diff options
Diffstat (limited to 'var')
193 files changed, 1177 insertions, 635 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index b1255be5a8..0ae69276b2 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -7,11 +7,15 @@ from spack import * class RA4(RPackage): - """Automated Affymetrix Array Analysis Umbrella Package.""" + """Automated Affymetrix Array Analysis Umbrella Package + + Umbrella package is available for the entire Automated Affymetrix Array + Analysis suite of package.""" homepage = "https://bioconductor.org/packages/a4" git = "https://git.bioconductor.org/packages/a4.git" + version('1.38.0', commit='5b7a9087bab10c55e24707e96e48046995236c94') version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712') version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d') version('1.28.0', commit='e81a8c15e1062ed9433e2d4d333f0484bc0e8bfb') diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index f6d8addd6d..08f6432e2e 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -7,25 +7,29 @@ from spack import * class RA4base(RPackage): - """Automated Affymetrix Array Analysis Base Package.""" + """Automated Affymetrix Array Analysis Base Package + + Base utility functions are available for the Automated Affymetrix Array + Analysis set of packages.""" homepage = "https://bioconductor.org/packages/a4Base" git = "https://git.bioconductor.org/packages/a4Base.git" + version('1.38.0', commit='4add242fa9c62795aca5b0dfca34a43484c5aa82') 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-a4preproc', type=('build', 'run')) + depends_on('r-a4core', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annaffy', type=('build', 'run')) depends_on('r-mpm', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) depends_on('r-glmnet', type=('build', 'run')) - depends_on('r-a4preproc', type=('build', 'run')) - depends_on('r-a4core', type=('build', 'run')) depends_on('r-gplots', type=('build', 'run')) + depends_on('r-annotationdbi', when='@:1.32.0', 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 1e668aaeec..9886e0023d 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -7,11 +7,16 @@ from spack import * class RA4classif(RPackage): - """Automated Affymetrix Array Analysis Classification Package.""" + """Automated Affymetrix Array Analysis Classification Package + + Functionalities for classification of Affymetrix microarray data, + integrating within the Automated Affymetrix Array Analysis set of + packages.""" homepage = "https://bioconductor.org/packages/a4Classif" git = "https://git.bioconductor.org/packages/a4Classif.git" + version('1.38.0', commit='c4d058813efb835774813b2d69c52912162f8e75') version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88') version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3') version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7') @@ -20,8 +25,9 @@ class RA4classif(RPackage): depends_on('r-a4core', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) - depends_on('r-mlinterfaces', type=('build', 'run')) + depends_on('r-biobase', when='@1.38.0:', type=('build', 'run')) depends_on('r-rocr', type=('build', 'run')) depends_on('r-pamr', type=('build', 'run')) depends_on('r-glmnet', type=('build', 'run')) depends_on('r-varselrf', type=('build', 'run')) + depends_on('r-mlinterfaces', when='@:1.32.0', 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 fad8ced723..0cfe0706ef 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -7,11 +7,15 @@ from spack import * class RA4core(RPackage): - """Automated Affymetrix Array Analysis Core Package.""" + """Automated Affymetrix Array Analysis Core Package + + Utility functions for the Automated Affymetrix Array Analysis set of + packages.""" homepage = "https://bioconductor.org/packages/a4Core" git = "https://git.bioconductor.org/packages/a4Core.git" + version('1.38.0', commit='a027dcd3486c64950815ec7c7271f1f65ba3d8a1') version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce') version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141') version('1.28.0', commit='39b6ee29bc2f2fdc5733438c14dc02f8abc6460b') diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index 4826f113d6..b0d3e8e1b9 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -7,15 +7,21 @@ from spack import * class RA4preproc(RPackage): - """Automated Affymetrix Array Analysis Preprocessing Package.""" + """Automated Affymetrix Array Analysis Preprocessing Package + + Utility functions to pre-process data for the Automated Affymetrix Array + Analysis set of packages.""" homepage = "https://bioconductor.org/packages/a4Preproc" git = "https://git.bioconductor.org/packages/a4Preproc.git" + version('1.38.0', commit='c93c223bd531bff090531a109b51f8dcd710d0cb') 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-annotationdbi', type=('build', 'run')) + depends_on('r-biocgenerics', when='@1.38.0:', type=('build', 'run')) + depends_on('r-biobase', when='@1.38.0:', type=('build', 'run')) + depends_on('r-annotationdbi', when='@:1.32.0', 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 c8cd2981b3..5f132f17ba 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -7,16 +7,20 @@ from spack import * class RA4reporting(RPackage): - """Automated Affymetrix Array Analysis Reporting Package.""" + """Automated Affymetrix Array Analysis Reporting Package + + Utility functions to facilitate the reporting of the Automated Affymetrix + Array Analysis Reporting set of packages.""" homepage = "https://bioconductor.org/packages/a4Reporting" git = "https://git.bioconductor.org/packages/a4Reporting.git" + version('1.38.0', commit='cd3cf244e7a299b2485684ed15519cbbda1c590f') 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-annaffy', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) + depends_on('r-annaffy', when='@:1.32.0', 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 778c73943a..d40325e79d 100644 --- a/var/spack/repos/builtin/packages/r-abadata/package.py +++ b/var/spack/repos/builtin/packages/r-abadata/package.py @@ -7,7 +7,7 @@ from spack import * class RAbadata(RPackage): - """Averaged gene expression in human brain regions from Allen Brain Atlas. + """Averaged gene expression in human brain regions from Allen Brain Atlas Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets @@ -21,6 +21,7 @@ class RAbadata(RPackage): homepage = "https://bioconductor.org/packages/ABAData" git = "https://git.bioconductor.org/packages/ABAData.git" + version('1.20.0', commit='c08a841ffb54d6555eb80b90a7a8afe7e48201b3') version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd') version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d') version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a') diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py index 207ac2c9a5..cf00e7def8 100644 --- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py +++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py @@ -7,7 +7,7 @@ from spack import * class RAbaenrichment(RPackage): - """Gene expression enrichment in human brain regions. + """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 @@ -25,19 +25,19 @@ class RAbaenrichment(RPackage): homepage = "https://bioconductor.org/packages/ABAEnrichment" git = "https://git.bioconductor.org/packages/ABAEnrichment.git" + version('1.20.0', commit='608433a0b07e6dd99915dc536a038d960f1be1d5') 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+X', type=('build', 'run')) depends_on('r@3.2:', type=('build', 'run')) + depends_on('r@3.4:', when='@1.8.0:', 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 b1d3a423f5..8a89c49be6 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -8,7 +8,7 @@ from spack import * class RAbsseq(RPackage): """ABSSeq: a new RNA-Seq analysis method based on modelling absolute - expression differences. + expression differences Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and @@ -18,6 +18,7 @@ class RAbsseq(RPackage): homepage = "https://bioconductor.org/packages/ABSSeq" git = "https://git.bioconductor.org/packages/ABSSeq.git" + version('1.44.0', commit='c202b4a059021ed1228ccee7303c69b0aa4ca1ee') version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce') version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a') version('1.34.1', commit='0c3a2514ef644c6e0de3714bc91959a302c9e006') diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 4ae329159a..47d8a802ed 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -7,7 +7,7 @@ from spack import * class RAcde(RPackage): - """Artificial Components Detection of Differentially Expressed Genes. + """Artificial Components Detection of Differentially Expressed Genes This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It @@ -23,6 +23,7 @@ class RAcde(RPackage): homepage = "https://bioconductor.org/packages/acde" git = "https://git.bioconductor.org/packages/acde.git" + version('1.20.0', commit='cefb4f2e2b0ef3c5f51944c0ece7a71294020350') version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417') version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4') version('1.10.0', commit='2c303dec45f3c70bf333a6eacae568a08d5ca010') diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index 7717c0e158..edf91d13e5 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -7,7 +7,7 @@ from spack import * class RAcgh(RPackage): - """Classes and functions for Array Comparative Genomic Hybridization data.. + """Classes and functions for Array Comparative Genomic Hybridization data Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these @@ -17,6 +17,7 @@ class RAcgh(RPackage): homepage = "https://bioconductor.org/packages/aCGH" git = "https://git.bioconductor.org/packages/aCGH.git" + version('1.68.0', commit='91f41a3917ddce43eb05e11c90eb99c467ba2247') version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f') version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21') version('1.58.0', commit='2decc79a21bff5a14d708cdc654e351515b20d3e') diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index f643a9bf31..025950a3d8 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -7,7 +7,7 @@ from spack import * class RAcme(RPackage): - """Algorithms for Calculating Microarray Enrichment (ACME). + """Algorithms for Calculating Microarray Enrichment (ACME) ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or @@ -22,6 +22,7 @@ class RAcme(RPackage): homepage = "https://bioconductor.org/packages/ACME" git = "https://git.bioconductor.org/packages/ACME.git" + version('2.46.0', commit='68f45c9f7d34c28adf6a0fc4245fdf63881109de') version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a') version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b') version('2.36.0', commit='39e056435b9775d35e7f7fc5446c2c3cafe15670') diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index ae538e9ba9..ad1ec8163c 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -7,7 +7,7 @@ from spack import * class RAdsplit(RPackage): - """Annotation-Driven Clustering. + """Annotation-Driven Clustering This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are @@ -17,6 +17,7 @@ class RAdsplit(RPackage): homepage = "https://bioconductor.org/packages/adSplit" git = "https://git.bioconductor.org/packages/adSplit.git" + version('1.60.0', commit='de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd') version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652') version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19') version('1.50.0', commit='a02e2c994e78ececd5a248575109c5ed36c969db') diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index 80d5cbfa05..c6b0adc57c 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -7,7 +7,7 @@ from spack import * class RAffxparser(RPackage): - """Affymetrix File Parsing SDK. + """Affymetrix File Parsing SDK Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix @@ -21,6 +21,7 @@ class RAffxparser(RPackage): homepage = "https://bioconductor.org/packages/affxparser" git = "https://git.bioconductor.org/packages/affxparser.git" + version('1.62.0', commit='b3e988e5c136c3f1a064e1da13730b403c8704c0') version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056') version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f') version('1.52.0', commit='8e0c4b89ee1cb4ff95f58a5dd947249dc718bc58') diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py index 8b26c397b3..47722b3496 100644 --- a/var/spack/repos/builtin/packages/r-affy/package.py +++ b/var/spack/repos/builtin/packages/r-affy/package.py @@ -7,7 +7,7 @@ from spack import * class RAffy(RPackage): - """Methods for Affymetrix Oligonucleotide Arrays. + """Methods for Affymetrix Oligonucleotide Arrays The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience @@ -16,6 +16,7 @@ class RAffy(RPackage): homepage = "https://bioconductor.org/packages/affy" git = "https://git.bioconductor.org/packages/affy.git" + version('1.68.0', commit='1664399610c9aa519399445a2ef8bb9ea2233eac') version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605') version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206') version('1.58.0', commit='4698231f45f225228f56c0708cd477ad450b4ee6') @@ -26,8 +27,7 @@ class RAffy(RPackage): 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-biocmanager', when='@1.60.0:', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - - depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run')) + depends_on('r-biocinstaller', when='@1.54.0:1.58.0', 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 5121ed2feb..af49dd6212 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -7,7 +7,7 @@ from spack import * class RAffycomp(RPackage): - """Graphics Toolbox for Assessment of Affymetrix Expression Measures. + """Graphics Toolbox for Assessment of Affymetrix Expression Measures The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.""" @@ -15,6 +15,7 @@ class RAffycomp(RPackage): homepage = "https://bioconductor.org/packages/affycomp" git = "https://git.bioconductor.org/packages/affycomp.git" + version('1.66.0', commit='388d01af8b1e6ab11051407f77d0206512df8424') version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c') version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef') version('1.56.0', commit='b0994da338be19396e647c680059fd35341b50a2') diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py index cac3fe77f6..324d239007 100644 --- a/var/spack/repos/builtin/packages/r-affycompatible/package.py +++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py @@ -7,7 +7,7 @@ from spack import * class RAffycompatible(RPackage): - """Affymetrix GeneChip software compatibility. + """Affymetrix GeneChip software compatibility This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to @@ -19,6 +19,7 @@ class RAffycompatible(RPackage): homepage = "https://bioconductor.org/packages/AffyCompatible" git = "https://git.bioconductor.org/packages/AffyCompatible.git" + version('1.50.0', commit='3b12d12bd6d1a9f0d45e012817231d137d47089e') version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476') version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8') version('1.40.0', commit='44838bdb5e8c26afbd898c49ed327ddd1a1d0301') diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index bafb957c4f..22c9ddbf12 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -7,7 +7,7 @@ from spack import * class RAffycontam(RPackage): - """structured corruption of affymetrix cel file data. + """structured corruption of affymetrix cel file data structured corruption of cel file data to demonstrate QA effectiveness""" @@ -15,6 +15,7 @@ class RAffycontam(RPackage): homepage = "https://bioconductor.org/packages/affyContam" git = "https://git.bioconductor.org/packages/affyContam.git" + version('1.48.0', commit='88387a2ad4be4234d36710c65f2ca3a5b06b67da') version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe') version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614') version('1.38.0', commit='84651e8eade61619afefc83bb290047da101a5bc') diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py index 46f1cfd7c7..822e2a574b 100644 --- a/var/spack/repos/builtin/packages/r-affycoretools/package.py +++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py @@ -8,7 +8,7 @@ from spack import * class RAffycoretools(RPackage): """Functions useful for those doing repetitive analyses with Affymetrix - GeneChips. + GeneChips Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.""" @@ -16,12 +16,14 @@ class RAffycoretools(RPackage): homepage = "https://bioconductor.org/packages/affycoretools" git = "https://git.bioconductor.org/packages/affycoretools.git" + version('1.62.0', commit='c9779e4da648fd174c9bd575c6020be1c03047c4') 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+X', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-affy', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) @@ -39,5 +41,5 @@ 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')) + depends_on('r-glimma', when='@1.62.0:', 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 0da27f1b3b..f43c8e603a 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -7,7 +7,7 @@ from spack import * class RAffydata(RPackage): - """Affymetrix Data for Demonstration Purpose. + """Affymetrix Data for Demonstration Purpose Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package @@ -16,6 +16,7 @@ class RAffydata(RPackage): homepage = "https://bioconductor.org/packages/affydata" git = "https://git.bioconductor.org/packages/affydata.git" + version('1.38.0', commit='b5e843b2514789d0d87bea44d762c89a95314ee7') version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd') version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea') version('1.28.0', commit='a106a5514c352bf0bbc624ded58a93886d4ce96f') diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py index f3100f4182..7f9ec7dfa0 100644 --- a/var/spack/repos/builtin/packages/r-affyexpress/package.py +++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py @@ -7,7 +7,7 @@ from spack import * class RAffyexpress(RPackage): - """Affymetrix Quality Assessment and Analysis Tool. + """Affymetrix Quality Assessment and Analysis Tool The purpose of this package is to provide a comprehensive and easy-to- use tool for quality assessment and to identify differentially expressed @@ -16,6 +16,7 @@ class RAffyexpress(RPackage): homepage = "https://bioconductor.org/packages/AffyExpress" git = "https://git.bioconductor.org/packages/AffyExpress.git" + version('1.56.0', commit='e07085833de2bbf81537410cad526d39f8a82478') version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96') version('1.48.0', commit='dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92') version('1.46.0', commit='2add4a4436e21aa20f1ededbfd5f1365a3d28c85') diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py index 8f91de4c00..aa772ab218 100644 --- a/var/spack/repos/builtin/packages/r-affyilm/package.py +++ b/var/spack/repos/builtin/packages/r-affyilm/package.py @@ -7,7 +7,7 @@ from spack import * class RAffyilm(RPackage): - """Linear Model of background subtraction and the Langmuir isotherm. + """Linear Model of background subtraction and the Langmuir isotherm affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to @@ -17,6 +17,7 @@ class RAffyilm(RPackage): homepage = "https://bioconductor.org/packages/affyILM" git = "https://git.bioconductor.org/packages/affyILM.git" + version('1.42.0', commit='b97b29786b866de38802ebbb995169be91e90942') version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132') version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564') version('1.32.0', commit='860f2ddada80435d309ba334eff3fab503817755') diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py index e53d1542ac..df46f43194 100644 --- a/var/spack/repos/builtin/packages/r-affyio/package.py +++ b/var/spack/repos/builtin/packages/r-affyio/package.py @@ -7,7 +7,7 @@ from spack import * class RAffyio(RPackage): - """Tools for parsing Affymetrix data files. + """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 @@ -16,6 +16,7 @@ class RAffyio(RPackage): homepage = "https://bioconductor.org/packages/affyio" git = "https://git.bioconductor.org/packages/affyio.git" + version('1.60.0', commit='ee20528b32700e99768da48143d6d45c9a7bbe91') version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f') version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963') version('1.50.0', commit='911ea4f8e4cdf7b649b87ef7ed1a5f5b111ef38a') diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py index d746b5c3f0..e837d04fea 100644 --- a/var/spack/repos/builtin/packages/r-affyplm/package.py +++ b/var/spack/repos/builtin/packages/r-affyplm/package.py @@ -7,7 +7,7 @@ from spack import * class RAffyplm(RPackage): - """Methods for fitting probe-level models. + """Methods for fitting probe-level models A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. @@ -18,6 +18,7 @@ class RAffyplm(RPackage): homepage = "https://bioconductor.org/packages/affyPLM" git = "https://git.bioconductor.org/packages/affyPLM.git" + version('1.66.0', commit='f0780c3d0e9dccaff83861b98beb5c1d324c4399') version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d') version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8') version('1.56.0', commit='13dfc558281af9a177d4d592c34cf7ace629af0e') diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py index 213beb5312..526f7c2410 100644 --- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py +++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py @@ -7,7 +7,7 @@ from spack import * class RAffyqcreport(RPackage): - """QC Report Generation for affyBatch objects. + """QC Report Generation for affyBatch objects 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 @@ -16,6 +16,7 @@ class RAffyqcreport(RPackage): homepage = "https://bioconductor.org/packages/affyQCReport" git = "https://git.bioconductor.org/packages/affyQCReport.git" + version('1.68.0', commit='34b42a16f87a90a595146f4a1802ed04f6bfccca') version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4') version('1.60.0', commit='d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa') version('1.58.0', commit='14be93a1e7a6d1a64c38ed2f53e0c52a389b2a1b') @@ -26,6 +27,7 @@ class RAffyqcreport(RPackage): depends_on('r-affy', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-affyplm', type=('build', 'run')) + depends_on('r-biobase', when='@1.68.0:', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-simpleaffy', 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 c4746cafca..adb6649f9a 100644 --- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py +++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py @@ -8,7 +8,7 @@ from spack import * class RAffyrnadegradation(RPackage): """Analyze and correct probe positional bias in microarray data due to RNA - degradation. + degradation The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a @@ -19,6 +19,7 @@ class RAffyrnadegradation(RPackage): homepage = "https://bioconductor.org/packages/AffyRNADegradation" git = "https://git.bioconductor.org/packages/AffyRNADegradation.git" + version('1.36.0', commit='89662b93076659db2967a526899184c12c156bc5') version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1') version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24') version('1.26.0', commit='6ab03ad624701464280bf7dfe345d200e846298a') diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py index 7473d5d4ef..4c34d5e317 100644 --- a/var/spack/repos/builtin/packages/r-agdex/package.py +++ b/var/spack/repos/builtin/packages/r-agdex/package.py @@ -7,7 +7,7 @@ from spack import * class RAgdex(RPackage): - """Agreement of Differential Expression Analysis. + """Agreement of Differential Expression Analysis A tool to evaluate agreement of differential expression for cross- species genomics""" @@ -15,6 +15,7 @@ class RAgdex(RPackage): homepage = "https://bioconductor.org/packages/AGDEX" git = "https://git.bioconductor.org/packages/AGDEX.git" + version('1.38.0', commit='7e2c1f5f27ccbea6a7157f5122212e40408b74da') version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf') version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b') version('1.28.0', commit='7d78ee424485018b73cd019ceaed7a2ed53adf3f') diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py index aaea3a2809..66527ad2bd 100644 --- a/var/spack/repos/builtin/packages/r-agilp/package.py +++ b/var/spack/repos/builtin/packages/r-agilp/package.py @@ -7,13 +7,14 @@ from spack import * class RAgilp(RPackage): - """Agilent expression array processing package. + """Agilent expression array processing package - More about what it does (maybe more than one line)""" + 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('3.22.0', commit='7d089d576752e0526f15a1007e94436089954313') version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47') version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61') version('3.12.0', commit='a86dea1b03b2b56c2c8317d4b10903fb8948ffcb') diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py index b41c98f785..01d44cc3d9 100644 --- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py +++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py @@ -8,17 +8,21 @@ from spack import * class RAgimicrorna(RPackage): """Processing and Differential Expression Analysis of Agilent microRNA - chips.""" + chips + + Processing and Analysis of Agilent microRNA data.""" homepage = "https://bioconductor.org/packages/AgiMicroRna" git = "https://git.bioconductor.org/packages/AgiMicroRna.git" + version('2.40.0', commit='cfa4acb2215da44767ab3a45845bcd587c309e74') 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+X', 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')) diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py index 99ead4adc8..e80f9f710a 100644 --- a/var/spack/repos/builtin/packages/r-aims/package.py +++ b/var/spack/repos/builtin/packages/r-aims/package.py @@ -7,7 +7,7 @@ from spack import * class RAims(RPackage): - """AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype. + """AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, @@ -18,6 +18,7 @@ class RAims(RPackage): homepage = "https://bioconductor.org/packages/AIMS" git = "https://git.bioconductor.org/packages/AIMS.git" + version('1.22.0', commit='34a38978b24377abb864eff7683bb36344ff171d') version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84') version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f') version('1.12.0', commit='d7eaa723d19a6aca37df244fd0b3d5426ed0a626') diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py index 90b958d06f..a930970424 100644 --- a/var/spack/repos/builtin/packages/r-aldex2/package.py +++ b/var/spack/repos/builtin/packages/r-aldex2/package.py @@ -7,7 +7,7 @@ from spack import * class RAldex2(RPackage): - """Analysis Of Differential Abundance Taking Sample Variation Into Account. + """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- @@ -24,16 +24,17 @@ class RAldex2(RPackage): homepage = "https://bioconductor.org/packages/ALDEx2" git = "https://git.bioconductor.org/packages/ALDEx2.git" + version('1.22.0', commit='ac7f0ab3f094ec52713da7620a27058b14c7181d') 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-s4vectors', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) + depends_on('r-zcompositions', when='@1.22.0:', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-s4vectors', 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 8639518f04..5d97d3081d 100644 --- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py +++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py @@ -7,7 +7,7 @@ from spack import * class RAllelicimbalance(RPackage): - """Investigates Allele Specific Expression. + """Investigates Allele Specific Expression Provides a framework for allelic specific expression investigation using RNA-seq data.""" @@ -15,6 +15,7 @@ class RAllelicimbalance(RPackage): homepage = "https://bioconductor.org/packages/AllelicImbalance" git = "https://git.bioconductor.org/packages/AllelicImbalance.git" + version('1.28.0', commit='ac5d13c9ee0935bf9500ee542792644e752a1fde') version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a') version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3') version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea') @@ -22,18 +23,29 @@ class RAllelicimbalance(RPackage): version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c') depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r@4.0.0:', when='@1.28.