear models and differential expression - for microarray data.""" + """Linear Models for Microarray Data. - homepage = "https://www.bioconductor.org/packages/limma/" + Data analysis, linear models and differential expression for microarray + data.""" + + homepage = "https://bioconductor.org/packages/limma" git = "https://git.bioconductor.org/packages/limma.git" - version('3.36.2', commit='0cd5c13e22565182226bd2937ffcf8c59de1ca59') - version('3.34.9', commit='6755278a929f942a49e2441fb002a3ed393e1139') + version('3.40.6', commit='3ae0767ecf7a764030e7b7d0b1d0f292c0b24055') + version('3.38.3', commit='77b292eb150cdedaa1db704bcfb01f0bb29e9849') + version('3.36.5', commit='3148d1cb7eea9c6bdd60351d51abcfd665332d44') + version('3.34.9', commit='6755278a929f942a49e2441fb002a3ed393e1139') version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60') - depends_on('r@3.5.0:3.5.9', when='@3.36.2') - depends_on('r@3.4.2:3.4.9', when='@3.34.9') - depends_on('r@3.4.0:3.4.9', when='@3.32.10') + depends_on('r@2.3.0:', type=('build', 'run')) + + depends_on('r@3.6.0:', when='@3.40.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py index ba51fcac20..cbd690e144 100644 --- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py +++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py @@ -7,18 +7,23 @@ from spack import * class RMakecdfenv(RPackage): - """This package has two functions. One reads a Affymetrix - chip description file (CDF) and creates a hash table environment - containing the location/probe set membership mapping. - The other creates a package that automatically loads - that environment.""" + """CDF Environment Maker. - homepage = "https://www.bioconductor.org/packages/makecdfenv/" + This package has two functions. One reads a Affymetrix chip description + file (CDF) and creates a hash table environment containing the + location/probe set membership mapping. The other creates a package that + automatically loads that environment.""" + + homepage = "https://bioconductor.org/packages/makecdfenv" git = "https://git.bioconductor.org/packages/makecdfenv.git" + version('1.60.0', commit='900ece3ecd7a0ade9f8a0374e5a03def4e079cb3') + version('1.58.0', commit='6f513e39c4920a6da10d22718fc3bf278fe5ffe2') + version('1.56.0', commit='f6b48e9a9f18598653d05bc0bdffeae7fefbb327') + version('1.54.0', commit='3ff646ddc4b028e46b1e091ff9c2d17ce77cec26') version('1.52.0', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-affyio', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mapplots/package.py b/var/spack/repos/builtin/packages/r-mapplots/package.py new file mode 100644 index 0000000000..e26ac5a68c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mapplots/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RMapplots(RPackage): + """mapplots: Data Visualisation on Maps""" + + homepage = "https://cloud.r-project.org/package=mapplots" + url = "https://cloud.r-project.org/src/contrib/mapplots_1.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mapplots" + + version('1.5.1', sha256='37e96d34f37922180e07bb63b4514e07d42eee5bbf0885b278286ee48cf142a3') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py index f85fa253fe..6f77ce328e 100644 --- a/var/spack/repos/builtin/packages/r-mergemaid/package.py +++ b/var/spack/repos/builtin/packages/r-mergemaid/package.py @@ -7,23 +7,29 @@ from spack import * class RMergemaid(RPackage): - """The functions in this R extension are intended for cross-study - comparison of gene expression array data. Required from the user is - gene expression matrices, their corresponding gene-id vectors and - other useful information, and they could be 'list','matrix', or - 'ExpressionSet'. The main function is 'mergeExprs' which transforms - the input objects into data in the merged format, such that common - genes in different datasets can be easily found. And the function - 'intcor' calculate the correlation coefficients. Other functions use - the output from 'modelOutcome' to graphically display the results and - cross-validate associations of gene expression data with survival.""" + """Merge Maid. - homepage = "https://www.bioconductor.org/packages/MergeMaid/" + The functions in this R extension are intended for cross-study + comparison of gene expression array data. Required from the user is gene + expression matrices, their corresponding gene-id vectors and other + useful information, and they could be 'list','matrix', or + 'ExpressionSet'. The main function is 'mergeExprs' which transforms the + input objects into data in the merged format, such that common genes in + different datasets can be easily found. And the function 'intcor' + calculate the correlation coefficients. Other functions use the output + from 'modelOutcome' to graphically display the results and cross- + validate associations of gene expression data with survival.""" + + homepage = "https://bioconductor.org/packages/MergeMaid" git = "https://git.bioconductor.org/packages/MergeMaid.git" + version('2.56.0', commit='c510d1d85bb39476e8397b24c4bc127780a17686') + version('2.54.0', commit='8e79bd2bd06b25138b3c5107681c89d714a3b194') + version('2.52.0', commit='88a1ddfd9cdbe902ba40fae0f39ee5665ac33a74') + version('2.50.0', commit='b77d7fcb8ac8cf9ee71303bb193ef1a36a7f6049') version('2.48.0', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.48.0') diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py index 0f6e1af6f8..1638f1dee2 100644 --- a/var/spack/repos/builtin/packages/r-minfi/package.py +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -7,21 +7,27 @@ from spack import * class RMinfi(RPackage): - """Tools to analyze & visualize Illumina Infinium methylation arrays.""" + """Analyze Illumina Infinium DNA methylation arrays. - homepage = "https://bioconductor.org/packages/minfi/" + Tools to analyze & visualize Illumina Infinium methylation arrays.""" + + homepage = "https://bioconductor.org/packages/minfi" git = "https://git.bioconductor.org/packages/minfi.git" + version('1.30.0', commit='a4c28e9388fe3b35e7d21a9669e39250ed6dcbcd') + version('1.28.4', commit='b5125b2f3e05d37d519eeb6fd44a60efdad388e7') + version('1.26.2', commit='ebb07b728b2453998d46e4e53d4fbf873e8e81fc') + version('1.24.0', commit='a4df428588ea86a1c79ddba76132014f0a39644e') version('1.22.1', commit='b2faf84bcbb291e32d470a0e029450093527545b') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-bumphunter', type=('build', 'run')) + depends_on('r-bumphunter@1.1.9:', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biobase@2.33.2:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-beanplot', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) @@ -31,7 +37,7 @@ class RMinfi(RPackage): depends_on('r-limma', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-illuminaio', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-matrixstats@0.50.0:', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) @@ -40,4 +46,14 @@ class RMinfi(RPackage): depends_on('r-quadprog', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-geoquery', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.22.1') + + depends_on('r-delayedmatrixstats', when='@1.26.2:', type=('build', 'run')) + depends_on('r-delayedarray@0.5.23:', when='@1.26.2:', type=('build', 'run')) + depends_on('r-hdf5array', when='@1.26.2:', type=('build', 'run')) + depends_on('r-biocparallel', when='@1.26.2:', type=('build', 'run')) + + depends_on('r-illuminaio@0.23.2:', when='@1.28.4:', type=('build', 'run')) + depends_on('r-delayedmatrixstats@1.3.4:', when='@1.28.4:', type=('build', 'run')) + depends_on('r-delayedarray@0.7.38:', when='@1.28.4:', type=('build', 'run')) + + depends_on('r-delayedarray@0.9.8:', when='@1.30.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py index 0d37551de5..c8601a399e 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -7,20 +7,31 @@ from spack import * class RMlinterfaces(RPackage): - """This package provides uniform interfaces to machine learning - code for data in R and Bioconductor containers.""" + """Uniform interfaces to R machine learning procedures for data in + Bioconductor containers. - homepage = "https://www.bioconductor.org/packages/MLInterfaces/" + This package provides uniform interfaces to machine learning code for + data in R and Bioconductor containers.""" + + homepage = "https://bioconductor.org/packages/MLInterfaces" git = "https://git.bioconductor.org/packages/MLInterfaces.git" + version('1.64.1', commit='0b081112d87771248bc33b3b82d5ca4685f986a1') + version('1.62.1', commit='6cf59a90b14779cf57a0b36f1087304082ae50fe') + version('1.60.1', commit='019e9ed44923e5d845a4800246aa044ddd59d548') + version('1.58.1', commit='4e2b5efa019fcb677dc82a58a1668c8a00cdfe07') version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f') - depends_on('r@3.4.0:3.4.9', when='@1.56.0') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.9:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.11:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-annotate', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) depends_on('r-pls', type=('build', 'run')) depends_on('r-sfsmisc', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) depends_on('r-rda', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-fpc', type=('build', 'run')) @@ -29,5 +40,7 @@ class RMlinterfaces(RPackage): depends_on('r-gbm', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-hwriter', type=('build', 'run')) - depends_on('r-threejs', type=('build', 'run')) + depends_on('r-threejs@0.2.2:', type=('build', 'run')) depends_on('r-mlbench', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.60.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py index b617d077ed..faf69a9855 100644 --- a/var/spack/repos/builtin/packages/r-msnbase/package.py +++ b/var/spack/repos/builtin/packages/r-msnbase/package.py @@ -7,19 +7,27 @@ from spack import * class RMsnbase(RPackage): - """Manipulation, processing and visualisation of mass spectrometry and - proteomics data.""" + """Base Functions and Classes for Mass Spectrometry and Proteomics. - homepage = "https://www.bioconductor.org/packages/MSnbase/" + MSnbase provides infrastructure for manipulation, processing and + visualisation of mass spectrometry and proteomics data, ranging from raw + to quantitative and annotated data.""" + + homepage = "https://bioconductor.org/packages/MSnbase" git = "https://git.bioconductor.org/packages/MSnbase.git" + version('2.10.1', commit='4d5899bc9c714f0b1a70cddd537cd4621b2b53b0') + version('2.8.3', commit='ef883752c5e92d445647bc5b5d23d5df320db415') + version('2.6.4', commit='46836860ce0281eef135303f2e2948303d67f68c') + version('2.4.2', commit='c045d65daa730c7837852e6343a05cae9644ab5e') version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-mzr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.7.1:', type=('build', 'run')) + depends_on('r-biobase@2.15.2:', type=('build', 'run')) + depends_on('r-mzr@2.7.6:', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-protgenerics', type=('build', 'run')) + depends_on('r-protgenerics@1.5.1:', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) @@ -27,12 +35,23 @@ class RMsnbase(RPackage): depends_on('r-affy', type=('build', 'run')) depends_on('r-impute', type=('build', 'run')) depends_on('r-pcamethods', type=('build', 'run')) - depends_on('r-mzid', type=('build', 'run')) - depends_on('r-maldiquant', type=('build', 'run')) + depends_on('r-mzid@1.5.2:', type=('build', 'run')) + depends_on('r-maldiquant@1.16:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.2.0') + + depends_on('r-mzr@2.11.11:', when='@2.4.2:', type=('build', 'run')) + depends_on('r-protgenerics@1.9.1:', when='@2.4.2:', type=('build', 'run')) + + depends_on('r-mzr@2.13.6:', when='@2.6.4:', type=('build', 'run')) + depends_on('r-iranges@2.13.28:', when='@2.6.4:', type=('build', 'run')) + depends_on('r-scales', when='@2.6.4:', type=('build', 'run')) + depends_on('r-mass', when='@2.6.4:', type=('build', 'run')) + + depends_on('r-mzr@2.15.1:', when='@2.8.3:', type=('build', 'run')) + + depends_on('r-mzr@2.17.3:', when='@2.10.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py index ce4b5502c3..09bb8dcaf3 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -7,13 +7,37 @@ from spack import * class RMulttest(RPackage): - """Resampling-based multiple hypothesis testing""" + """Resampling-based multiple hypothesis testing. - homepage = "https://www.bioconductor.org/packages/multtest/" + Non-parametric bootstrap and permutation resampling-based multiple + testing procedures (including empirical Bayes methods) for controlling + the family-wise error rate (FWER), generalized family-wise error rate + (gFWER), tail probability of the proportion of false positives (TPPFP), + and false discovery rate (FDR). Several choices of bootstrap-based null + distribution are implemented (centered, centered and scaled, quantile- + transformed). Single-step and step-wise methods are available. Tests + based on a variety of t- and F-statistics (including t-statistics based + on regression parameters from linear and survival models as well as + those based on correlation parameters) are included. When probing + hypotheses with t-statistics, users may also select a potentially faster + null distribution which is multivariate normal with mean zero and + variance covariance matrix derived from the vector influence function. + Results are reported in terms of adjusted p-values, confidence regions + and test statistic cutoffs. The procedures are directly applicable to + identifying differentially expressed genes in DNA microarray + experiments.""" + + homepage = "https://bioconductor.org/packages/multtest" git = "https://git.bioconductor.org/packages/multtest.git" + version('2.40.0', commit='5f00017c2d3a31e05e1cfe06d9f7afdee19f8473') + version('2.38.0', commit='4dfe71cecfb298a94521088fb7bd83c5498d2915') + version('2.36.0', commit='babb15e8d110eb72300ad59cf7e53386237a4198') + version('2.34.0', commit='6ef873e05e6c93ede54f3421424f56eda057cd54') version('2.32.0', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a') - depends_on('r@3.4.0:3.4.9', when='@2.32.0') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py index 321ef53455..e32ad934be 100644 --- a/var/spack/repos/builtin/packages/r-mzid/package.py +++ b/var/spack/repos/builtin/packages/r-mzid/package.py @@ -7,15 +7,21 @@ from spack import * class RMzid(RPackage): - """A parser for mzIdentML files implemented using the XML package. The + """An mzIdentML parser for R. + + A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.""" - homepage = "https://www.bioconductor.org/packages/mzID/" + homepage = "https://bioconductor.org/packages/mzID" git = "https://git.bioconductor.org/packages/mzID.git" + version('1.22.0', commit='382d9cf11f0cba996911a9d79e193d28f3ac6042') + version('1.20.1', commit='819582646944440ddd9ed3724ae964841573e54c') + version('1.18.0', commit='7d8924ae95585eb8cf472d21619a7603d291d652') + version('1.16.0', commit='fc203832a4cbbbe20f6dd826c6bf2128f2c271c4') version('1.14.0', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115') depends_on('r-xml', type=('build', 'run')) @@ -24,4 +30,3 @@ class RMzid(RPackage): depends_on('r-foreach', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 4ff0958eea..a50b7fc27f 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -7,22 +7,34 @@ from spack import * class RMzr(RPackage): - """mzR provides a unified API to the common file formats and parsers + """parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass + spectrometry data). + + mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.""" - homepage = "https://www.bioconductor.org/packages/mzR/" + homepage = "https://bioconductor.org/packages/mzR" git = "https://git.bioconductor.org/packages/mzR.git" + version('2.18.1', commit='13f9f9b1149859c3e29cfce941d958cc4f680546') + version('2.16.2', commit='22d7dad98f46b5bed7f6f7b3a703dcdf5997f709') + version('2.14.0', commit='bf1154bc45101d95b5a67c66980856a779b84bd4') + version('2.12.0', commit='f05eb27ae31c3d019cca10fc3b9ee513cbcdfc5a') version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388') + depends_on('r-rcpp@0.10.1:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.6:', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('netcdf-c') - depends_on('r@3.4.0:3.4.9', when='@2.10.0') + + depends_on('r-protgenerics@1.9.1:', when='@2.12.0:', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@2.14.0:', type=('build', 'run')) + + depends_on('r-ncdf4', when='@2.16.2:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py index 1ed8e1d4d3..4b7f3a5a9a 100644 --- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py +++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py @@ -7,25 +7,36 @@ from spack import * class ROligoclasses(RPackage): - """This package contains class definitions, validity checks, - and initialization methods for classes used by the oligo and - crlmm packages.""" + """Classes for high-throughput arrays supported by oligo and crlmm. - homepage = "https://www.bioconductor.org/packages/oligoClasses/" + This package contains class definitions, validity checks, and + initialization methods for classes used by the oligo and crlmm + packages.""" + + homepage = "https://bioconductor.org/packages/oligoClasses" git = "https://git.bioconductor.org/packages/oligoClasses.git" + version('1.46.0', commit='325684f66fc92f778098f24bcfbef0ce3da9717c') + version('1.44.0', commit='d3e1134cdbea5f95b83215dc66e5f7b6a1cd0638') + version('1.42.0', commit='ef125700d487b470281a9c1e985390633c4dd2bd') + version('1.40.0', commit='32f40617e62d05c457baaebc7e27585b852848ed') version('1.38.0', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962') - depends_on('r@3.4.0:3.4.9', when='@1.38.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r@2.14:', type=('build', 'run')) + depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + depends_on('r-biobase@2.17.8:', type=('build', 'run')) + depends_on('r-iranges@2.5.17:', type=('build', 'run')) + depends_on('r-genomicranges@1.23.7:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-affyio', type=('build', 'run')) + depends_on('r-biostrings@2.23.6:', type=('build', 'run')) + depends_on('r-affyio@1.23.2:', type=('build', 'run')) depends_on('r-ff', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.38.0:1.42.0', type=('build', 'run')) + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) + + depends_on('r-dbi', when='@1.40.0:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.27.1:', when='@1.44.0:', type=('build', 'run')) + depends_on('r-biocmanager', when='@1.44.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py index 0677d405f1..6506801f0a 100644 --- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py +++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py @@ -8,12 +8,16 @@ from spack import * class ROrgHsEgDb(RPackage): """Genome wide annotation for Human, primarily based on mapping - using Entrez Gene identifiers.""" + using Entrez Gene identifiers.""" homepage = "https://bioconductor.org/packages/org.Hs.eg.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" + version('3.8.2', sha256='a0a16b7428f9e3d6ba54ebf4e05cd97a7bd298510ec4cf46ed2bed3e8f80db02', + url='https://www.bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Hs.eg.db_3.8.2.tar.gz') version('3.4.1', sha256='0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00') - depends_on('r@3.4.0:3.4.9', when='@3.4.1') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', when='@3.4.1:', type=('build', 'run')) + + depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run')) + depends_on('r-annotationdbi@1.43.1:', when='@3.8.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py index f9b4b68769..58079db4b1 100644 --- a/var/spack/repos/builtin/packages/r-organismdbi/package.py +++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py @@ -7,24 +7,35 @@ from spack import * class ROrganismdbi(RPackage): - """The package enables a simple unified interface to several annotation + """Software to enable the smooth interfacing of different database + packages. + + The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.""" - homepage = "https://bioconductor.org/packages/OrganismDbi/" + homepage = "https://bioconductor.org/packages/OrganismDbi" git = "https://git.bioconductor.org/packages/OrganismDbi.git" + version('1.26.0', commit='495b4a8f8264d06d827537d43b3c6cc705244bb5') + version('1.24.0', commit='3428952dc0f267a01e256a1c0873656cfbfde7f8') + version('1.22.0', commit='24e953eb3847222d8018103b79b9fc72483cc513') + version('1.20.0', commit='d42e06a24777e5ffb966ad5addb4f46dfffa2269') version('1.18.1', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-annotationdbi@1.33.15:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.23.31:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.18.1:1.22.0', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-rbgl', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.18.1') + depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.13:', when='@1.22.0:', type=('build', 'run')) + + depends_on('r-biocmanager', when='@1.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py index cb753e51d8..67d20ef890 100644 --- a/var/spack/repos/builtin/packages/r-pathview/package.py +++ b/var/spack/repos/builtin/packages/r-pathview/package.py @@ -7,26 +7,32 @@ from spack import * class RPathview(RPackage): - """Pathview is a tool set for pathway based data integration and - visualization. It maps and renders a wide variety of biological data on - relevant pathway graphs. All users need is to supply their data and - specify the target pathway. Pathview automatically downloads the pathway - graph data, parses the data file, maps user data to the pathway, and - render pathway graph with the mapped data. In addition, Pathview also - seamlessly integrates with pathway and gene set (enrichment) analysis - tools for large-scale and fully automated analysis.""" + """a tool set for pathway based data integration and visualization. - homepage = "https://www.bioconductor.org/packages/pathview/" + Pathview is a tool set for pathway based data integration and + visualization. It maps and renders a wide variety of biological data on + relevant pathway graphs. All users need is to supply their data and + specify the target pathway. Pathview automatically downloads the pathway + graph data, parses the data file, maps user data to the pathway, and + render pathway graph with the mapped data. In addition, Pathview also + seamlessly integrates with pathway and gene set (enrichment) analysis + tools for large-scale and fully automated analysis.""" + + homepage = "https://bioconductor.org/packages/pathview" git = "https://git.bioconductor.org/packages/pathview.git" + version('1.24.0', commit='e4401c1425c980ce2e6e478a4602a9f6d36ccd8d') + version('1.22.3', commit='ff86f9e166a5b03bbed1a0ad276778958c3045ce') + version('1.20.0', commit='a195afa6ba6c7917af2c7f77170f0644c46880c7') + version('1.18.2', commit='d2048981696564ec75f661ed665977d3a6e09188') version('1.16.7', commit='fc560ed15ef7393a73d35e714716cc24dc835339') - depends_on('r-keggrest', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-org-hs-eg-db', type=('build', 'run')) + depends_on('r-kegggraph', type=('build', 'run')) + depends_on('r-xml', type=('build', 'run')) + depends_on('r-rgraphviz', type=('build', 'run')) + depends_on('r-graph', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-graph', type=('build', 'run')) - depends_on('r-rgraphviz', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-kegggraph', type=('build', 'run')) - depends_on('r-org-hs-eg-db', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.16.7') + depends_on('r-keggrest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py index a61b08a850..a3cc30f91b 100644 --- a/var/spack/repos/builtin/packages/r-pcamethods/package.py +++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py @@ -7,23 +7,28 @@ from spack import * class RPcamethods(RPackage): - """Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse - Non-Linear PCA and the conventional SVD PCA. A cluster based method for - missing value estimation is included for comparison. BPCA, PPCA and - NipalsPCA may be used to perform PCA on incomplete data as well as for - accurate missing value estimation. A set of methods for printing and - plotting the results is also provided. All PCA methods make use of the - same data structure (pcaRes) to provide a common interface to the PCA - results. Initiated at the Max-Planck Institute for Molecular Plant - Physiology, Golm, Germany.""" + """A collection of PCA methods. - homepage = "http://bioconductor.org/packages/pcaMethods/" + Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear + PCA and the conventional SVD PCA. A cluster based method for missing + value estimation is included for comparison. BPCA, PPCA and NipalsPCA + may be used to perform PCA on incomplete data as well as for accurate + missing value estimation. A set of methods for printing and plotting the + results is also provided. All PCA methods make use of the same data + structure (pcaRes) to provide a common interface to the PCA results. + Initiated at the Max-Planck Institute for Molecular Plant Physiology, + Golm, Germany.""" + + homepage = "https://bioconductor.org/packages/pcaMethods" git = "https://git.bioconductor.org/packages/pcaMethods.git" + version('1.76.0', commit='5db995330ced37dfd5ddad6ad1d90b4815d3127a') + version('1.74.0', commit='1b8f0a5cdfe3664119d0d7e926a2e0fe7320133c') + version('1.72.0', commit='1bb8c7d056645e62ee5179f6bb30b6594ebf3bfd') + version('1.70.0', commit='3368fad48ea930775505fd26e4179d7714d633d8') version('1.68.0', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab') depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.68.0') diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index 67d06960ae..64f66ef845 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -13,7 +13,10 @@ class RPfamDb(RPackage): homepage = "https://www.bioconductor.org/packages/PFAM.db/" url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" + version('3.10.0', sha256='038888f95ce69230ac0e0b08aa3bcb09965682415520d437a7fb0a031eefe158') version('3.4.1', sha256='fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f') - depends_on('r@3.4.0:3.4.9', when='@3.4.1') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', when='@3.4.1:', type=('build', 'run')) + depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run')) + + depends_on('r-annotationdbi@1.47.1:', when='@3.