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run')) depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run')) depends_on('r-genomicalignments', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', 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-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) + depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run')) depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run')) depends_on('r-genomicfeatures', type=('build', 'run')) + depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run')) depends_on('r-gviz', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-latticeextra', type=('build', 'run')) @@ -41,15 +53,3 @@ 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 c298b0ca82..2be92fe260 100644 --- a/var/spack/repos/builtin/packages/r-alpine/package.py +++ b/var/spack/repos/builtin/packages/r-alpine/package.py @@ -7,7 +7,7 @@ from spack import * class RAlpine(RPackage): - """alpine. + """alpine Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.""" @@ -15,6 +15,7 @@ class RAlpine(RPackage): homepage = "https://bioconductor.org/packages/alpine" git = "https://git.bioconductor.org/packages/alpine.git" + version('1.16.0', commit='aee397774ac6cd17ad45dc05be14c526647f3c13') version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c') version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4') version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274') diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py index feaca54b95..35c04521d1 100644 --- a/var/spack/repos/builtin/packages/r-alsace/package.py +++ b/var/spack/repos/builtin/packages/r-alsace/package.py @@ -7,7 +7,7 @@ from spack import * class RAlsace(RPackage): - """ALS for the Automatic Chemical Exploration of mixtures. + """ALS for the Automatic Chemical Exploration of mixtures Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first @@ -19,6 +19,7 @@ class RAlsace(RPackage): homepage = "https://bioconductor.org/packages/alsace" git = "https://git.bioconductor.org/packages/alsace.git" + version('1.26.0', commit='40a76404acb1466723a78a55d87c67eec3e6f306') version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389') version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191') version('1.16.0', commit='5a51a19aeccbba0123222201cb7a228559f29653') diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py index 4432127554..0724e52243 100644 --- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py +++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py @@ -7,13 +7,14 @@ from spack import * class RAltcdfenvs(RPackage): - """alternative CDF environments (aka probeset mappings). + """alternative CDF environments (aka probeset mappings) - Convenience data structures and functions to handle cdfenvs""" + Convenience data structures and functions to handle cdfenvs.""" homepage = "https://bioconductor.org/packages/altcdfenvs" git = "https://git.bioconductor.org/packages/altcdfenvs.git" + version('2.52.0', commit='21329abf82eae26f84b7c0270e81c8e089c548ce') version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b') version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133') version('2.42.0', commit='00ec6461877a063d938494b8ed0cd273a3b20b85') diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py index e995f1d8ce..cbd5f7cf4a 100644 --- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py +++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py @@ -21,6 +21,7 @@ class RAmpliqueso(RPackage): version('1.16.0', commit='25d2543ff9dedef4f966f999c95cdf87185d3bb3') version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b') + depends_on('r+X', 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')) diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py index 5c02517a36..ecd641d3cd 100644 --- a/var/spack/repos/builtin/packages/r-anaquin/package.py +++ b/var/spack/repos/builtin/packages/r-anaquin/package.py @@ -7,7 +7,7 @@ from spack import * class RAnaquin(RPackage): - """Statistical analysis of sequins. + """Statistical analysis of sequins The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan @@ -18,6 +18,7 @@ class RAnaquin(RPackage): homepage = "https://bioconductor.org/packages/Anaquin" git = "https://git.bioconductor.org/packages/Anaquin.git" + version('2.14.0', commit='d0a34c931a0e72080bff91dacb37dbbe26b45386') version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601') version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6') version('2.4.0', commit='0d6ae80ff622151a782e4774ca274f06024a71d2') diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py index 3513ed5b30..31894e53dc 100644 --- a/var/spack/repos/builtin/packages/r-aneufinder/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py @@ -7,7 +7,7 @@ from spack import * class RAneufinder(RPackage): - """Analysis of Copy Number Variation in Single-Cell-Sequencing Data. + """Analysis of Copy Number Variation in Single-Cell-Sequencing Data AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole @@ -16,6 +16,7 @@ class RAneufinder(RPackage): homepage = "https://bioconductor.org/packages/AneuFinder" git = "https://git.bioconductor.org/packages/AneuFinder.git" + version('1.18.0', commit='76ec9af947f97212084ca478e8e82f9e0eb79de9') version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e') version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd') version('1.8.0', commit='36a729d244add5aafbe21c37a1baaea6a50354d3') @@ -23,27 +24,26 @@ class RAneufinder(RPackage): version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e') depends_on('r@3.3:', type=('build', 'run')) + depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-ggplot2', 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', when='@1.4.0:1.6.0', type=('build', 'run')) + depends_on('r-biocgenerics@0.31.6:', when='@1.18.0:', type=('build', 'run')) depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-rsamtools', type=('build', 'run')) depends_on('r-bamsignals', type=('build', 'run')) depends_on('r-dnacopy', type=('build', 'run')) + depends_on('r-ecp', when='@1.8.0:', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-genomicalignments', type=('build', 'run')) - 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-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 4e538f6652..5189efaf29 100644 --- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py @@ -7,7 +7,7 @@ from spack import * class RAneufinderdata(RPackage): - """WGSCS Data for Demonstration Purposes. + """WGSCS Data for Demonstration Purposes Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.""" @@ -15,6 +15,7 @@ class RAneufinderdata(RPackage): homepage = "https://bioconductor.org/packages/AneuFinderData" git = "https://git.bioconductor.org/packages/AneuFinderData.git" + version('1.18.0', commit='1bf1657b28fc8c1425e611980a692da952ce3d1e') version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1') version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035') version('1.8.0', commit='4f00f8d5f2e968fea667a7feafc0a4607d6e0c6e') diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index 4581bfb60c..964fbb3b9f 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -7,7 +7,7 @@ from spack import * class RAnnaffy(RPackage): - """Annotation tools for Affymetrix biological metadata. + """Annotation tools for Affymetrix biological metadata Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental @@ -17,6 +17,7 @@ class RAnnaffy(RPackage): homepage = "https://bioconductor.org/packages/annaffy" git = "https://git.bioconductor.org/packages/annaffy.git" + version('1.62.0', commit='ad9c37e0e7e45e0f35c208ce528ba48000b37432') version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233') version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484') version('1.52.0', commit='ef84030163045f702941c8d5a59fbd4a09f30e2c') diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index 6a42312909..6544684005 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -7,13 +7,14 @@ from spack import * class RAnnotate(RPackage): - """Annotation for microarrays. + """Annotation for microarrays Using R enviroments for annotation.""" homepage = "https://bioconductor.org/packages/annotate" git = "https://git.bioconductor.org/packages/annotate.git" + version('1.68.0', commit='98cdb12c612b3f3fc06329a89a1ffb0a92b555c0') version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd') version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16') version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc') @@ -27,4 +28,5 @@ class RAnnotate(RPackage): depends_on('r-dbi', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) depends_on('r-biocgenerics@0.13.8:', type=('build', 'run')) - depends_on('r-rcurl', type=('build', 'run')) + depends_on('r-httr', when='@1.68.0:', type=('build', 'run')) + depends_on('r-rcurl', when='@:1.62.0', 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 12128ed00a..61a9fa9669 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -7,7 +7,7 @@ from spack import * class RAnnotationdbi(RPackage): - """Manipulation of SQLite-based annotations in Bioconductor. + """Manipulation of SQLite-based annotations in Bioconductor Implements a user-friendly interface for querying SQLite-based annotation data packages.""" @@ -15,6 +15,7 @@ class RAnnotationdbi(RPackage): homepage = "https://bioconductor.org/packages/AnnotationDbi" git = "https://git.bioconductor.org/packages/AnnotationDbi.git" + version('1.52.0', commit='c4e0ca9bd65362ae9cad6a98d90f54267b0ae838') version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9') version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac') version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3') @@ -23,12 +24,10 @@ class RAnnotationdbi(RPackage): depends_on('r@2.7.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.15.10:', 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')) 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 942fe4fd57..ba5ae683ad 100644 --- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py +++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py @@ -7,7 +7,7 @@ from spack import * class RAnnotationfilter(RPackage): - """Facilities for Filtering Bioconductor Annotation Resources. + """Facilities for Filtering Bioconductor Annotation Resources This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters @@ -16,6 +16,7 @@ class RAnnotationfilter(RPackage): homepage = "https://bioconductor.org/packages/AnnotationFilter" git = "https://git.bioconductor.org/packages/AnnotationFilter.git" + version('1.14.0', commit='6ee3a13ed93a535ed452cbc8c118151a2cbb732c') version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed') version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3') version('1.4.0', commit='acbd3309f478843a7899bd9773af5f19f986b829') diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py index c16583f312..6840dedf8f 100644 --- a/var/spack/repos/builtin/packages/r-annotationforge/package.py +++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py @@ -7,7 +7,7 @@ from spack import * class RAnnotationforge(RPackage): - """Tools for building SQLite-based annotation data packages. + """Tools for building SQLite-based annotation data packages Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.""" @@ -15,6 +15,7 @@ class RAnnotationforge(RPackage): homepage = "https://bioconductor.org/packages/AnnotationForge" git = "https://git.bioconductor.org/packages/AnnotationForge.git" + version('1.32.0', commit='3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7') version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e') version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d') version('1.22.2', commit='8eafb1690c1c02f6291ccbb38ac633d54b8217f8') diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py index fb2b479880..457d541d06 100644 --- a/var/spack/repos/builtin/packages/r-annotationhub/package.py +++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py @@ -7,7 +7,7 @@ from spack import * class RAnnotationhub(RPackage): - """Client to access AnnotationHub resources. + """Client to access AnnotationHub resources This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location @@ -21,6 +21,7 @@ class RAnnotationhub(RPackage): homepage = "https://bioconductor.org/packages/AnnotationHub" git = "https://git.bioconductor.org/packages/AnnotationHub.git" + version('2.22.0', commit='3ab7dceebbc31ac14ca931f66c662cf9538b7d0a') version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed') version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12') version('2.12.1', commit='471407bd9cdc612e01deb071c91bd9e5f1ea5e55') @@ -28,18 +29,16 @@ class RAnnotationhub(RPackage): version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c') depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) + depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) + depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run')) + depends_on('r-biocversion', when='@2.22.0:', type=('build', 'run')) + depends_on('r-curl', when='@2.10.1:', type=('build', 'run')) + depends_on('r-rappdirs', when='@2.16.1:', 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-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')) + depends_on('r-biocinstaller', when='@:2.16.