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py index 1a9016bcb1..f23693fa2c 100644 --- a/var/spack/repos/builtin/packages/r-phyloseq/package.py +++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py @@ -7,28 +7,43 @@ from spack import * class RPhyloseq(RPackage): - """phyloseq provides a set of classes and tools to facilitate the import, - storage, analysis, and graphical display of microbiome census data.""" + """Handling and analysis of high-throughput microbiome census data. - homepage = "https://www.bioconductor.org/packages/phyloseq/" + phyloseq provides a set of classes and tools to facilitate the import, + storage, analysis, and graphical display of microbiome census data.""" + + homepage = "https://bioconductor.org/packages/phyloseq" git = "https://git.bioconductor.org/packages/phyloseq.git" + version('1.28.0', commit='a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d') + version('1.26.1', commit='a084072bc9e057b90adfbd59e27db2a1ecee151c') + version('1.24.2', commit='829992f88c79de48bb8749678624e2bbd3b66645') + version('1.22.3', commit='c695323f2963636d16acda9f05a583bd58e31344') version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0') - depends_on('r@3.4.0:3.4.9', when='@1.20.0') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-ade4', type=('build', 'run')) - depends_on('r-ape', type=('build', 'run')) - depends_on('r-biomformat', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-data-table', type=('build', 'run')) - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-multtest', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) - depends_on('r-vegan', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.18.0:', type=('build', 'run')) + depends_on('r-ade4@1.7.4:', type=('build', 'run')) + depends_on('r-ape@3.4:', type=('build', 'run')) + depends_on('r-biomformat@1.0.0:', type=('build', 'run')) + depends_on('r-biostrings@2.40.0:', type=('build', 'run')) + depends_on('r-cluster@2.0.4:', type=('build', 'run')) + depends_on('r-data-table@1.9.6:', type=('build', 'run')) + depends_on('r-foreach@1.4.3:', type=('build', 'run')) + depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) + depends_on('r-igraph@1.0.1:', type=('build', 'run')) + depends_on('r-multtest@2.28.0:', type=('build', 'run')) + depends_on('r-plyr@1.8.3:', type=('build', 'run')) + depends_on('r-reshape2@1.4.1:', type=('build', 'run')) + depends_on('r-scales@0.4.0:', type=('build', 'run')) + depends_on('r-vegan@2.3.5:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-ape@5.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biobase@2.36.2:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-data-table@1.10.4:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-vegan@2.4:', when='@1.22.3:', type=('build', 'run')) + + depends_on('r-vegan@2.5:', when='@1.24.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-polyclip/package.py b/var/spack/repos/builtin/packages/r-polyclip/package.py new file mode 100644 index 0000000000..6a6d059c41 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-polyclip/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPolyclip(RPackage): + """polyclip: Polygon Clipping""" + + homepage = "https://cloud.r-project.org/package=polyclip" + url = "https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/polyclip" + + version('1.10-0', sha256='74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py index bed1fa0fc0..6e375916ca 100644 --- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py +++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py @@ -7,12 +7,15 @@ from spack import * class RPreprocesscore(RPackage): - """A library of core preprocessing routines""" + """A collection of pre-processing functions. - homepage = "https://bioconductor.org/packages/preprocessCore/" + A library of core preprocessing routines.""" + + homepage = "https://bioconductor.org/packages/preprocessCore" git = "https://git.bioconductor.org/packages/preprocessCore.git" + version('1.46.0', commit='8cfc3938c1b08424587f437ed6cd2ec43512500e') + version('1.44.0', commit='dc1dc61fc562aaff3fd9b11ab0d48c2d6b3a5b81') + version('1.42.0', commit='2e3a8baeacfaa1526d51252642772ea951015bba') + version('1.40.0', commit='969bb0e5cbd63d569502ae4e6eaadc1e216646dd') version('1.38.1', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc') - version('1.44.0', branch='RELEASE_3_8') - - depends_on('r@3.4.0:3.4.9', when='@1.38.1') diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py index 2bd18088ca..753dbb18ff 100644 --- a/var/spack/repos/builtin/packages/r-protgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py @@ -7,11 +7,15 @@ from spack import * class RProtgenerics(RPackage): - """S4 generic functions needed by Bioconductor proteomics packages.""" + """S4 generic functions for Bioconductor proteomics infrastructure. - homepage = "https://bioconductor.org/packages/ProtGenerics/" + S4 generic functions needed by Bioconductor proteomics packages.""" + + homepage = "https://bioconductor.org/packages/ProtGenerics" git = "https://git.bioconductor.org/packages/ProtGenerics.git" + version('1.16.0', commit='960a5fdc586898513b5ae9c48fffba5c5d703723') + version('1.14.0', commit='c85940b70a16ad69275c4facb3ef673d20a1c998') + version('1.12.0', commit='e84382a4b1730409f572fb681b5070017d00d30d') + version('1.10.0', commit='9ae2c3710b77381571900f0f25c6c8fda65795ac') version('1.8.0', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3') - - depends_on('r@3.4.0:3.4.9', when='@1.8.0') diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py index 637d741ecb..b27de06266 100644 --- a/var/spack/repos/builtin/packages/r-quantro/package.py +++ b/var/spack/repos/builtin/packages/r-quantro/package.py @@ -7,18 +7,25 @@ from spack import * class RQuantro(RPackage): - """A data-driven test for the assumptions of quantile normalization using + """A test for when to use quantile normalization. + + A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, - MethylSet). Group level information about each sample (such as - Tumor / Normal status) must also be provided because the test assesses - if there are global differences in the distributions between the - user-defined groups.""" + MethylSet). Group level information about each sample (such as Tumor / + Normal status) must also be provided because the test assesses if there + are global differences in the distributions between the user-defined + groups.""" - homepage = "https://www.bioconductor.org/packages/quantro/" + homepage = "https://bioconductor.org/packages/quantro" git = "https://git.bioconductor.org/packages/quantro.git" + version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359') + version('1.16.0', commit='cfc2e853bdc3cc90fd35e153fe243892d50d61c6') + version('1.14.0', commit='2d43264b2a95ae8ca51a69d7768fe43b9f1b77bb') + version('1.12.0', commit='1cfcc73875cf4ecc2618e5e45fda89bd075a5d12') version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9') + depends_on('r@3.1.3:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-minfi', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) @@ -26,4 +33,3 @@ class RQuantro(RPackage): depends_on('r-iterators', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.10.0') diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py index 2e1b8e56b3..7b07bb0276 100644 --- a/var/spack/repos/builtin/packages/r-qvalue/package.py +++ b/var/spack/repos/builtin/packages/r-qvalue/package.py @@ -7,27 +7,29 @@ from spack import * class RQvalue(RPackage): - """This package takes a list of p-values resulting from the - simultaneous testing of many hypotheses and estimates their - q-values and local FDR values. The q-value of a test measures - the proportion of false positives incurred (called the false - discovery rate) when that particular test is called significant. - The local FDR measures the posterior probability the null - hypothesis is true given the test's p-value. Various plots are - automatically generated, allowing one to make sensible - significance cut-offs. Several mathematical results have - recently been shown on the conservative accuracy of the - estimated q-values from this software. The software can be - applied to problems in genomics, brain imaging, astrophysics, - and data mining.""" + """Q-value estimation for false discovery rate control. - homepage = "https://www.bioconductor.org/packages/qvalue/" + This package takes a list of p-values resulting from the simultaneous + testing of many hypotheses and estimates their q-values and local FDR + values. The q-value of a test measures the proportion of false positives + incurred (called the false discovery rate) when that particular test is + called significant. The local FDR measures the posterior probability the + null hypothesis is true given the test's p-value. Various plots are + automatically generated, allowing one to make sensible significance cut- + offs. Several mathematical results have recently been shown on the + conservative accuracy of the estimated q-values from this software. The + software can be applied to problems in genomics, brain imaging, + astrophysics, and data mining.""" + + homepage = "https://bioconductor.org/packages/qvalue" git = "https://git.bioconductor.org/packages/qvalue.git" + version('2.16.0', commit='5efbe20ef522a45a7a04b681f72bb9a12e2747ae') + version('2.14.1', commit='b694e4b264f25250eb1d1115e70c07f65767c20e') version('2.12.0', commit='7df64ebfcbe69dcbf8b88cb6ef0068bf16979673') + version('2.10.0', commit='581e5664b4356440a96310897398f01a98ceb81b') version('2.8.0', commit='c7bf3315619d42d800f57a36670c25a7495ded72') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.8.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@2.12.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py index d5390e9a5b..f63046a95d 100644 --- a/var/spack/repos/builtin/packages/r-rbgl/package.py +++ b/var/spack/repos/builtin/packages/r-rbgl/package.py @@ -7,16 +7,20 @@ from spack import * class RRbgl(RPackage): - """A fairly extensive and comprehensive interface to the graph - algorithms contained in the BOOST library.""" + """An interface to the BOOST graph library. - homepage = "https://www.bioconductor.org/packages/RBGL/" + A fairly extensive and comprehensive interface to the graph algorithms + contained in the BOOST library.""" + + homepage = "https://bioconductor.org/packages/RBGL" git = "https://git.bioconductor.org/packages/RBGL.git" version('1.60.0', commit='ef24c17c411659b8f030602bd9781c534d6ec93b') + version('1.58.2', commit='086ad0c6bab7be29311b6ae14fd39df7a21331a6') + version('1.56.0', commit='a1fa9d89c6a3401892c5dd1493df6a14031f0912') + version('1.54.0', commit='e9c743d380e83c155495cb8732102f01f213c905') version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0') - depends_on('r@3.4.0:3.4.9', when='@1.52.0') - depends_on('r@3.6.0:', when='@1.60.0', type=('build', 'run')) - depends_on('r-bh', when='@1.60.0', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) + + depends_on('r-bh', when='@1.60.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpphnsw/package.py b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py new file mode 100644 index 0000000000..f6addea265 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcpphnsw/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRcpphnsw(RPackage): + """RcppHNSW: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate + NearestNeighbors""" + + homepage = "https://cloud.r-project.org/package=RcppHNSW" + url = "https://cloud.r-project.org/src/contrib/RcppHNSW_0.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppHNSW" + + version('0.1.0', sha256='75a54c30953845dec685764c7b3b4cd7315197c91aef4ab3b4eb0a6293010a95') + + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index de4930c4c8..b8e25053a8 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -7,42 +7,45 @@ from spack import * class RReportingtools(RPackage): - """The ReportingTools software package enables users to easily - display reports of analysis results generated from sources such - as microarray and sequencing data. The package allows users to - create HTML pages that may be viewed on a web browser such as - Safari, or in other formats readable by programs such as Excel. - Users can generate tables with sortable and filterable columns, - make and display plots, and link table entries to other data - sources such as NCBI or larger plots within the HTML page. Using - the package, users can also produce a table of contents page to - link various reports together for a particular project that can - be viewed in a web browser. For more examples, please visit our - site: http:// research-pub.gene.com/ReportingTools.""" + """Tools for making reports in various formats. - homepage = "https://bioconductor.org/packages/ReportingTools/" + The ReportingTools software package enables users to easily display + reports of analysis results generated from sources such as microarray + and sequencing data. The package allows users to create HTML pages that + may be viewed on a web browser such as Safari, or in other formats + readable by programs such as Excel. Users can generate tables with + sortable and filterable columns, make and display plots, and link table + entries to other data sources such as NCBI or larger plots within the + HTML page. Using the package, users can also produce a table of contents + page to link various reports together for a particular project that can + be viewed in a web browser. For more examples, please visit our site: + http:// research-pub.gene.com/ReportingTools.""" + + homepage = "https://bioconductor.org/packages/ReportingTools" git = "https://git.bioconductor.org/packages/ReportingTools.git" + version('2.24.0', commit='d114c658affba9b682a37b4e2caf4341cf8da6cf') + version('2.22.1', commit='dce6af6c6a1cddff077fe61368f2c13e5a0e7bab') + version('2.20.0', commit='77e14ae13fdc16654300852dfd94e6cef58009da') + version('2.17.3', commit='b2e379cd5b813d8ccca37ec25f0660deec943622') version('2.16.0', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663') - depends_on('r@3.4.0:3.4.9', when='@2.16.0') depends_on('r-knitr', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-hwriter', type=('build', 'run')) depends_on('r-category', type=('build', 'run')) depends_on('r-gostats', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) - depends_on('r-limma', type=('build', 'run')) + depends_on('r-limma@3.17.5:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-edger', type=('build', 'run')) depends_on('r-annotate', type=('build', 'run')) depends_on('r-pfam-db', type=('build', 'run')) depends_on('r-gseabase', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.6:', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-r-utils', type=('build', 'run')) - depends_on('r-deseq2', type=('build', 'run')) + depends_on('r-deseq2@1.3.41:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggbio', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py index 34936da7e3..d61b62218b 100644 --- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py +++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py @@ -7,13 +7,21 @@ from spack import * class RRgraphviz(RPackage): - """Interfaces R with the AT and T graphviz library for plotting - R graph objects from the graph package.""" + """Provides plotting capabilities for R graph objects. - homepage = "http://bioconductor.org/packages/Rgraphviz/" + Interfaces R with the AT and T graphviz library for plotting R graph + objects from the graph package.""" + + homepage = "https://bioconductor.org/packages/Rgraphviz" git = "https://git.bioconductor.org/packages/Rgraphviz.git" + version('2.28.0', commit='c1f57c11f037c977f1d17f227f12a09a999e8c0b') + version('2.26.0', commit='e9b08c77121a45c65129d94a12b5c0b31c65617f') + version('2.24.0', commit='7d1fb00afed0d44e32b4a46f10137ab34f100577') + version('2.22.0', commit='5b8ebbf9b38574c08959dd4632e802b3fbccc121') version('2.20.0', commit='eface6298150667bb22eac672f1a45e52fbf8c90') - depends_on('r@3.4.0:3.4.9', when='@2.20.0') + depends_on('r@2.6.0:', type=('build', 'run')) depends_on('r-graph', type=('build', 'run')) + + depends_on('graphviz@2.16:', type='run') 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') diff --git a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py new file mode 100644 index 0000000000..1c1fe6d2ce --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRhdf5lib(RPackage): + """hdf5 library as an R package. + + Provides C and C++ hdf5 libraries.""" + + homepage = "https://bioconductor.org/packages/Rhdf5lib" + git = "https://git.bioconductor.org/packages/Rhdf5lib.git" + + version('1.6.3', commit='11ac3069f28b0068002db9c645817401f6c5b3c4') + version('1.4.3', commit='f6be8c2659b2daa17541506058917b7981490d65') + version('1.2.1', commit='dbf85dbedb736d5a696794d52875729c8514494e') + version('1.0.0', commit='79608038c2016a518ba747fe6a2bf02ce53a75f9') + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py index e2286b4847..834df729a3 100644 --- a/var/spack/repos/builtin/packages/r-rhtslib/package.py +++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py @@ -7,17 +7,26 @@ from spack import * class RRhtslib(RPackage): - """This package provides version 1.1 of the 'HTSlib' C library - for high-throughput sequence analysis. The package is primarily - useful to developers of other R packages who wish to make use - of HTSlib. Motivation and instructions for use of this package - are in the vignette, vignette(package="Rhtslib", "Rhtslib").""" + """HTSlib high-throughput sequencing library as an R package. - homepage = "https://www.bioconductor.org/packages/Rhtslib/" + This package provides version 1.7 of the 'HTSlib' C library for high- + throughput sequence analysis. The package is primarily useful to + developers of other R packages who wish to make use of HTSlib. + Motivation and instructions for use of this package are in the vignette, + vignette(package="Rhtslib", "Rhtslib").""" + + homepage = "https://bioconductor.org/packages/Rhtslib" git = "https://git.bioconductor.org/packages/Rhtslib.git" + version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4') + version('1.14.1', commit='4be260720f845a34d0ac838278fce1363f645230') + version('1.12.1', commit='e3487b1355995d09b28fde5d0a7504a3e79a7203') + version('1.10.0', commit='53dcf7dfe35d735283956c77c011a97ca3f4eb26') version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79') - depends_on('r@3.4.0:3.4.9', when='@1.8.0') depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('autoconf@2.67:', type='build') + + depends_on('bzip2', type=('build', 'link', 'run')) + depends_on('xz', type=('build', 'link', 'run')) + depends_on('curl', type=('build', 'link', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py new file mode 100644 index 0000000000..a1a0b2aefe --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRnaseqmap(RPackage): + """rnaSeq secondary analyses. + + The rnaSeqMap library provides classes and functions to analyze the RNA- + sequencing data using the coverage profiles in multiple samples at a + time""" + + homepage = "https://bioconductor.org/packages/rnaSeqMap" + git = "https://git.bioconductor.org/packages/rnaSeqMap.git" + + version('2.42.0', commit='3a3a1030cc38d79d04536e0ab16114e4fa6721cf') + version('2.40.1', commit='c122d645b3503fb1a061f5515e4f8cf2863b3ba3') + version('2.38.0', commit='5eb9583bfacd375161739a8ae6057204487f8b9e') + version('2.36.0', commit='69c46fa467be0ac30776ede85a521f7622539b7e') + version('2.34.0', commit='7881bc00600ed824ac437edf3cfba35573261e46') + + depends_on('r@2.11.0:', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-deseq', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py index 32564c1fe7..fd26c483d4 100644 --- a/var/spack/repos/builtin/packages/r-rots/package.py +++ b/var/spack/repos/builtin/packages/r-rots/package.py @@ -7,14 +7,20 @@ from spack import * class RRots(RPackage): - """Calculates the Reproducibility-Optimized Test Statistic (ROTS) - for differential testing in omics data.""" + """Reproducibility-Optimized Test Statistic. - homepage = "https://bioconductor.org/packages/release/bioc/html/ROTS.html" + Calculates the Reproducibility-Optimized Test Statistic (ROTS) for + differential testing in omics data.""" + + homepage = "https://bioconductor.org/packages/ROTS" git = "https://git.bioconductor.org/packages/ROTS.git" + version('1.12.0', commit='7e2c96fd8fd36710321498745f24cc6b59ac02f0') + version('1.10.1', commit='1733d3f868cef4d81af6edfc102221d80793937b') version('1.8.0', commit='02e3c6455bb1afe7c4cc59ad6d4d8bae7b01428b') + version('1.6.0', commit='3567ac1142ba97770b701ee8e5f9e3e6c781bd56') + version('1.4.0', commit='2e656514a4bf5a837ee6e14ce9b28a61dab955e7') - depends_on('r@3.5.0:3.5.9', when='@1.8.0:', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py index 7292fcf1cd..3fbf2bef54 100644 --- a/var/spack/repos/builtin/packages/r-rsamtools/package.py +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -7,33 +7,41 @@ from spack import * class RRsamtools(RPackage): - """This package provides an interface to the 'samtools', 'bcftools', and - 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence - Alignment / Map), FASTA, binary variant call (BCF) and compressed - indexed tab-delimited (tabix) files.""" + """Binary alignment (BAM), FASTA, variant call (BCF), and tabix file + import. - homepage = "https://bioconductor.org/packages/Rsamtools/" + This package provides an interface to the 'samtools', 'bcftools', and + 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), + FASTA, binary variant call (BCF) and compressed indexed tab-delimited + (tabix) files.""" + + homepage = "https://bioconductor.org/packages/Rsamtools" git = "https://git.bioconductor.org/packages/Rsamtools.git" - version('1.32.2', commit='2b3254ccdeb24dc6ad95a93c2eb527021631797e') + version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70') + version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c') + version('1.32.3', commit='0aa3f134143b045aa423894de81912becf64e4c2') + version('1.30.0', commit='61b365fe3762e796b3808cec7238944b7f68d7a6') version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472') - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.1.3:', when='@1.32.2', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomicranges@1.31.8:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@1.32.2', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.32.2', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.12:', when='@1.32.2', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-xvector@0.15.1:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.28.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run')) + + depends_on('r-rhtslib@1.16.3:', when='@2.0.3:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py index e272d6a80d..a83f1ea5ec 100644 --- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py +++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py @@ -7,39 +7,48 @@ from spack import * class RRtracklayer(RPackage): - """Extensible framework for interacting with multiple genome browsers + """R interface to genome annotation files and the UCSC genome browser. + + Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.""" - homepage = "http://bioconductor.org/packages/rtracklayer/" + homepage = "https://bioconductor.org/packages/rtracklayer" git = "https://git.bioconductor.org/packages/rtracklayer.git" - version('1.40.5', commit='4e5b06daccd0bca1ddcd93052deca896ade58fd6') + version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3') + version('1.42.2', commit='76702f671faea736807d54aeecfbadcd152d94c5') + version('1.40.6', commit='ba9a6e711504a702147383bc7abfcc36eb304df7') + version('1.38.3', commit='f20db703c09dc7e808c09e9b78c15aec9e546248') version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131') - depends_on('r-xml', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.25.1:', when='@1.40.5', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.40.5', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.13:', when='@1.40.5', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-xvector@0.19.7:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.15.2:', when='@1.40.5', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-biostrings@2.47.6:', when='@1.40.5', type=('build', 'run')) + depends_on('r@3.