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aroma-light/package.py b/var/spack/repos/builtin/packages/r-aroma-light/package.py index e0462bac6b..00be416162 100644 --- a/var/spack/repos/builtin/packages/r-aroma-light/package.py +++ b/var/spack/repos/builtin/packages/r-aroma-light/package.py @@ -7,17 +7,23 @@ from spack import * class RAromaLight(RPackage): - """Methods for microarray analysis that take basic data types such as + """Light-Weight Methods for Normalization and Visualization of Microarray + Data using Only Basic R Data Types + + Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.""" homepage = "https://www.aroma-project.org/" git = "https://git.bioconductor.org/packages/aroma.light" + version('3.20.0', commit='02cde7fa166259bce73c396a87dca2ecc8249c39') version('3.16.0', commit='fc16179fc4bee8954c5415d7cd13e3112b75b4fd') depends_on('r@2.15.2:', type=('build', 'run')) depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) depends_on('r-r-oo@1.22.0:', type=('build', 'run')) + depends_on('r-r-oo@1.23.0:', when='@3.20.0:', type=('build', 'run')) depends_on('r-r-utils@2.9.0:', type=('build', 'run')) depends_on('r-matrixstats@0.54.0:', type=('build', 'run')) + depends_on('r-matrixstats@0.55.0:', when='@3.20.0:', 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 b45fec7c27..5deebb1697 100644 --- a/var/spack/repos/builtin/packages/r-bamsignals/package.py +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -7,7 +7,7 @@ from spack import * class RBamsignals(RPackage): - """Extract read count signals from bam files. + """Extract read count signals from bam files This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it @@ -17,6 +17,7 @@ class RBamsignals(RPackage): homepage = "https://bioconductor.org/packages/bamsignals" git = "https://git.bioconductor.org/packages/bamsignals.git" + version('1.22.0', commit='5f533969c84212406bcb3ebf725ebb6d77e9947a') version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657') version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d') version('1.12.1', commit='06b6282df377cf9db58e8016be4ac8ddcc960939') @@ -30,7 +31,9 @@ class RBamsignals(RPackage): 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')) + depends_on('gmake', type='build') + + # this is no listed but is needed + depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py index fd8726311a..2008fd0b69 100644 --- a/var/spack/repos/builtin/packages/r-beachmat/package.py +++ b/var/spack/repos/builtin/packages/r-beachmat/package.py @@ -7,7 +7,7 @@ from spack import * class RBeachmat(RPackage): - """Compiling Bioconductor to Handle Each Matrix Type. + """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 @@ -18,23 +18,24 @@ class RBeachmat(RPackage): homepage = "https://bioconductor.org/packages/beachmat" git = "https://git.bioconductor.org/packages/beachmat.git" + version('2.6.4', commit='7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb') 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', 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-delayedarray@0.15.14:', when='@2.6.4', type=('build', 'run')) depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run')) + depends_on('r-matrix', when='@2.6.4:', type=('build', 'run')) + depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run')) + depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run')) + depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run')) + depends_on('r-hdf5array@1.9.5:', when='@1.4.0', 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')) diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py index e08d76e3ea..c359050afb 100644 --- a/var/spack/repos/builtin/packages/r-biobase/package.py +++ b/var/spack/repos/builtin/packages/r-biobase/package.py @@ -7,7 +7,7 @@ from spack import * class RBiobase(RPackage): - """Biobase: Base functions for Bioconductor. + """Biobase: Base functions for Bioconductor Functions that are needed by many other packages or which replace R functions.""" @@ -15,6 +15,7 @@ class RBiobase(RPackage): homepage = "https://bioconductor.org/packages/Biobase" git = "https://git.bioconductor.org/packages/Biobase.git" + version('2.50.0', commit='9927f90d0676382f2f99e099d8d2c8e2e6f1b4de') version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3') version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d') version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5') @@ -23,5 +24,4 @@ class RBiobase(RPackage): 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 index ee961a00ac..4bcdcf7023 100644 --- a/var/spack/repos/builtin/packages/r-biocfilecache/package.py +++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py @@ -7,7 +7,7 @@ from spack import * class RBiocfilecache(RPackage): - """Manage Files Across Sessions. + """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 @@ -17,6 +17,7 @@ class RBiocfilecache(RPackage): homepage = "https://bioconductor.org/packages/BiocFileCache" git = "https://git.bioconductor.org/packages/BiocFileCache.git" + version('1.14.0', commit='cdcde4b59ae73dda12aa225948dbd0a058d9be6d') version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0') version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba') version('1.4.0', commit='a2c473d17f78899c7899b9638faea8c30735eb80') @@ -24,11 +25,10 @@ class RBiocfilecache(RPackage): 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-dbplyr@1.0.0:', when='@1.2.3:', 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')) + depends_on('r-httr', 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 2c564ccf4f..6558fb633c 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -7,13 +7,14 @@ from spack import * class RBiocgenerics(RPackage): - """S4 generic functions used in Bioconductor. + """S4 generic functions used in Bioconductor The package defines S4 generic functions used in Bioconductor.""" homepage = "https://bioconductor.org/packages/BiocGenerics" git = "https://git.bioconductor.org/packages/BiocGenerics.git" + version('0.36.0', commit='0d5d169d7d64d648a22f9043837c93bc784e71ed') version('0.34.0', commit='f7c2020') version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8') version('0.28.0', commit='041fc496504f2ab1d4d863fffb23372db214394b') @@ -22,3 +23,4 @@ class RBiocgenerics(RPackage): version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad') depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run')) + depends_on('r@4.0.0:', when='@0.36.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py index 964c4ed779..50cbf21970 100644 --- a/var/spack/repos/builtin/packages/r-biocneighbors/package.py +++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py @@ -7,7 +7,7 @@ from spack import * class RBiocneighbors(RPackage): - """Nearest Neighbor Detection for Bioconductor Packages. + """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 @@ -22,14 +22,15 @@ class RBiocneighbors(RPackage): homepage = "https://bioconductor.org/packages/BiocNeighbors" git = "https://git.bioconductor.org/packages/BiocNeighbors.git" + version('1.8.2', commit='889bc91f8cb45d210b47ae5c0b9cfb86fb071ca2') 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-biocparallel', type=('build', 'run')) + depends_on('r-matrix', when='@1.8.2:', type=('build', 'run')) depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rcppannoy', when='@:1.2.0', type=('build', 'run')) + depends_on('r-biocgenerics', 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 2ac2552227..b1849c5420 100644 --- a/var/spack/repos/builtin/packages/r-biocparallel/package.py +++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py @@ -7,7 +7,7 @@ from spack import * class RBiocparallel(RPackage): - """Bioconductor facilities for parallel evaluation. + """Bioconductor facilities for parallel evaluation This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor @@ -16,6 +16,7 @@ class RBiocparallel(RPackage): homepage = "https://bioconductor.org/packages/BiocParallel" git = "https://git.bioconductor.org/packages/BiocParallel.git" + version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f') version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e') version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4') version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299') @@ -24,5 +25,4 @@ class RBiocparallel(RPackage): depends_on('r-futile-logger', type=('build', 'run')) depends_on('r-snow', 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 index a5b05f2ed3..355aab3563 100644 --- a/var/spack/repos/builtin/packages/r-biocsingular/package.py +++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py @@ -7,7 +7,7 @@ from spack import * class RBiocsingular(RPackage): - """Singular Value Decomposition for Bioconductor Packages. + """Singular Value Decomposition for Bioconductor Packages Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that @@ -18,6 +18,7 @@ class RBiocsingular(RPackage): homepage = "https://bioconductor.org/packages/BiocSingular" git = "https://git.bioconductor.org/packages/BiocSingular.git" + version('1.6.0', commit='11baf1080d6f791439cd5d97357589d6451643d9') version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833') depends_on('r-biocgenerics', 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 1db2838247..a2f0988910 100644 --- a/var/spack/repos/builtin/packages/r-biocstyle/package.py +++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py @@ -7,7 +7,7 @@ from spack import * class RBiocstyle(RPackage): - """Standard styles for vignettes and other Bioconductor documents. + """Standard styles for vignettes and other Bioconductor documents Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.""" @@ -15,15 +15,17 @@ class RBiocstyle(RPackage): homepage = "https://bioconductor.org/packages/BiocStyle" git = "https://git.bioconductor.org/packages/BiocStyle.git" + version('2.18.1', commit='956f0654e8e18882ba09305742401128c9c7d47d') 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+X', type=('build', 'run')) depends_on('r-bookdown', type=('build', 'run')) depends_on('r-knitr@1.12:', type=('build', 'run')) + depends_on('r-knitr@1.30:', when='@2.18.1:', type=('build', 'run')) depends_on('r-rmarkdown@1.2:', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) - depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py new file mode 100644 index 0000000000..4d021a161f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-biocversion/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2021 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 RBiocversion(RPackage): + """Set the appropriate version of Bioconductor packages + + This package provides repository information for the appropriate + version of Bioconductor.""" + + homepage = "https://bioconductor.org/packages/BiocVersion/" + git = "https://git.bioconductor.org/packages/BiocVersion" + + version('3.12.0', commit='23b971963c6b73550a7e330dab5a046d58ce0223') + + depends_on('r@4.0.0:', 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 c878bdb70f..d1c4387288 100644 --- a/var/spack/repos/builtin/packages/r-biomart/package.py +++ b/var/spack/repos/builtin/packages/r-biomart/package.py @@ -7,7 +7,7 @@ from spack import * class RBiomart(RPackage): - """Interface to BioMart databases (i.e. Ensembl). + """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 @@ -25,6 +25,7 @@ class RBiomart(RPackage): homepage = "https://bioconductor.org/packages/biomaRt" git = "https://git.bioconductor.org/packages/biomaRt.git" + version('2.46.2', commit='90d6abfdfa04259006f7b47efb10271ada76aec1') version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68') version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658') version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f') @@ -32,9 +33,12 @@ class RBiomart(RPackage): version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f') 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', 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')) + depends_on('r-openssl', when='@2.46.2:', type=('build', 'run')) + depends_on('r-biocfilecache', when='@2.46.2:', type=('build', 'run')) + depends_on('r-rappdirs', when='@2.46.2:', type=('build', 'run')) + depends_on('r-xml2', when='@2.46.2:', type=('build', 'run')) + depends_on('r-rcurl', when='@:2.40.5', 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 ef84947fc7..ba8a137e81 100644 --- a/var/spack/repos/builtin/packages/r-biomformat/package.py +++ b/var/spack/repos/builtin/packages/r-biomformat/package.py @@ -7,7 +7,7 @@ from spack import * class RBiomformat(RPackage): - """An interface package for the BIOM file format. + """An interface package for the BIOM file format This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and @@ -22,6 +22,7 @@ class RBiomformat(RPackage): homepage = "https://bioconductor.org/packages/biomformat" git = "https://git.bioconductor.org/packages/biomformat.git" + version('1.18.0', commit='dc18859c139f4d76805adb6f01e199573cdd5a8b') version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a') version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09') version('1.8.0', commit='acd207377b24e4d8310eaff06c16dcfe6c04509a') diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py index 80cbd662ef..7ae78acdc4 100644 --- a/var/spack/repos/builtin/packages/r-biostrings/package.py +++ b/var/spack/repos/builtin/packages/r-biostrings/package.py @@ -7,7 +7,7 @@ from spack import * class RBiostrings(RPackage): - """Efficient manipulation of biological strings. + """Efficient manipulation of biological strings Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or @@ -16,6 +16,7 @@ class RBiostrings(RPackage): homepage = "https://bioconductor.org/packages/Biostrings" git = "https://git.bioconductor.org/packages/Biostrings.git" + version('2.58.0', commit='0ec1a5455d5e9eebd14b26228906bb04e2abb197') version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5') version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2') version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b') @@ -23,18 +24,19 @@ class RBiostrings(RPackage): version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200') depends_on('r@2.8.0:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run')) depends_on('r-biocgenerics@0.15.