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.20:', type=('build', 'run')) + depends_on('r-xml@1.98-0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-xvector@0.9.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.3.14:', type=('build', 'run')) + depends_on('r-biostrings@2.43.7:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-rsamtools@1.31.2:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-genomicalignments@1.15.6:', when='@1.40.5', type=('build', 'run')) - depends_on('r-genomicranges@1.21.20:', when='@1.36.3', type=('build', 'run')) - depends_on('r-genomicranges@1.31.8:', when='@1.40.5', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.36.6', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.40.5', type=('build', 'run')) + depends_on('r-rcurl@1.4-2:', type=('build', 'run')) + depends_on('r-rsamtools@1.17.8:', type=('build', 'run')) + depends_on('r-genomicalignments@1.5.4:', type=('build', 'run')) + + depends_on('r-iranges@2.11.12:', when='@1.38.3:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.8:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.40.6:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.22:', when='@1.42.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py index 1a4ca70513..67ea5f7268 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -7,23 +7,27 @@ from spack import * class RS4vectors(RPackage): - """The S4Vectors package defines the Vector and List virtual classes and - a set of generic functions that extend the semantic of ordinary - vectors and lists in R. Package developers can easily implement - vector-like or list-like objects as concrete subclasses of Vector or - List. In addition, a few low-level concrete subclasses of general - interest (e.g. DataFrame, Rle, and Hits) are implemented in the - S4Vectors package itself (many more are implemented in the IRanges - package and in other Bioconductor infrastructure packages).""" - - homepage = "https://bioconductor.org/packages/S4Vectors/" + """Foundation of vector-like and list-like containers in Bioconductor. + + The S4Vectors package defines the Vector and List virtual classes and a + set of generic functions that extend the semantic of ordinary vectors + and lists in R. Package developers can easily implement vector-like or + list-like objects as concrete subclasses of Vector or List. In addition, + a few low-level concrete subclasses of general interest (e.g. DataFrame, + Rle, and Hits) are implemented in the S4Vectors package itself (many + more are implemented in the IRanges package and in other Bioconductor + infrastructure packages).""" + + homepage = "https://bioconductor.org/packages/S4Vectors" git = "https://git.bioconductor.org/packages/S4Vectors.git" + version('0.22.1', commit='d25e517b48ca4184a4c2ee1f8223c148a55a8b8a') + version('0.20.1', commit='1878b2909086941e556c5ea953c6fd86aebe9b02') version('0.18.3', commit='d6804f94ad3663828440914920ac933b934aeff1') version('0.16.0', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d') version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23') - depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@0.14.7') - depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0:') - depends_on('r@3.4.0:3.4.9', when='@0.14.7', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.18.3', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.21.1:', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@0.16.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py new file mode 100644 index 0000000000..380f3966e3 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scater/package.py @@ -0,0 +1,63 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RScater(RPackage): + """Single-Cell Analysis Toolkit for Gene Expression Data in R. + + A collection of tools for doing various analyses of single-cell RNA-seq + gene expression data, with a focus on quality control and + visualization.""" + + homepage = "https://bioconductor.org/packages/scater" + git = "https://git.bioconductor.org/packages/scater.git" + + version('1.12.2', commit='1518dc27a87c79181c34107d639e95fe55e55092') + version('1.10.1', commit='2e6694af2929092f263c2b0830d48b3f9632e70c') + version('1.8.4', commit='d560a9a378541d53d17990d2aa2cd28874df3dcd') + version('1.6.3', commit='964effb4e883102d7c8cae627dbac4ba5d216a75') + version('1.4.0', commit='90a2eab66ff82ba6dd7fbb33e41cd0ded20fa218') + + depends_on('r@3.3:', when='@1.4.0', type=('build', 'run')) + depends_on('r-biobase', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-biomart', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-data-table', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-dplyr', when='@1.4.0:1.12.2', type=('build', 'run')) + depends_on('r-edger', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-ggbeeswarm', type=('build', 'run')) + depends_on('r-limma', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-matrixstats', when='@1.4.0:1.6.3', type=('build', 'run')) + depends_on('r-plyr', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-reshape2', when='@1.4.0:1.10.1', type=('build', 'run')) + depends_on('r-rhdf5', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-rjson', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-shiny', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-shinydashboard', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-tximport', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) + + depends_on('r@3.4:', when='@1.6.3', type=('build', 'run')) + depends_on('r-singlecellexperiment', when='@1.6.3:', type=('build', 'run')) + depends_on('r-summarizedexperiment', when='@1.6.3:', type=('build', 'run')) + depends_on('r-s4vectors', when='@1.6.3:', type=('build', 'run')) + depends_on('r-rcpp', when='@1.6.3:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.6.3:1.10.1', type=('build', 'run')) + depends_on('r-beachmat', when='@1.6.3:', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.8.4', type=('build', 'run')) + depends_on('r-delayedmatrixstats', when='@1.8.4:', type=('build', 'run')) + depends_on('r-rcpp@0.12.14:', when='@1.8.4:', type=('build', 'run')) + depends_on('r-delayedarray', when='@1.8.4:', type=('build', 'run')) + + depends_on('r-biocparallel', when='@1.10.1:', type=('build', 'run')) + + depends_on('r@3.6:', when='@1.12.2', type=('build', 'run')) + depends_on('r-biocneighbors', when='@1.12.2:', type=('build', 'run')) + depends_on('r-biocsingular', when='@1.12.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scrime/package.py b/var/spack/repos/builtin/packages/r-scrime/package.py new file mode 100644 index 0000000000..bd5ce70b67 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scrime/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RScrime(RPackage): + """scrime: Analysis of High-Dimensional Categorical Data Such as SNP + Data""" + + homepage = "https://cloud.r-project.org/package=scrime" + url = "https://cloud.r-project.org/src/contrib/scrime_1.3.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/scrime" + + version('1.3.5', sha256='5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578') diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py index b264ad50e8..d3b88b102c 100644 --- a/var/spack/repos/builtin/packages/r-seqlogo/package.py +++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py @@ -7,13 +7,17 @@ from spack import * class RSeqlogo(RPackage): - """seqLogo takes the position weight matrix of a DNA sequence motif and + """Sequence logos for DNA sequence alignments. + + seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).""" - homepage = "https://bioconductor.org/packages/seqLogo/" + homepage = "https://bioconductor.org/packages/seqLogo" git = "https://git.bioconductor.org/packages/seqLogo.git" + version('1.50.0', commit='57986221c90c3920f9829756c4b3ee566dc1e14d') + version('1.48.0', commit='dde85582e7fd0c08c5b8bc73f9aed8f23b727d9d') + version('1.46.0', commit='e78be03db5f6a516138aeea6aa9512685633a4a2') version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac') - - depends_on('r@3.4.3:3.4.9', when='@1.44.0') + version('1.42.0', commit='d7e04726c813282aa3f47a9ee98c5e1cec9bdddd') diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py index b42f2b715f..19150bde9b 100644 --- a/var/spack/repos/builtin/packages/r-shortread/package.py +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -7,30 +7,46 @@ from spack import * class RShortread(RPackage): - """This package implements sampling, iteration, and input of FASTQ - files. The package includes functions for filtering and trimming - reads, and for generating a quality assessment report. Data are - represented as DNAStringSet-derived objects, and easily manipulated - for a diversity of purposes. The package also contains legacy support - for early single-end, ungapped alignment formats.""" - - homepage = "https://www.bioconductor.org/packages/ShortRead/" + """FASTQ input and manipulation. + + This package implements sampling, iteration, and input of FASTQ files. + The package includes functions for filtering and trimming reads, and for + generating a quality assessment report. Data are represented as + DNAStringSet-derived objects, and easily manipulated for a diversity of + purposes. The package also contains legacy support for early single-end, + ungapped alignment formats.""" + + homepage = "https://bioconductor.org/packages/ShortRead" git = "https://git.bioconductor.org/packages/ShortRead.git" + version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908') + version('1.40.0', commit='0cbe4b62b0be4c5f2e2670da17493423446e008f') + version('1.38.0', commit='e9498f04b7b4bf0212bbb10ec7e3de2d7699f4bf') + version('1.36.1', commit='176c34eddf4a416d30c69cb4ac197141ba42e66f') version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd') - depends_on('r@3.4.0:3.4.9', when='@1.34.2') - depends_on('r-latticeextra', type=('build', 'run')) - depends_on('r-lattice', type=('build', 'run')) - depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r-hwriter', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) - depends_on('r-genomicalignments', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.1:', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) + depends_on('r-genomicalignments@1.5.4:', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.1.19:', type=('build', 'run')) + depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-hwriter', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-latticeextra', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + + depends_on('r-biocgenerics@0.23.3:', when='@1.36.1:', type=('build', 'run')) + + depends_on('r-biostrings@2.47.6:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.38.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.38.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py index a619f1902c..f9617e6eb9 100644 --- a/var/spack/repos/builtin/packages/r-siggenes/package.py +++ b/var/spack/repos/builtin/packages/r-siggenes/package.py @@ -7,16 +7,23 @@ from spack import * class RSiggenes(RPackage): - """Identification of differentially expressed genes and estimation of the + """Multiple Testing using SAM and Efron's Empirical Bayes Approaches. + + Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).""" - homepage = "http://bioconductor.org/packages/siggenes/" + homepage = "https://bioconductor.org/packages/siggenes" git = "https://git.bioconductor.org/packages/siggenes.git" + version('1.58.0', commit='69500158d69942cf7c62f583830933cf8baf89a1') + version('1.56.0', commit='3e929feaa76311be07ff51ad807e657b0b521f6f') + version('1.54.0', commit='1630e42652192e3e4e48e9e78e53665a120cfc7f') + version('1.52.0', commit='dc46cf4b6053ea99c6c841d661f97390653c2e71') version('1.50.0', commit='b1818f26e1449005ffd971df6bda8da0303080bc') depends_on('r-biobase', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.50.0') + + depends_on('r-scrime@1.2.5:', when='@1.58.