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.31.5:', when='@2.58.0:', 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-s4vectors@0.21.13:', when='@2.52.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@2.58.0:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', when='@2.44.2:', type=('build', 'run')) + depends_on('r-iranges@2.13.24:', when='@2.48.0:', type=('build', 'run')) + depends_on('r-iranges@2.23.9:', when='@2.58.0:', type=('build', 'run')) + depends_on('r-xvector@0.11.6:', 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')) + depends_on('r-xvector@0.29.2:', when='@2.58.0:', type=('build', 'run')) + depends_on('r-crayon', when='@2.58.0:', 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 ae823fedc9..0f0dbad6e0 100644 --- a/var/spack/repos/builtin/packages/r-biovizbase/package.py +++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py @@ -7,7 +7,7 @@ from spack import * class RBiovizbase(RPackage): - """Basic graphic utilities for visualization of genomic data.. + """Basic graphic utilities for visualization of genomic data. The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for @@ -17,6 +17,7 @@ class RBiovizbase(RPackage): homepage = "https://bioconductor.org/packages/biovizBase" git = "https://git.bioconductor.org/packages/biovizBase.git" + version('1.38.0', commit='d0f3362e0ad0e90b4b1d3e47b13ed57907d03403') version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8') version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82') version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063') @@ -24,12 +25,14 @@ class RBiovizbase(RPackage): version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c') depends_on('r@2.10:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@1.38.0:', 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@0.9.25:', type=('build', 'run')) + depends_on('r-s4vectors@0.23.19:', when='@1.38.0:', 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')) @@ -42,5 +45,4 @@ class RBiovizbase(RPackage): 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-hsapiens-ucsc-hg19/package.py b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py index 14100d56b1..bd6f8ee30a 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py @@ -7,13 +7,22 @@ from spack import * class RBsgenomeHsapiensUcscHg19(RPackage): - """Full genome sequences for Homo sapiens (Human) as provided by UCSC + """Full genome sequences for Homo sapiens (UCSC version hg19, based on + GRCh37.p13) + + Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.""" # This is a bioconductor package but there is no available git repo. - homepage = "http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html" + homepage = "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/" url = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" - version('1.4.0', sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8') + version('1.4.3', + sha256='5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a', + url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz') + version('1.4.0', + sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8', + url='https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz') depends_on('r-bsgenome@1.33.5:', type=('build', 'run')) + depends_on('r-bsgenome@1.54.0:', when='@1.4.3:', 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 6949579451..bf23766f83 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py @@ -8,11 +8,14 @@ from spack import * class RBsgenome(RPackage): """Software infrastructure for efficient representation of full genomes and - their SNPs.""" + their SNPs + + Infrastructure shared by all the Biostrings-based genome data packages.""" homepage = "https://bioconductor.org/packages/BSgenome" git = "https://git.bioconductor.org/packages/BSgenome.git" + version('1.58.0', commit='3a4926e03a7a1d7140a10c1b2bf6090808470145') version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b') version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9') version('1.48.0', commit='092a1b90482ace329cbd8ca2a338e91449acb93e') @@ -22,21 +25,22 @@ class RBsgenome(RPackage): 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-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run')) 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-xvector', type=('build', 'run')) - 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@1.11.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run')) depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.25.6:', when='@1.58.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run')) depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-biostrings@2.35.3:', type=('build', 'run')) depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-rtracklayer@1.25.8:', type=('build', 'run')) depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run')) + depends_on('r-matrixstats', when='@1.58.0:', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + depends_on('r-xvector@0.29.3:', when='@1.58.0:', type=('build', 'run')) + depends_on('r-rsamtools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py index 029bbce542..fe8cebe8fd 100644 --- a/var/spack/repos/builtin/packages/r-bsseq/package.py +++ b/var/spack/repos/builtin/packages/r-bsseq/package.py @@ -7,49 +7,52 @@ from spack import * class RBsseq(RPackage): - """A collection of tools for analyzing and visualizing bisulfite sequencing + """Analyze, manage and store bisulfite sequencing data + + A collection of tools for analyzing and visualizing bisulfite sequencing data.""" homepage = "https://github.com/kasperdanielhansen/bsseq" git = "https://git.bioconductor.org/packages/bsseq" + version('1.26.0', commit='fae32292687625012a2938a48c93df55ad4257b5') version('1.24.4', commit='8fe7a03') version('1.22.0', commit='d4f7301') version('1.20.0', commit='07e398b') depends_on('r@3.5:', type=('build', 'run')) - + depends_on('r@4.0:', when='@1.26.0:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) - depends_on('r-genomicranges@1.29.14:', type=('build', 'run')) depends_on('r-genomicranges@1.33.6:', when='@1.24.4:', type=('build', 'run')) - + depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', type=('build', 'run')) depends_on('r-summarizedexperiment@1.9.18:', type=('build', 'run')) depends_on('r-summarizedexperiment@1.17.4:', when='@1.24.4:', type=('build', 'run')) - + depends_on('r-summarizedexperiment@1.19.5:', when='@1.26.0:', type=('build', 'run')) depends_on('r-iranges@2.11.16:', type=('build', 'run')) depends_on('r-iranges@2.22.2:', when='@1.24.4:', type=('build', 'run')) - + depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-locfit', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) depends_on('r-data-table@1.11.8:', type=('build', 'run')) - depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-s4vectors@0.23.11:', when='@1.22.0:', type=('build', 'run')) - depends_on('r-s4vectors@0.25.14:', when='@1.24.4', type=('build', 'run')) - + depends_on('r-s4vectors@0.25.14:', when='@1.24.4:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', type=('build', 'run')) depends_on('r-r-utils@2.0.0:', type=('build', 'run')) depends_on('r-delayedmatrixstats@1.5.2:', type=('build', 'run')) depends_on('r-permute', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) depends_on('r-delayedarray@0.9.8:', type=('build', 'run')) + depends_on('r-delayedarray@0.15.16:', when='@1.26.0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-bsgenome', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-hdf5array@1.11.9:', type=('build', 'run')) + depends_on('r-hdf5array@1.15.19:', when='@1.26.0:', type=('build', 'run')) depends_on('r-rhdf5', type=('build', 'run')) depends_on('r-beachmat', 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 7d788550fd..0768927a8c 100644 --- a/var/spack/repos/builtin/packages/r-bumphunter/package.py +++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py @@ -7,13 +7,14 @@ from spack import * class RBumphunter(RPackage): - """Bump Hunter. + """Bump Hunter Tools for finding bumps in genomic data""" homepage = "https://bioconductor.org/packages/bumphunter" git = "https://git.bioconductor.org/packages/bumphunter.git" + version('1.32.0', commit='b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0') version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa') version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b') version('1.22.0', commit='fb71b193f4ef7fa12d100441e6eb498765f7afde') @@ -21,6 +22,8 @@ class RBumphunter(RPackage): version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a') depends_on('r@2.10:', type=('build', 'run')) + depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run')) + depends_on('r@3.5:', when='@1.24.5:', 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')) @@ -34,7 +37,3 @@ 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:', 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 163892d80a..f5546a2da3 100644 --- a/var/spack/repos/builtin/packages/r-category/package.py +++ b/var/spack/repos/builtin/packages/r-category/package.py @@ -7,7 +7,7 @@ from spack import * class RCategory(RPackage): - """Category Analysis. + """Category Analysis A collection of tools for performing category (gene set enrichment) analysis.""" @@ -15,6 +15,7 @@ class RCategory(RPackage): homepage = "https://bioconductor.org/packages/Category" git = "https://git.bioconductor.org/packages/Category.git" + version('2.56.0', commit='ad478caa9d693dbc2770608e79dd852375b9a223') version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9') version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5') version('2.46.0', commit='c8aeee4dee3fb120f25e0647dd06e895a3ffbc2a') diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py index c78138ce64..7f6c6be3eb 100644 --- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py +++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py @@ -8,7 +8,7 @@ from spack import * class RClusterprofiler(RPackage): """statistical analysis and visualization of functional profiles for genes - and gene clusters. + and gene clusters This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.""" @@ -16,6 +16,7 @@ class RClusterprofiler(RPackage): homepage = "https://bioconductor.org/packages/clusterProfiler" git = "https://git.bioconductor.org/packages/clusterProfiler.git" + version('3.18.0', commit='064a6e612ce27e260e33af78b907bee4065ff821') version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2') version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c') version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36') @@ -23,20 +24,23 @@ class RClusterprofiler(RPackage): version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7') depends_on('r@3.3.1:', type=('build', 'run')) - depends_on('r-dose@3.1.3:', type=('build', 'run')) + depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-downloader', when='@3.18.0:', type=('build', 'run')) + depends_on('r-dose@3.1.3:', type=('build', 'run')) + depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run')) + depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-dose@3.13.1:', when='@3.18.0:', type=('build', 'run')) + depends_on('r-dplyr', when='@3.18.0:', type=('build', 'run')) + depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run')) + depends_on('r-enrichplot@1.9.3:', when='@3.18.0:', 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-gosemsim@2.0.0:', when='@3.4.4:3.6.0', 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-rlang', when='@3.18.0:', 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')) + depends_on('r-ggplot2', when='@:3.12.0', 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 db8f4b9722..6f652c74b1 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -7,7 +7,7 @@ from spack import * class RCner(RPackage): - """CNE Detection and Visualization. + """CNE Detection and Visualization Large-scale identification and advanced visualization of sets of conserved noncoding elements.""" @@ -15,6 +15,7 @@ class RCner(RPackage): homepage = "https://bioconductor.org/packages/CNEr" git = "https://git.bioconductor.org/packages/CNEr.git" + version('1.26.0', commit='e5e582da6feeae0618c4460f16ece724215e3b20') version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5') version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606') version('1.16.1', commit='a2bec4b98d5938709f959a69c151f553ef357941') @@ -22,14 +23,16 @@ class RCner(RPackage): version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017') depends_on('r@3.2.2:', type=('build', 'run')) + depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run')) depends_on('r-biostrings@2.33.4:', type=('build', 'run')) + depends_on('r-dbi@0.6:', type=('build', 'run')) + depends_on('r-dbi@0.7:', when='@1.14.0:', 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')) @@ -41,6 +44,3 @@ class RCner(RPackage): depends_on('r-go-db@3.3.0:', type=('build', 'run')) depends_on('r-r-utils@2.3.0:', type=('build', 'run')) 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-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py index f4ecc915a2..02ad9e9496 100644 --- a/var/spack/repos/builtin/packages/r-codex/package.py +++ b/var/spack/repos/builtin/packages/r-codex/package.py @@ -7,7 +7,10 @@ from spack import * class RCodex(RPackage): - """A normalization and copy number variation calling procedure for whole + """A Normalization and Copy Number Variation Detection Method for Whole + Exome Sequencing + + A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX @@ -20,6 +23,7 @@ class RCodex(RPackage): homepage = "http://www.bioconductor.org/packages/release/bioc/html/CODEX.html" git = "https://git.bioconductor.org/packages/CODEX" + version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb') version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc') depends_on('r@3.2.3:', 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 bcf1268dde..71309ea39f 100644 --- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py @@ -7,7 +7,7 @@ from spack import * class RComplexheatmap(RPackage): - """Make Complex Heatmaps. + """Make Complex Heatmaps Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the @@ -17,6 +17,7 @@ class RComplexheatmap(RPackage): homepage = "https://bioconductor.org/packages/ComplexHeatmap" git = "https://git.bioconductor.org/packages/ComplexHeatmap.git" + version('2.6.2', commit='0383bada2c76dc3dde71cf6a625016b619aec4d3') version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4') version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f') version('1.18.1', commit='be0dd9d666a219c61335efe0dac50b2eed2a8825') @@ -25,16 +26,18 @@ class RComplexheatmap(RPackage): depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-circlize@0.3.4:', type=('build', 'run')) + depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run')) + depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run')) depends_on('r-getoptlong', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) + depends_on('r-clue', when='@2.0.0:', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - 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')) + depends_on('r-cairo', when='@2.6.2:', type=('build', 'run')) + depends_on('r-digest', when='@2.6.2:', type=('build', 'run')) + depends_on('r-s4vectors@0.26.1:', when='@2.6.2:', type=('build', 'run')) + depends_on('r-iranges', when='@2.6.2:', type=('build', 'run')) + depends_on('r-matrixstats', when='@2.6.2:', type=('build', 'run')) + depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', 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 96c0b966ff..2eedb9d528 100644 --- a/var/spack/repos/builtin/packages/r-ctc/package.py +++ b/var/spack/repos/builtin/packages/r-ctc/package.py @@ -7,7 +7,7 @@ from spack import * class RCtc(RPackage): - """Cluster and Tree Conversion.. + """Cluster and Tree Conversion. Tools for export and import classification trees and clusters to other programs""" @@ -15,6 +15,7 @@ class RCtc(RPackage): homepage = "https://bioconductor.org/packages/ctc" git = "https://git.bioconductor.org/packages/ctc.git" + version('1.64.0', commit='35dbe620a21056b8f69890e6f9a7c320528d8621') version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb') version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f') version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e') diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py index 419d5167e1..4da3f90c1f 100644 --- a/var/spack/repos/builtin/packages/r-decipher/package.py +++ b/var/spack/repos/builtin/packages/r-decipher/package.py @@ -7,11 +7,14 @@ from spack import * class RDecipher(RPackage): - """Tools for curating, analyzing, and manipulating biological sequences.""" + """Tools for curating, analyzing, and manipulating biological sequences + + A toolset for deciphering and managing biological sequences.""" homepage = "https://bioconductor.org/packages/DECIPHER" git = "https://git.bioconductor.org/packages/DECIPHER.git" + version('2.18.1', commit='6a708421550e6705d05e2fb50a0f5ab4f9041cb0') version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f') version('2.10.2', commit='db7b017c9050a7ec1d4daa15352994890095e9c3') version('2.8.1', commit='35aa66f48e06b93a98d1060c90c44d34ce05ccd9') @@ -19,6 +22,7 @@ class RDecipher(RPackage): version('2.4.0', commit='1a57b8e4c7d7dec1c233f79c9a88d3705e0ad432') depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@2.18.1:', type=('build', 'run')) depends_on('r-biostrings@2.35.12:', type=('build', 'run')) depends_on('r-rsqlite@1.1:', type=('build', 'run')) depends_on('r-dbi', 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 e9087183a0..ad8c4f0f60 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -8,7 +8,7 @@ from spack import * class RDelayedarray(RPackage): """A unified framework for working transparently with on-disk and in-memory - array-like datasets. + 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 @@ -21,6 +21,7 @@ class RDelayedarray(RPackage): homepage = "https://bioconductor.org/packages/DelayedArray" git = "https://git.bioconductor.org/packages/DelayedArray.git" + version('0.16.1', commit='c95eba771ad3fee1b49ec38c51cd8fd1486feadc') version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a') version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f') version('0.6.6', commit='bdb0ac0eee71edd40ccca4808f618fa77f595a64') @@ -28,21 +29,20 @@ class RDelayedarray(RPackage): version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4') depends_on('r@3.4:', type=('build', 'run')) + depends_on('r-matrix', when='@0.10.0:', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.31.5:', when='@0.16.1:', type=('build', 'run')) + depends_on('r-matrixgenerics@1.1.3:', when='@0.16.1:', type=('build', 'run')) depends_on('r-s4vectors@0.14.3:', type=('build', 'run')) - depends_on('r-iranges', type=('build', 'run')) - depends_on('r-matrixstats', 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-s4vectors@0.27.2:', when='@0.16.1:', 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-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run')) - depends_on('r-matrix', when='@0.10.0:', type=('build', 'run')) + depends_on('r-matrixstats', when='@:0.10.0', type=('build', 'run')) + depends_on('r-biocparallel', when='@0.6.6:0.10.0', 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 index 01acefecb3..4f8ac5e4cd 100644 --- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py @@ -7,7 +7,7 @@ from spack import * class RDelayedmatrixstats(RPackage): - """Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects. + """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 @@ -16,26 +16,29 @@ class RDelayedmatrixstats(RPackage): for subsetted calculations such that both memory usage and processing time is minimized.""" - homepage = "https://bioconductor.org/packages/DelayedMatrixStats" + homepage = "https://github.com/PeteHaitch/DelayedMatrixStats" git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git" + version('1.12.3', commit='2b3091dfa9b3bab914e3a4157182063714ba86ae') 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-matrixgenerics', when='@1.12.2:', type=('build', 'run')) depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run')) + depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.15.3:', when='@1.12.2:', type=('build', 'run')) depends_on('r-matrixstats@0.53.1:', type=('build', 'run')) + depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run')) + depends_on('r-matrixstats@0.56.0:', when='@1.12.2:', type=('build', 'run')) + depends_on('r-sparsematrixstats', when='@1.12.2:', 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-iranges', type=('build', 'run')) depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run')) + depends_on('r-hdf5array@1.17.2:', when='@1.12.2:', 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 d10435ac10..169828fc00 100644 --- a/var/spack/repos/builtin/packages/r-deseq/package.py +++ b/var/spack/repos/builtin/packages/r-deseq/package.py @@ -8,7 +8,7 @@ from spack import * class RDeseq(RPackage): """Differential gene expression analysis based on the negative binomial - distribution. + distribution Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model @@ -17,6 +17,7 @@ class RDeseq(RPackage): homepage = "https://bioconductor.org/packages/DESeq" git = "https://git.bioconductor.org/packages/DESeq.git" + version('1.42.0', commit='da76bc64e8c4073b58eaf1c93aa4e89bec5c4e50') version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e') version('1.34.1', commit='e86f1b03a30bc02de4bfd4a0759af2f65cb48c62') version('1.32.0', commit='e3d623b815b53d79eae7cdd09d097cc6098d28c9') diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index 55d71a51f1..a547f1cd9c 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -8,7 +8,7 @@ from spack import * class RDeseq2(RPackage): """Differential gene expression analysis based on the negative binomial - distribution. + distribution Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model @@ -17,6 +17,7 @@ class RDeseq2(RPackage): homepage = "https://bioconductor.org/packages/DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" + version('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77') version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf') version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce') version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c') @@ -24,6 +25,7 @@ class RDeseq2(RPackage): version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb') depends_on('r-s4vectors@0.9.25:', type=('build', 'run')) + depends_on('r-s4vectors@0.23.18:', when='@1.30.0:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-summarizedexperiment@1.1.6:', 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 712ecbe21e..9b5fcf2d35 100644 --- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py +++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py @@ -8,7 +8,7 @@ from spack import * class RDirichletmultinomial(RPackage): """Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome - Data. + Data Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code @@ -19,6 +19,7 @@ class RDirichletmultinomial(RPackage): homepage = "https://bioconductor.org/packages/DirichletMultinomial" git = "https://git.bioconductor.org/packages/DirichletMultinomial.git" + version('1.32.0', commit='6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16') version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f') version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35') version('1.22.0', commit='5864f4298105d12f345f27df77ad13bae4061ca5') diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py index 2b2f2ca065..00358abc46 100644 --- a/var/spack/repos/builtin/packages/r-dnacopy/package.py +++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py @@ -7,7 +7,7 @@ from spack import * class RDnacopy(RPackage): - """DNA copy number data analysis. + """DNA copy number data analysis Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy @@ -16,6 +16,7 @@ class RDnacopy(RPackage): homepage = "https://bioconductor.org/packages/DNAcopy" git = "https://git.bioconductor.org/packages/DNAcopy.git" + version('1.64.0', commit='01650266ea7a4e5c600de545fe70a1103e79b2d8') version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23') version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a') version('1.54.0', commit='fe2657936afbce8ee03221461dff4265e3ded4c4') diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py index cc685ceef4..5b09a3e727 100644 --- a/var/spack/repos/builtin/packages/r-do-db/package.py +++ b/var/spack/repos/builtin/packages/r-do-db/package.py @@ -7,7 +7,9 @@ from spack import * class RDoDb(RPackage): - """A set of annotation maps describing the entire Disease + """A set of annotation maps describing the entire Disease Ontology + + A set of annotation maps describing the entire Disease Ontology assembled using data from DO.""" homepage = "https://bioconductor.org/packages/DO.db/" @@ -15,4 +17,5 @@ class RDoDb(RPackage): version('2.9', sha256='762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881') + depends_on('r@2.7.0:', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py index e2bdad9aa0..0de5b437e1 100644 --- a/var/spack/repos/builtin/packages/r-dose/package.py +++ b/var/spack/repos/builtin/packages/r-dose/package.py @@ -7,7 +7,7 @@ from spack import * class RDose(RPackage): - """Disease Ontology Semantic and Enrichment analysis. + """Disease Ontology Semantic and Enrichment analysis This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities @@ -19,6 +19,7 @@ class RDose(RPackage): homepage = "https://bioconductor.org/packages/DOSE" git = "https://git.bioconductor.org/packages/DOSE.git" + version('3.16.0', commit='a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd') version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3') version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639') version('3.6.1', commit='f2967f0482cea39222bfd15767d0f4a5994f241b') @@ -26,18 +27,17 @@ class RDose(RPackage): version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b') depends_on('r@3.3.1:', type=('build', 'run')) + depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@3.16.0:', 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-s4vectors', when='@:3.10.2', 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')) + depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dss/package.py b/var/spack/repos/builtin/packages/r-dss/package.py index 00c599ceb0..02de075e17 100644 --- a/var/spack/repos/builtin/packages/r-dss/package.py +++ b/var/spack/repos/builtin/packages/r-dss/package.py @@ -7,7 +7,7 @@ from spack import * class RDss(RPackage): - """Dispersion shrinkage for sequencing data. + """Dispersion shrinkage for sequencing data DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from @@ -19,12 +19,13 @@ class RDss(RPackage): homepage = "http://bioconductor.org/packages/DSS/" git = "https://git.bioconductor.org/packages/DSS" + version('2.38.0', commit='82e65b92e6e227f1f99620362db8b03059e07e98') version('2.36.0', commit='841c7ed') version('2.34.0', commit='f9819c7') version('2.32.0', commit='ffb502d') depends_on('r@3.3:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-bsseq', type=('build', 'run')) depends_on('r-biocparallel', when='@2.36.0:', type=('build', 'run')) + depends_on('r-bsseq', type=('build', 'run')) depends_on('r-delayedarray', when='@2.36.0:', 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 8a4e83bb5a..f8cc2dbf8e 100644 --- a/var/spack/repos/builtin/packages/r-edger/package.py +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -7,7 +7,7 @@ from spack import * class REdger(RPackage): - """Empirical Analysis of Digital Gene Expression Data in R. + """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 @@ -20,6 +20,7 @@ class REdger(RPackage): homepage = "https://bioconductor.org/packages/edgeR" git = "https://git.bioconductor.org/packages/edgeR.git" + version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a') version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f') version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d') version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902') @@ -27,10 +28,9 @@ class REdger(RPackage): version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495') depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) - depends_on('r-locfit', type=('build', 'run')) - depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run')) + depends_on('r-limma@3.41.5:', when='@3.32.1:', type=('build', 'run')) + depends_on('r-locfit', 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 index 366bc0a640..4521f4b953 100644 --- a/var/spack/repos/builtin/packages/r-enrichplot/package.py +++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py @@ -7,7 +7,7 @@ from spack import * class REnrichplot(RPackage): - """Visualization of Functional Enrichment Result. + """Visualization of Functional Enrichment Result The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA @@ -17,24 +17,30 @@ class REnrichplot(RPackage): homepage = "https://bioconductor.org/packages/enrichplot" git = "https://git.bioconductor.org/packages/enrichplot.git" + version('1.10.2', commit='77ee04f60a07cc31151f8f47f8ee64f3a43c9760') 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@3.5.0:', when='@1.10.2:', type=('build', 'run')) depends_on('r-cowplot', type=('build', 'run')) - depends_on('r-dose@3.5.1:', type=('build', 'run')) + depends_on('r-dose', type=('build', 'run')) + depends_on('r-dose@3.5.1:', when='@:1.4.0', 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-plyr', when='@1.10.2:', 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')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-scatterpie', when='@1.10.2:', type=('build', 'run')) + depends_on('r-shadowtext', when='@1.10.2:', type=('build', 'run')) + depends_on('r-gosemsim', type=('build', 'run')) + depends_on('r-magrittr', when='@1.10.2:', type=('build', 'run')) + depends_on('r-ggridges', when='@:1.4.0', type=('build', 'run')) + depends_on('r-upsetr', when='@:1.4.0', type=('build', 'run')) + depends_on('r-annotationdbi', when='@:1.4.0', type=('build', 'run')) + depends_on('r-europepmc', when='@1.2.0:1.4.0', type=('build', 'run')) + depends_on('r-ggplotify', when='@1.2.0:1.4.0', type=('build', 'run')) + depends_on('r-gridextra', when='@1.2.0:1.4.0', 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 3aa08ef7fe..03f782030e 100644 --- a/var/spack/repos/builtin/packages/r-ensembldb/package.py +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -7,7 +7,7 @@ from spack import * class REnsembldb(RPackage): - """Utilities to create and use Ensembl-based annotation databases. + """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 @@ -25,6 +25,7 @@ class REnsembldb(RPackage): homepage = "https://bioconductor.org/packages/ensembldb" git = "https://git.bioconductor.org/packages/ensembldb.git" + version('2.14.0', commit='c7150519ed4ef38e5eac1043209863dbc7be43a1') version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0') version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c') version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327') @@ -33,8 +34,12 @@ class REnsembldb(RPackage): depends_on('r-biocgenerics@0.15.10:', type=('build', 'run')) depends_on('r-genomicranges@1.23.21:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run')) depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run')) depends_on('r-annotationfilter@0.99.7:', type=('build', 'run')) + depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run')) + depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', 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')) @@ -42,19 +47,13 @@ class REnsembldb(RPackage): 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', when='@2.0.4:2.2.2', type=('build', 'run')) + depends_on('r-s4vectors@0.23.10:', when='@2.14.0:', 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-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-protgenerics', type=('build', 'run')) + depends_on('r-biostrings', 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')) + depends_on('r-curl', type=('build', 'run')) + depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-exomecopy/package.py b/var/spack/repos/builtin/packages/r-exomecopy/package.py index 112793b865..63cea83434 100644 --- a/var/spack/repos/builtin/packages/r-exomecopy/package.py +++ b/var/spack/repos/builtin/packages/r-exomecopy/package.py @@ -7,7 +7,9 @@ from spack import * class RExomecopy(RPackage): - """Detection of copy number variants (CNV) from exome sequencing samples, + """Copy number variant detection from exome sequencing read depth + + Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into @@ -16,6 +18,7 @@ class RExomecopy(RPackage): homepage = "http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html" git = "https://git.bioconductor.org/packages/exomeCopy" + version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26') version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6') depends_on('r-iranges@2.5.27:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py index 0cfeb1e3da..59907838af 100644 --- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py @@ -7,7 +7,9 @@ from spack import * class RFdbInfiniummethylationHg18(RPackage): - """Compiled HumanMethylation27 and HumanMethylation450 annotations""" + """Annotation package for Illumina Infinium DNA methylation probes + + Compiled HumanMethylation27 and HumanMethylation450 annotations""" # This is a bioconductor package but there is no available git repository homepage = "http://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg18.html" diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py index a2f9797784..0c9d2459b5 100644 --- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py @@ -7,7 +7,9 @@ from spack import * class RFdbInfiniummethylationHg19(RPackage): - """Compiled HumanMethylation27 and HumanMethylation450 annotations.""" + """Annotation package for Illumina Infinium DNA methylation probes + + Compiled HumanMethylation27 and HumanMethylation450 annotations.""" # No available git repository homepage = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg19.html" diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py index 9b56def563..80ab4145c8 100644 --- a/var/spack/repos/builtin/packages/r-fgsea/package.py +++ b/var/spack/repos/builtin/packages/r-fgsea/package.py @@ -7,7 +7,7 @@ from spack import * class RFgsea(RPackage): - """Fast Gene Set Enrichment Analysis. + """Fast Gene Set Enrichment Analysis The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and @@ -17,6 +17,7 @@ class RFgsea(RPackage): homepage = "https://bioconductor.org/packages/fgsea" git = "https://git.bioconductor.org/packages/fgsea.git" + version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318') version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3') version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b') version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d') @@ -30,7 +31,5 @@ class RFgsea(RPackage): 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 f5e5cc9d10..2ef16bbdd4 100644 --- a/var/spack/repos/builtin/packages/r-gcrma/package.py +++ b/var/spack/repos/builtin/packages/r-gcrma/package.py @@ -7,11 +7,14 @@ from spack import * class RGcrma(RPackage): - """Background Adjustment Using Sequence Information.""" + """Background Adjustment Using Sequence Information + + Background adjustment using sequence information.""" homepage = "https://bioconductor.org/packages/gcrma" git = "https://git.bioconductor.org/packages/gcrma.git" + version('2.62.0', commit='b91bdf5bf4e875defedb4d4e3e1e75867773287a') version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224') version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc') version('2.52.0', commit='d6e90b05432d2a8b0583d3fed001811ecdf49d7d') @@ -24,6 +27,5 @@ class RGcrma(RPackage): depends_on('r-affyio@1.13.3:', type=('build', 'run')) depends_on('r-xvector', type=('build', 'run')) depends_on('r-biostrings@2.11.32:', type=('build', 'run')) - depends_on('r-biocinstaller', type=('build', 'run')) - depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run')) + depends_on('r-biocinstaller', when='@:2.52.0', 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 d8de168207..c4cd3e9ae4 100644 --- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -7,7 +7,7 @@ from spack import * class RGdsfmt(RPackage): - """R Interface to CoreArray Genomic Data Structure (GDS) Files. + """R Interface to CoreArray Genomic Data Structure (GDS) Files This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with @@ -25,6 +25,7 @@ class RGdsfmt(RPackage): homepage = "https://bioconductor.org/packages/gdsfmt" git = "https://git.bioconductor.org/packages/gdsfmt.git" + version('1.26.1', commit='bd180b21b1ace120035f0da255cbf6f13088f069') version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00') version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9') version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95') diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index f9adf27e34..a50b89da99 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -7,12 +7,14 @@ from spack import * class RGenefilter(RPackage): - """genefilter: methods for filtering genes from high-throughput - experiments.""" + """genefilter: methods for filtering genes from high-throughput experiments + + Some basic functions for filtering genes.""" homepage = "https://bioconductor.org/packages/genefilter" git = "https://git.bioconductor.org/packages/genefilter.git" + version('1.72.1', commit='b01b00a766982ef7d80b90a252085c8c4f085e1b') version('1.72.0', commit='8cb0b2e73531a417d53e5625bcf436265cdbe101') version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf') version('1.64.0', commit='82e91b7751bae997b9c898c219ea201fd02a8512') @@ -20,9 +22,9 @@ class RGenefilter(RPackage): version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4') version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2') - depends_on('r-biocgenerics@0.31.2:', type=('build', 'run'), when='@1.68.0:') - depends_on('r-s4vectors@0.9.42:', type=('build', 'run'), when='@:1.66.0') + depends_on('r-biocgenerics@0.31.2:', when='@1.68.0:', 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-survival', type=('build', 'run')) + depends_on('r-s4vectors@0.9.42:', when='@:1.66.0', 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 fb150d011d..b9f00c16cc 100644 --- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py +++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py @@ -7,7 +7,7 @@ from spack import * class RGenelendatabase(RPackage): - """Lengths of mRNA transcripts for a number of genomes. + """Lengths of mRNA transcripts for a number of genomes Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser""" @@ -15,6 +15,7 @@ class RGenelendatabase(RPackage): homepage = "https://bioconductor.org/packages/geneLenDataBase" git = "https://git.bioconductor.org/packages/geneLenDataBase.git" + version('1.26.0', commit='2724715ae23a6647d1c0c6e934720aad9377d65e') version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4') version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07') version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198') diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py index 3302356223..2a9f67c3b8 100644 --- a/var/spack/repos/builtin/packages/r-genemeta/package.py +++ b/var/spack/repos/builtin/packages/r-genemeta/package.py @@ -7,7 +7,7 @@ from spack import * class RGenemeta(RPackage): - """MetaAnalysis for High Throughput Experiments. + """MetaAnalysis for High Throughput Experiments A collection of meta-analysis tools for analysing high throughput experimental data""" @@ -15,6 +15,7 @@ class RGenemeta(RPackage): homepage = "https://bioconductor.org/packages/GeneMeta" git = "https://git.bioconductor.org/packages/GeneMeta.git" + version('1.62.0', commit='eb4273ff5867e39592f50b97b454fa5e32b4a9bf') version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d') version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7') version('1.52.0', commit='1f21759984a5852c42a19e89ee53ffd72053d49c') diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py index d74db0b681..d52bce1c6f 100644 --- a/var/spack/repos/builtin/packages/r-geneplotter/package.py +++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py @@ -7,11 +7,14 @@ from spack import * class RGeneplotter(RPackage): - """Graphics related functions for Bioconductor.""" + """Graphics related functions