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py index a5798e0575..070bf60d69 100644 --- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py +++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py @@ -7,20 +7,26 @@ from spack import * class RSimpleaffy(RPackage): - """Provides high level functions for reading Affy .CEL files, - phenotypic data, and then computing simple things with it, such as - t-tests, fold changes and the like. Makes heavy use of the affy - library. Also has some basic scatter plot functions and mechanisms - for generating high resolution journal figures...""" + """Very simple high level analysis of Affymetrix data. - homepage = "http://bioconductor.org/packages/simpleaffy/" + Provides high level functions for reading Affy .CEL files, phenotypic + data, and then computing simple things with it, such as t-tests, fold + changes and the like. Makes heavy use of the affy library. Also has some + basic scatter plot functions and mechanisms for generating high + resolution journal figures...""" + + homepage = "https://bioconductor.org/packages/simpleaffy" git = "https://git.bioconductor.org/packages/simpleaffy.git" + version('2.60.0', commit='b32b5e7d5c65e43c10f98ab8684a1086a06d04f9') + version('2.58.0', commit='70cf1199bad620f60eaa288279632110bb571200') + version('2.56.0', commit='a05d768180b8713ad9e1dc46d491b7ef389b299d') + version('2.54.0', commit='6876e028d412b14504ad3915cbec1a189e9c6478') version('2.52.0', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385') - depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.1.12:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-affy', type=('build', 'run')) + depends_on('r-affy@1.33.6:', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-gcrma', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.52.0') diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py new file mode 100644 index 0000000000..71b58ecc9f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSinglecellexperiment(RPackage): + """S4 Classes for Single Cell Data. + + Defines a S4 class for storing data from single-cell experiments. This + includes specialized methods to store and retrieve spike-in information, + dimensionality reduction coordinates and size factors for each cell, + along with the usual metadata for genes and libraries.""" + + homepage = "https://bioconductor.org/packages/SingleCellExperiment" + git = "https://git.bioconductor.org/packages/SingleCellExperiment.git" + + version('1.6.0', commit='baa51d77a8dacd2a22e7293095a8cffaaa3293b4') + version('1.4.1', commit='b1efcb338e9176ae6829bb897957aa37e74d4870') + version('1.2.0', commit='fe512259da79e0c660b322b5387e9bb16f2e6321') + version('1.0.0', commit='545e974aa7ca7855e039bf9e3030290cd71d9031') + + depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + + depends_on('r@3.5:', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py index a78a59236c..1a71934f03 100644 --- a/var/spack/repos/builtin/packages/r-snprelate/package.py +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -7,27 +7,34 @@ from spack import * class RSnprelate(RPackage): - """Genome-wide association studies (GWAS) are widely used to investigate + """Parallel Computing Toolset for Relatedness and Principal Component + Analysis of SNP Data. + + Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many - computational challenges. We developed an R package SNPRelate to - provide a binary format for single-nucleotide polymorphism (SNP) data - in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. - The GDS format offers the efficient operations specifically designed - for integers with two bits, since a SNP could occupy only two bits. + computational challenges. We developed an R package SNPRelate to provide + a binary format for single-nucleotide polymorphism (SNP) data in GWAS + utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS + format offers the efficient operations specifically designed for + integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 - classes and generic functions. The extended GDS format is implemented - in the SeqArray package to support the storage of single nucleotide + classes and generic functions. The extended GDS format is implemented in + the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.""" homepage = "https://bioconductor.org/packages/SNPRelate" git = "https://git.bioconductor.org/packages/SNPRelate.git" + version('1.18.1', commit='81c581bf76392efdc8ba237ca2e42ca1dba788ca') + version('1.16.0', commit='0e38e8df4af87dff6c27a23af2867661998c0d85') + version('1.14.0', commit='9501cbfc411aa320e58654a865fda2e9077977af') version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe') + version('1.10.2', commit='3f5c4010871df742e7a460586b38ad0c2fd37aeb') - depends_on('r@3.4.0:3.4.9', when='@1.12.2') + depends_on('r@2.15:', type=('build', 'run')) depends_on('r-gdsfmt@1.8.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py index 7a1c8b2ca3..a907249f35 100644 --- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -7,16 +7,23 @@ from spack import * class RSomaticsignatures(RPackage): - """The SomaticSignatures package identifies mutational signatures of - single nucleotide variants (SNVs). It provides a infrastructure related - to the methodology described in Nik-Zainal (2012, Cell), with - flexibility in the matrix decomposition algorithms.""" + """Somatic Signatures. - homepage = "https://bioconductor.org/packages/SomaticSignatures/" + The SomaticSignatures package identifies mutational signatures of single + nucleotide variants (SNVs). It provides a infrastructure related to the + methodology described in Nik-Zainal (2012, Cell), with flexibility in + the matrix decomposition algorithms.""" + + homepage = "https://bioconductor.org/packages/SomaticSignatures" git = "https://git.bioconductor.org/packages/SomaticSignatures.git" + version('2.20.0', commit='dbedc30d92b600b3a17de596ebe38d15982c70c6') + version('2.18.0', commit='facccd67eee5202fcbe6ad32e667546546e7ccff') + version('2.16.0', commit='4ae348d9fa096c0ec307df95149991edf6044977') + version('2.14.0', commit='b12d24f86e96a7c6a17cbbad21ca14fa3aa7c60f') version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-nmf', type=('build', 'run')) @@ -30,4 +37,3 @@ class RSomaticsignatures(RPackage): depends_on('r-pcamethods', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.12.1') diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py index c5417ffa2b..d157e1f478 100644 --- a/var/spack/repos/builtin/packages/r-spem/package.py +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -7,14 +7,20 @@ from spack import * class RSpem(RPackage): - """This package can optimize the parameter in S-system models given time - series data""" + """S-system parameter estimation method. - homepage = "https://bioconductor.org/packages/SPEM/" + This package can optimize the parameter in S-system models given time + series data""" + + homepage = "https://bioconductor.org/packages/SPEM" git = "https://git.bioconductor.org/packages/SPEM.git" + version('1.24.0', commit='537ed19e466008f2972a246479b327c95177a99e') + version('1.22.0', commit='fddb7cd1f81e47eae603724ea149c2adca5b3eb4') + version('1.20.0', commit='b0e1049c61a35da00882d21026f4c1eb03b17517') version('1.18.0', commit='3ab425dd9889885eac328d26b73366a875cd250b') + version('1.16.0', commit='9c0a96374086765db9c81e36a662999067fa4cc7') + depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-rsolnp', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.18.0') diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py index fb36786018..324cdb31f8 100644 --- a/var/spack/repos/builtin/packages/r-sseq/package.py +++ b/var/spack/repos/builtin/packages/r-sseq/package.py @@ -7,13 +7,28 @@ from spack import * class RSseq(RPackage): - """Shrinkage estimation of dispersion in Negative Binomial models for - RNA-seq experiments with small sample size""" + """Shrinkage estimation of dispersion in Negative Binomial models for RNA- + seq experiments with small sample size. - homepage = "https://www.bioconductor.org/packages/sSeq/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/sSeq_1.20.0.tar.gz" + The purpose of this package is to discover the genes that are + differentially expressed between two conditions in RNA-seq experiments. + Gene expression is measured in counts of transcripts and modeled with + the Negative Binomial (NB) distribution using a shrinkage approach for + dispersion estimation. The method of moment (MM) estimates for + dispersion are shrunk towards an estimated target, which minimizes the + average squared difference between the shrinkage estimates and the + initial estimates. The exact per-gene probability under the NB model is + calculated, and used to test the hypothesis that the expected expression + of a gene in two conditions identically follow a NB distribution.""" - version('1.20.0', sha256='0fddcb238a6c401987843debe5b46dc03c22a1ee04df670f0d502e86a4f2144f') + homepage = "https://bioconductor.org/packages/sSeq" + git = "https://git.bioconductor.org/packages/sSeq.git" + + version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc') + version('1.20.1', commit='91f31440323612cb04beb44404ab0a1bcb3ad87d') + version('1.18.0', commit='1f65e5a55ce0d51672b785450031872e6db5ca0f') + version('1.16.0', commit='b7f2b99dbd4a12ee9d18b0ec9898f13f1038479e') + version('1.14.0', commit='20ccffeb60196914975aa1feef902ddba659c571') depends_on('r@3.0:', type=('build', 'run')) depends_on('r-catools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py index d9aaa00ee7..f7607ee67b 100644 --- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py @@ -7,31 +7,39 @@ from spack import * class RSummarizedexperiment(RPackage): - """The SummarizedExperiment container contains one or more assays, each + """SummarizedExperiment container. + + The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows - typically represent genomic ranges of interest and the columns - represent samples.""" + typically represent genomic ranges of interest and the columns represent + samples.""" - homepage = "https://bioconductor.org/packages/SummarizedExperiment/" + homepage = "https://bioconductor.org/packages/SummarizedExperiment" git = "https://git.bioconductor.org/packages/SummarizedExperiment.git" - version('1.10.0', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b') + version('1.14.1', commit='2c68d99e11c7345e5ed388370822ea48395c64a4') + version('1.12.0', commit='5f8416864636add121ec1d6737ebb89a42227fd7') + version('1.10.1', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b') version('1.8.1', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7') version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0') - depends_on('r-genomicranges@1.27.22:', when='@1.6.5', type=('build', 'run')) - depends_on('r-genomicranges@1.29.14:', when='@1.8.1', type=('build', 'run')) - depends_on('r-genomicranges@1.31.17:', when='@1.10.0', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.22:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-delayedarray@0.1.9:', when='@1.6.5', type=('build', 'run')) - depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.1.9:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.25:', when='@1.10.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.16:', when='@1.10.0', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomeinfodb@1.13.1:', when='@1.10.0', type=('build', 'run')) - depends_on('r-biocgenerics@0.15.3:', when='@1.6.5:', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.6.5:1.9.9', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.10.0', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.7.2:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + + depends_on('r-genomicranges@1.29.14:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-iranges@2.11.17:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.8.1:', type=('build', 'run')) + + depends_on('r-genomicranges@1.31.17:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@1.10.1:', type=('build', 'run')) + + depends_on('r-genomicranges@1.33.6:', when='@1.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py index e6ec8b9715..547bfdd27b 100644 --- a/var/spack/repos/builtin/packages/r-sva/package.py +++ b/var/spack/repos/builtin/packages/r-sva/package.py @@ -7,14 +7,37 @@ from spack import * class RSva(RPackage): - """Surrogate Variable Analysis.""" + """Surrogate Variable Analysis. - homepage = "https://www.bioconductor.org/packages/sva/" + The sva package contains functions for removing batch effects and other + unwanted variation in high-throughput experiment. Specifically, the sva + package contains functions for the identifying and building surrogate + variables for high-dimensional data sets. Surrogate variables are + covariates constructed directly from high-dimensional data (like gene + expression/RNA sequencing/methylation/brain imaging data) that can be + used in subsequent analyses to adjust for unknown, unmodeled, or latent + sources of noise. The sva package can be used to remove artifacts in + three ways: (1) identifying and estimating surrogate variables for + unknown sources of variation in high-throughput experiments (Leek and + Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch + effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) + removing batch effects with known control probes (Leek 2014 biorXiv). + Removing batch effects and using surrogate variables in differential + expression analysis have been shown to reduce dependence, stabilize + error rate estimates, and improve reproducibility, see (Leek and Storey + 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews + Genetics).""" + + homepage = "https://bioconductor.org/packages/sva" git = "https://git.bioconductor.org/packages/sva.git" + version('3.32.1', commit='1b8286734d00533b49d9f1456b6523cc778bb744') + version('3.30.1', commit='fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c') + version('3.28.0', commit='dd4937229dbccd2f383a04d5237fe147a884728d') + version('3.26.0', commit='3cc5e75413c35ed5511892f5c36a8b5cb454937e') version('3.24.4', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73') - depends_on('r@3.4.0:3.4.9', when='@3.24.4') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py index 393071cb67..e9c74cea4e 100644 --- a/var/spack/repos/builtin/packages/r-tfbstools/package.py +++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py @@ -7,25 +7,25 @@ from spack import * class RTfbstools(RPackage): - """TFBSTools is a package for the analysis and manipulation of - transcription factor binding sites. + """Software Package for Transcription Factor Binding Site (TFBS) Analysis. - It includes matrices conversion between Position Frequency Matirx (PFM), - Position Weight Matirx (PWM) and Information Content Matrix (ICM). It - can also scan putative TFBS from sequence/alignment, query JASPAR - database and provides a wrapper of de novo motif discovery software. TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS - from sequence/alignment, query JASPAR database and provides a wrapper - of de novo motif discovery software.""" + from sequence/alignment, query JASPAR database and provides a wrapper of + de novo motif discovery software.""" - homepage = "http://bioconductor.org/packages/TFBSTools/" + homepage = "https://bioconductor.org/packages/TFBSTools" git = "https://git.bioconductor.org/packages/TFBSTools.git" + version('1.22.0', commit='613d3567fd662b65269bd200c5aa5f87ac6a4612') + version('1.20.0', commit='74035fc6beb1af82f171c11ef2b0a8817714c5bc') + version('1.18.0', commit='17e12b9f3dcb9059d414307ec0bc23ed1ee33294') version('1.16.0', commit='565436a5a674d4dea7279e796a20c5bd2034f65a') + version('1.14.2', commit='e429fdefb6f7ee4585dd2a8ca3d0ced7a5bed4ff') + depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-biobase@2.28:', type=('build', 'run')) depends_on('r-biostrings@2.36.4:', type=('build', 'run')) depends_on('r-biocgenerics@0.14.0:', type=('build', 'run')) @@ -46,4 +46,3 @@ class RTfbstools(RPackage): depends_on('r-tfmpvalue@0.0.5:', type=('build', 'run')) depends_on('r-xml@3.98-1.3:', type=('build', 'run')) depends_on('r-xvector@0.8.0:', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.16.0') diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py index 0ac49d576e..71da1a51db 100644 --- a/var/spack/repos/builtin/packages/r-tmixclust/package.py +++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py @@ -7,17 +7,24 @@ from spack import * class RTmixclust(RPackage): - """Implementation of a clustering method for time series gene expression - data based on mixed-effects models with Gaussian variables and - non-parametric cubic splines estimation. The method can robustly account - for the high levels of noise present in typical gene expression time - series datasets.""" + """Time Series Clustering of Gene Expression with Gaussian Mixed-Effects + Models and Smoothing Splines. - homepage = "https://bioconductor.org/packages/TMixClust/" + Implementation of a clustering method for time series gene expression + data based on mixed-effects models with Gaussian variables and non- + parametric cubic splines estimation. The method can robustly account for + the high levels of noise present in typical gene expression time series + datasets.""" + + homepage = "https://bioconductor.org/packages/TMixClust" git = "https://git.bioconductor.org/packages/TMixClust.git" + version('1.6.0', commit='9f5f78e52538d15f402c8f6e4c60f7212c7bc548') + version('1.4.0', commit='a52fcae6e7a5dd41e7afbe128f35397e8bc8cb12') + version('1.2.0', commit='0250c0b238f08077b5b9ff17c2f3b7633c67dc3c') version('1.0.1', commit='0ac800210e3eb9da911767a80fb5582ab33c0cad') + depends_on('r@3.4:', type=('build', 'run')) depends_on('r-gss', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) @@ -26,4 +33,3 @@ class RTmixclust(RPackage): depends_on('r-flexclust', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-spem', type=('build', 'run')) - depends_on('r@3.4.3:3.4.9', when='@1.0.1') diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py index 7822f1f543..b476638246 100644 --- a/var/spack/repos/builtin/packages/r-topgo/package.py +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -7,24 +7,29 @@ from spack import * class RTopgo(RPackage): - """topGO package provides tools for testing GO terms while accounting - for the topology of the GO graph. Different test statistics and - different methods for eliminating local similarities and dependencies - between GO terms can be implemented and applied.""" + """Enrichment Analysis for Gene Ontology. - homepage = "https://www.bioconductor.org/packages/topGO/" + topGO package provides tools for testing GO terms while accounting for + the topology of the GO graph. Different test statistics and different + methods for eliminating local similarities and dependencies between GO + terms can be implemented and applied.""" + + homepage = "https://bioconductor.org/packages/topGO" git = "https://git.bioconductor.org/packages/topGO.git" + version('2.36.0', commit='c2f6c187b41c4aa44cc92ac781fdd878491a4019') + version('2.34.0', commit='44cb5eaba515b365b7b2a8c22df0a45883db6b4d') + version('2.32.0', commit='78ce3068fc06ae38d55219759fa177e2fcb3f596') version('2.30.1', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa') version('2.28.0', commit='066a975d460046cce33fb27e74e6a0ebc33fd716') - depends_on('r@3.4.0:3.4.9') - depends_on('r-dbi', type=('build', 'run')) - depends_on('r-matrixstats', type=('build', 'run')) - depends_on('r-lattice', type=('build', 'run')) - depends_on('r-sparsem@0.73:', type=('build', 'run')) - depends_on('r-annotationdbi@1.7.19:', type=('build', 'run')) - depends_on('r-go-db@2.3.0:', type=('build', 'run')) - depends_on('r-biobase@2.0.0:', type=('build', 'run')) - depends_on('r-graph@1.14.0:', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.13.6:', type=('build', 'run')) + depends_on('r-graph@1.14.0:', type=('build', 'run')) + depends_on('r-biobase@2.0.0:', type=('build', 'run')) + depends_on('r-go-db@2.3.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.7.19:', type=('build', 'run')) + depends_on('r-sparsem@0.73:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tweenr/package.py b/var/spack/repos/builtin/packages/r-tweenr/package.py new file mode 100644 index 0000000000..af10b88998 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tweenr/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTweenr(RPackage): + """tweenr: Interpolate Data for Smooth Animations""" + + homepage = "https://github.com/thomasp85/tweenr" + url = "https://cloud.r-project.org/src/contrib/tweenr_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tweenr" + + version('1.0.1', sha256='efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-farver', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-rcpp@0.12.3:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py new file mode 100644 index 0000000000..748096b6cc --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tximport/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTximport(RPackage): + """Import and summarize transcript-level estimates for transcript- and + gene-level analysis. + + Imports transcript-level abundance, estimated counts and transcript + lengths, and summarizes into matrices for use with downstream gene-level + analysis packages. Average transcript length, weighted by sample- + specific transcript abundance estimates, is provided as a matrix which + can be used as an offset for different expression of gene-level + counts.""" + + homepage = "https://bioconductor.org/packages/tximport" + git = "https://git.bioconductor.org/packages/tximport.git" + + version('1.12.3', commit='acbdead961471c3b910d720f73bd0af1b7a07c57') + version('1.10.1', commit='cd8f81cf7140f61d4a4f25f89451fb49e2cd4bd3') + version('1.8.0', commit='cc91b8389ca4c16b0f588bdeb63d051a11e8a705') + version('1.6.0', commit='0b1ba6c6622e02b954812c88454c28e8efb75e0b') + version('1.4.0', commit='bfbd2436eca21acf212b76a658b49cfb5e116d6b') diff --git a/var/spack/repos/builtin/packages/r-upsetr/package.py b/var/spack/repos/builtin/packages/r-upsetr/package.py new file mode 100644 index 0000000000..a40a872dcd --- /dev/null +++ b/var/spack/repos/builtin/packages/r-upsetr/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUpsetr(RPackage): + """UpSetR: A More Scalable Alternative to Venn and Euler Diagrams + forVisualizing Intersecting Sets""" + + homepage = "http://github.com/hms-dbmi/UpSetR" + url = "https://cloud.r-project.org/src/contrib/UpSetR_1.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/UpSetR" + + version('1.4.0', sha256='351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py index 5293b84150..2dc08887b9 100644 --- a/var/spack/repos/builtin/packages/r-variantannotation/package.py +++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py @@ -7,28 +7,53 @@ from spack import * class RVariantannotation(RPackage): - """Annotate variants, compute amino acid coding changes, predict coding + """Annotation of Genetic Variants. + + Annotate variants, compute amino acid coding changes, predict coding outcomes.""" - homepage = "https://www.bioconductor.org/packages/VariantAnnotation/" + homepage = "https://bioconductor.org/packages/VariantAnnotation" git = "https://git.bioconductor.org/packages/VariantAnnotation.git" + version('1.30.1', commit='fb1ab00872570afb280522c4663e347dafc07a9e') + version('1.28.13', commit='0393347b8ce2d5edf1a61589be93e6a93eda3419') + version('1.26.1', commit='60ae67598cc3d7ed20ee6417920f8c209085faaf') + version('1.24.5', commit='468d7f53fd743e04c9af853d58e871b4cc13a090') version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-genomeinfodb', type=('build', 'run')) - depends_on('r-genomicranges', type=('build', 'run')) - depends_on('r-summarizedexperiment', type=('build', 'run')) - depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run')) + depends_on('r-rsamtools@1.23.10:', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-xvector', type=('build', 'run')) - depends_on('r-biostrings', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-bsgenome', type=('build', 'run')) - depends_on('r-rtracklayer', type=('build', 'run')) - depends_on('r-genomicfeatures', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.22.3') + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.3.25:', type=('build', 'run')) + depends_on('r-xvector@0.5.6:', type=('build', 'run')) + depends_on('r-biostrings@2.33.5:', type=('build', 'run')) + depends_on('r-annotationdbi@1.27.9:', type=('build', 'run')) + depends_on('r-bsgenome@1.37.6:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.16:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.27.4:', type=('build', 'run')) + + depends_on('r-genomeinfodb@1.15.2:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.9.9:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.24:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-bsgenome@1.47.3:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.31.3:', when='@1.26.1:', type=('build', 'run')) + + depends_on('r-rsamtools@1.33.6:', when='@1.28.13:', type=('build', 'run')) + + depends_on('r-rsamtools@1.99.0:', when='@1.30.1:', type=('build', 'run')) + depends_on('r-rhtslib', when='@1.30.1:', type=('build', 'run')) + + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-vioplot/package.py b/var/spack/repos/builtin/packages/r-vioplot/package.py new file mode 100644 index 0000000000..bc9daef0e9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vioplot/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RVioplot(RPackage): + """vioplot: Violin Plot""" + + homepage = "https://cloud.r-project.org/package=vioplot" + url = "https://cloud.r-project.org/src/contrib/vioplot_0.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vioplot" + + version('0.3.2', sha256='7b51d0876903a3c315744cb051ac61920eeaa1f0694814959edfae43ce956e8e') + + depends_on('r-sm', type=('build', 'run')) + depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py index 5db8fec045..d9272d8efb 100644 --- a/var/spack/repos/builtin/packages/r-vsn/package.py +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -7,28 +7,36 @@ from spack import * class RVsn(RPackage): - """The package implements a method for normalising microarray intensities, - and works for single- and multiple-color arrays. It can also be used - for data from other technologies, as long as they have similar format. - The method uses a robust variant of the maximum-likelihood estimator - for an additive-multiplicative error model and affine calibration. The - model incorporates data calibration step (a.k.a. normalization), a - model for the dependence of the variance on the mean intensity and a - variance stabilizing data transformation. Differences between - transformed intensities are analogous to "normalized log-ratios". - However, in contrast to the latter, their variance is independent of - the mean, and they are usually more sensitive and specific in detecting - differential transcription.""" - - homepage = "https://www.bioconductor.org/packages/vsn/" + """Variance stabilization and calibration for microarray data. + + The package implements a method for normalising microarray intensities, + and works for single- and multiple-color arrays. It can also be used for + data from other technologies, as long as they have similar format. The + method uses a robust variant of the maximum-likelihood estimator for an + additive-multiplicative error model and affine calibration. The model + incorporates data calibration step (a.k.a. normalization), a model for + the dependence of the variance on the mean intensity and a variance + stabilizing data transformation. Differences between transformed + intensities are analogous to "normalized log-ratios". However, in + contrast to the latter, their variance is independent of the mean, and + they are usually more sensitive and specific in detecting differential + transcription.""" + + homepage = "https://bioconductor.org/packages/vsn" git = "https://git.bioconductor.org/packages/vsn.git" + version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe') + version('3.50.0', commit='ad49fcc288c6065d0f04040acd688e7f0d7d927e') + version('3.48.1', commit='d57f64112004b1d73b3be625949830209de027eb') + version('3.46.0', commit='7ecfd20452348da27d6fcc052cbff2b9be777792') version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-hexbin', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@3.44.0') + depends_on('r-hexbin', when='@3.44.0', type=('build', 'run')) + + depends_on('r@3.4.0:', when='@3.46.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py index f36835b58c..17fc9d67f0 100644 --- a/var/spack/repos/builtin/packages/r-xde/package.py +++ b/var/spack/repos/builtin/packages/r-xde/package.py @@ -7,18 +7,26 @@ from spack import * class RXde(RPackage): - """Multi-level model for cross-study detection of differential gene - expression.""" + """XDE: a Bayesian hierarchical model for cross-study analysis of + differential gene expression.""" - homepage = "https://www.bioconductor.org/packages/XDE/" + homepage = "https://bioconductor.org/packages/XDE" git = "https://git.bioconductor.org/packages/XDE.git" + version('2.30.0', commit='058af6f1e431522778f970bf61f834620d3d7dd7') + version('2.28.0', commit='b8cc7d0840ce1324644e8b4a750fbb964884498b') + version('2.26.0', commit='7bf6368037937c53542447175061c2e2059ee3be') + version('2.24.0', commit='fd5f245f82893657dc36e5a67a1d3b8255772462') version('2.22.0', commit='25bcec965ae42a410dd285a9db9be46d112d8e81') - depends_on('r-biobase', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-biobase@2.5.5:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) depends_on('r-mergemaid', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@2.22.0') + + depends_on('r-rcolorbrewer', when='@2.24.0:', type=('build', 'run')) + depends_on('r-genemeta', when='@2.24.0:', type=('build', 'run')) + depends_on('r-siggenes', when='@2.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py index 661017ba75..b718a85d97 100644 --- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py +++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py @@ -7,12 +7,18 @@ from spack import * class RXmapbridge(RPackage): - """xmapBridge can plot graphs in the X:Map genome browser. This package + """Export plotting files to the xmapBridge for visualisation in X:Map. + + xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.""" - homepage = "https://www.bioconductor.org/packages/xmapbridge/" + homepage = "https://bioconductor.org/packages/xmapbridge" git = "https://git.bioconductor.org/packages/xmapbridge.git" + version('1.42.0', commit='d79c80dfc1a0ed3fd6d3e7a7c3a4aff778537ca9') + version('1.40.0', commit='00a2993863f28711e237bc937fa0ba2d05f81684') + version('1.38.0', commit='08138f00385fa0c669ff4cc33d7eac3d29cd615d') + version('1.36.0', commit='e44f648c9da9eaa130849a738d90dc11685050e2') version('1.34.0', commit='f162e1f72ead5f5a1aede69032d5771a6572d965') - depends_on('r@3.4.0:3.4.9', when='@1.34.0') + depends_on('r@2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py index 9623be17c0..9cfe599d55 100644 --- a/var/spack/repos/builtin/packages/r-xvector/package.py +++ b/var/spack/repos/builtin/packages/r-xvector/package.py @@ -7,21 +7,33 @@ from spack import * class RXvector(RPackage): - """Memory efficient S4 classes for storing sequences "externally" (behind - an R external pointer, or on disk).""" + """Foundation of external vector representation and manipulation in + Bioconductor. - homepage = "https://bioconductor.org/packages/XVector/" + Provides memory efficient S4 classes for storing sequences "externally" + (e.g. behind an R external pointer, or on disk).""" + + homepage = "https://bioconductor.org/packages/XVector" git = "https://git.bioconductor.org/packages/XVector.git" + version('0.24.0', commit='e5109cb2687724b9fddddf296c07a82bae4c551d') + version('0.22.0', commit='b5e107a5fd719e18374eb836eb498b529afa4473') version('0.20.0', commit='a83a7ea01f6a710f0ba7d9fb021cfa795b291cb4') + version('0.18.0', commit='27acf47282c9880b54d04dff46c1e50f0c87fa6b') version('0.16.0', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f') - depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-biocgenerics@0.19.2:', when='@0.20.0', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) - depends_on('r-s4vectors@0.17.24:', when='@0.20.0', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-iranges@2.13.16:', when='@0.20.0', type=('build', 'run')) + depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.19.2:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@0.16.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@0.20.0', type=('build', 'run')) + + depends_on('r-s4vectors@0.15.14:', when='@0.18.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.17.24:', when='@0.20.0:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@0.20.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.19.15:', when='@0.22.0:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@0.22.0:', type=('build', 'run')) + + depends_on('r-s4vectors@0.21.13:', when='@0.24.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py index c41dca0f4d..b1f0cd1316 100644 --- a/var/spack/repos/builtin/packages/r-yapsa/package.py +++ b/var/spack/repos/builtin/packages/r-yapsa/package.py @@ -7,18 +7,25 @@ from spack import * class RYapsa(RPackage): - """This package provides functions and routines useful in the analysis of + """Yet Another Package for Signature Analysis. + + This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.""" - homepage = "http://bioconductor.org/packages/YAPSA/" + homepage = "https://bioconductor.org/packages/YAPSA" git = "https://git.bioconductor.org/packages/YAPSA.git" + version('1.10.0', commit='06af18e424868eb0f0be6c80e90cbab1eabf3d73') + version('1.8.0', commit='402f3f7774fdf8afc7883579ad651c26df0f8fdb') + version('1.6.0', commit='2455d272b076835ddb36ad21c01ef15af66abc36') + version('1.4.0', commit='6f24150a0689d5215983975ece96c8c205923c72') version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d') + depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-lsei', type=('build', 'run')) @@ -30,8 +37,8 @@ class RYapsa(RPackage): depends_on('r-corrplot', type=('build', 'run')) depends_on('r-dendextend', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) + depends_on('r-circlize', type=('build', 'run')) depends_on('r-gtrellis', type=('build', 'run')) depends_on('r-pmcmr', type=('build', 'run')) depends_on('r-complexheatmap', type=('build', 'run')) depends_on('r-keggrest', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py index 342fea2b18..cbab1bb902 100644 --- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py +++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py @@ -7,14 +7,19 @@ from spack import * class RYaqcaffy(RPackage): - """Quality control of Affymetrix GeneChip expression data and + """Affymetrix expression data quality control and reproducibility analysis. + + Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.""" - homepage = "http://bioconductor.org/packages/yaqcaffy/" + homepage = "https://bioconductor.org/packages/yaqcaffy" git = "https://git.bioconductor.org/packages/yaqcaffy.git" + version('1.44.0', commit='00898f3ec9ac0beadbcf57bda3d3c1c99fb0c3c0') + version('1.42.0', commit='a4af673774165e087499ecc35f96aab6bbfbeea1') + version('1.40.0', commit='0c78f8ff8f675305f6fa4b052d2482e9aee551bb') + version('1.38.0', commit='d57100862c2dc0f5e7684f318b9ceda7349352be') version('1.36.0', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6') - depends_on('r-simpleaffy', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.36.0') + depends_on('r-simpleaffy@2.19.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py index 12ffca6910..4623c73c81 100644 --- a/var/spack/repos/builtin/packages/r-yarn/package.py +++ b/var/spack/repos/builtin/packages/r-yarn/package.py @@ -7,16 +7,22 @@ from spack import * class RYarn(RPackage): - """Expedite large RNA-Seq analyses using a combination of previously + """YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization. + + Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.""" - homepage = "https://bioconductor.org/packages/yarn/" + homepage = "https://bioconductor.org/packages/yarn" git = "https://git.bioconductor.org/packages/yarn.git" + version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472') + version('1.8.1', commit='ee0723d4dbf082b4469ca9c22cce4f1a2ac81c04') + version('1.6.0', commit='19d1b2ef275f294bd318b86e0d237c271880117d') + version('1.4.0', commit='36100f40b9e520c072d0d5ebf963723b813f7db0') version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697') depends_on('r-biobase', type=('build', 'run')) @@ -30,4 +36,3 @@ class RYarn(RPackage): depends_on('r-readr', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-quantro', type=('build', 'run')) - depends_on('r@3.4.0:3.4.9', when='@1.2.0') diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py index 3b36a02b16..a4b830e3db 100644 --- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py +++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py @@ -7,17 +7,18 @@ from spack import * class RZlibbioc(RPackage): - """This package uses the source code of zlib-1.2.5 to create libraries - for systems that do not have these available via other means (most - Linux and Mac users should have system-level access to zlib, and no - direct need for this package). See the vignette for instructions - on use.""" + """An R packaged zlib-1.2.5. - homepage = "http://bioconductor.org/packages/release/bioc/html/zlibbioc.html" + This package uses the source code of zlib-1.2.5 to create libraries for + systems that do not have these available via other means (most Linux and + Mac users should have system-level access to zlib, and no direct need + for this package). See the vignette for instructions on use.""" + + homepage = "https://bioconductor.org/packages/zlibbioc" git = "https://git.bioconductor.org/packages/zlibbioc.git" + version('1.30.0', commit='99eae5b05968bf6abc9b54b9031afd93517381e0') + version('1.28.0', commit='b825b042742ba45455fc284b988ff4cd2a33222c') version('1.26.0', commit='2e3ab097caa09a5e3ddaa3469b13e19a7224da0d') + version('1.24.0', commit='2990059338d1b987d098c009b0bfa806bd24afec') version('1.22.0', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5') - - depends_on('r@3.4.0:3.4.9', when='@1.22.0', type=('build', 'run')) - depends_on('r@3.5.0:3.5.9', when='@1.26.0', type=('build', 'run')) |