for Bioconductor + + Functions for plotting genomic data.""" homepage = "https://bioconductor.org/packages/geneplotter" git = "https://git.bioconductor.org/packages/geneplotter.git" + version('1.68.0', commit='f1fea7e468fb24fdfa93ef4493600a4d8d183f69') version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48') version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad') version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde') diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py index 2594915cf6..819983efa9 100644 --- a/var/spack/repos/builtin/packages/r-genie3/package.py +++ b/var/spack/repos/builtin/packages/r-genie3/package.py @@ -7,7 +7,7 @@ from spack import * class RGenie3(RPackage): - """GEne Network Inference with Ensemble of trees. + """GEne Network Inference with Ensemble of trees This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.""" @@ -15,6 +15,7 @@ class RGenie3(RPackage): homepage = "https://bioconductor.org/packages/GENIE3" git = "https://git.bioconductor.org/packages/GENIE3.git" + version('1.12.0', commit='14289cee9bed113ab35ba03bcaac4a30e5784497') version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502') version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08') version('1.2.1', commit='1b56fe8184d521d1bb247f000efe9e2b540604c9') diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index cd079f4c60..3b45b55f0b 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -8,7 +8,7 @@ from spack import * class RGenomeinfodb(RPackage): """Utilities for manipulating chromosome names, including modifying them to - follow a particular naming style. + follow a particular naming style Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus @@ -18,6 +18,7 @@ class RGenomeinfodb(RPackage): homepage = "https://bioconductor.org/packages/GenomeInfoDb" git = "https://git.bioconductor.org/packages/GenomeInfoDb.git" + version('1.26.2', commit='96dd27a7e3ef476790b1475aab50dbbed7df67a2') version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265') version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f') version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa') @@ -27,9 +28,9 @@ class RGenomeinfodb(RPackage): 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-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.25.12:', when='@1.26.2:', type=('build', 'run')) depends_on('r-iranges@1.99.26:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) depends_on('r-genomeinfodbdata', 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-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py index a637d28996..fb3a12639c 100644 --- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py +++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py @@ -7,7 +7,7 @@ from spack import * class RGenomicalignments(RPackage): - """Representation and manipulation of short genomic alignments. + """Representation and manipulation of short genomic alignments Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference @@ -17,6 +17,7 @@ class RGenomicalignments(RPackage): homepage = "https://bioconductor.org/packages/GenomicAlignments" git = "https://git.bioconductor.org/packages/GenomicAlignments.git" + version('1.26.0', commit='6c74c74ee53efcd880171126366fee4bd72357bc') version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd') version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab') version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974') @@ -26,25 +27,26 @@ class RGenomicalignments(RPackage): 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-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', 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-biostrings@2.37.1:', type=('build', 'run')) - depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) - depends_on('r-biocparallel', 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-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run')) depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run')) + depends_on('r-genomicranges@1.27.19:', 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-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', 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-biostrings@2.55.7:', when='@1.26.0:', 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-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')) + depends_on('r-biocparallel', 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 f96c952f6d..ce4c878c18 100644 --- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -7,7 +7,7 @@ from spack import * class RGenomicfeatures(RPackage): - """Conveniently import and query gene models. + """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 @@ -21,6 +21,7 @@ class RGenomicfeatures(RPackage): homepage = "https://bioconductor.org/packages/GenomicFeatures" git = "https://git.bioconductor.org/packages/GenomicFeatures.git" + version('1.42.1', commit='2e82891974138b0e976799d64a8938f0be61284d') version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555') version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387') version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1') @@ -29,29 +30,28 @@ class RGenomicfeatures(RPackage): depends_on('r-biocgenerics@0.1.0:', type=('build', 'run')) depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run')) depends_on('r-iranges@2.9.19:', type=('build', 'run')) + depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run')) depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.25.7:', when='@1.42.1:', type=('build', 'run')) depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run')) depends_on('r-annotationdbi@1.33.15:', type=('build', 'run')) + depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run')) depends_on('r-dbi', 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='@1.32.3:', type=('build', 'run')) depends_on('r-biostrings@2.23.3:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) depends_on('r-rtracklayer@1.29.24:', type=('build', 'run')) + depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', 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 21bcbdb65a..ad364e78c1 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -7,7 +7,7 @@ from spack import * class RGenomicranges(RPackage): - """Representation and manipulation of genomic intervals. + """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 @@ -23,6 +23,7 @@ class RGenomicranges(RPackage): homepage = "https://bioconductor.org/packages/GenomicRanges" git = "https://git.bioconductor.org/packages/GenomicRanges.git" + version('1.42.0', commit='32baca734b599d60fa13bdbe31c5712e648f538d') version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a') version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd') version('1.32.7', commit='4c56dc836dbfd0d228dc810e8d401811cdbc267c') @@ -31,21 +32,20 @@ class RGenomicranges(RPackage): 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='@1.32.7:', type=('build', 'run')) depends_on('r-s4vectors@0.9.47:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@1.42.0:', 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-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')) + depends_on('r-iranges@2.23.9:', when='@1.42.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.5:', 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='@1.32.7:', type=('build', 'run')) + depends_on('r-xvector', type=('build', 'run')) + depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run')) + depends_on('r-xvector@0.29.2:', when='@1.42.0:', 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 97eb0ba775..60a02bedcc 100644 --- a/var/spack/repos/builtin/packages/r-geoquery/package.py +++ b/var/spack/repos/builtin/packages/r-geoquery/package.py @@ -7,7 +7,7 @@ from spack import * class RGeoquery(RPackage): - """Get data from NCBI Gene Expression Omnibus (GEO). + """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 @@ -17,6 +17,7 @@ class RGeoquery(RPackage): homepage = "https://bioconductor.org/packages/GEOquery" git = "https://git.bioconductor.org/packages/GEOquery.git" + version('2.58.0', commit='6332ca3791ddcfb233b9ad75b5904b3d60f49b93') version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643') version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97') version('2.48.0', commit='6a8d1ca195b5c26fb717ae93beb1a8d9b7031c5e') @@ -24,15 +25,13 @@ class RGeoquery(RPackage): version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb') depends_on('r-biobase', 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-readr', when='@2.46.15:', type=('build', 'run')) + depends_on('r-readr@1.3.1:', when='@2.50.5:', 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')) + depends_on('r-xml', when='@2.42.0', type=('build', 'run')) + depends_on('r-rcurl', when='@2.42.0', 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 a218dcde24..f285243cf6 100644 --- a/var/spack/repos/builtin/packages/r-ggbio/package.py +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -7,7 +7,7 @@ from spack import * class RGgbio(RPackage): - """Visualization tools for genomic data. + """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 @@ -22,6 +22,7 @@ class RGgbio(RPackage): homepage = "https://bioconductor.org/packages/ggbio" git = "https://git.bioconductor.org/packages/ggbio.git" + version('1.38.0', commit='c39c51993f419cfc2f094e664477f25f5212a242') version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88') version('1.30.0', commit='8b05258b089b06a743352e92058edda06c24cfb7') version('1.28.5', commit='594521ca556ef7d97cf4882ecfa54d22c2a2faba') @@ -36,11 +37,15 @@ class RGgbio(RPackage): depends_on('r-gtable', type=('build', 'run')) depends_on('r-hmisc', type=('build', 'run')) depends_on('r-biovizbase@1.23.3:', type=('build', 'run')) + depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run')) + depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) + depends_on('r-iranges@2.11.16:', when='@1.26.1:', 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-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run')) depends_on('r-summarizedexperiment', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) depends_on('r-rsamtools@1.17.28:', type=('build', 'run')) @@ -49,17 +54,10 @@ class RGgbio(RPackage): 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-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run')) depends_on('r-organismdbi', type=('build', 'run')) depends_on('r-ggally', 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-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-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py index fe0efb4902..7d59544072 100644 --- a/var/spack/repos/builtin/packages/r-glimma/package.py +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -7,7 +7,7 @@ from spack import * class RGlimma(RPackage): - """Interactive HTML graphics. + """Interactive HTML graphics This package generates interactive visualisations for analysis of RNA- sequencing data using output from limma, edgeR or DESeq2 packages in an @@ -18,6 +18,7 @@ class RGlimma(RPackage): homepage = "https://bioconductor.org/packages/Glimma" git = "https://git.bioconductor.org/packages/Glimma.git" + version('2.0.0', commit='40bebaa79e8c87c5686cff7285def4461c11bca9') version('1.12.0', commit='d02174239fe0b47983d6947ed42a1a53b24caecb') version('1.10.1', commit='ffc7abc36190396598fadec5e9c653441e47be72') version('1.8.2', commit='7696aca2c023f74d244b6c908a6e7ba52bfcb34b') @@ -25,10 +26,14 @@ class RGlimma(RPackage): version('1.4.0', commit='c613c5334ed7868f36d5716b97fdb6234fb291f8') 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@3.4.0:', when='@1.6.0:', type=('build', 'run')) + depends_on('r@4.0.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-htmlwidgets', when='@2.0.0:', type=('build', 'run')) depends_on('r-edger', type=('build', 'run')) + depends_on('r-deseq2', when='@2.0.0:', type=('build', 'run')) + depends_on('r-limma', when='@2.0.0:', type=('build', 'run')) + depends_on('r-summarizedexperiment', when='@2.0.0:', 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')) + depends_on('r-biobase', when='@1.4.0:1.6.0', type=('build', 'run')) + depends_on('r-scater', when='@1.4.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index db52277bbb..e15bf99802 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -7,11 +7,21 @@ from spack import * class RGoDb(RPackage): - """A set of annotation maps describing the entire Gene + """A set of annotation maps describing the entire Gene Ontology + + A set of annotation maps describing the entire Gene Ontology assembled using data from GO.""" homepage = "https://www.bioconductor.org/packages/GO.db/" - url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" + url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" + + version('3.12.1', + sha256='e0316959d3d32096f9432c897413dff74fce53e15ead7917a7724467d971dab9', + url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GO.db_3.12.1.tar.gz') + version('3.4.1', + sha256='2fc2048e9d26edb98e35e4adc4d18c6df54f44836b5cc4a482d36ed99e058cc1', + url='https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz') - version('3.4.1', sha256='2fc2048e9d26edb98e35e4adc4d18c6df54f44836b5cc4a482d36ed99e058cc1') - depends_on('r-annotationdbi', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.37.4:', type=('build', 'run')) + depends_on('r-annotationdbi@1.51.3:', when='@3.12.1:', 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 index 219f68bc32..8df9f00ff0 100644 --- a/var/spack/repos/builtin/packages/r-gofuncr/package.py +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -7,7 +7,7 @@ from spack import * class RGofuncr(RPackage): - """Gene ontology enrichment using FUNC. + """Gene ontology enrichment using FUNC GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from @@ -29,16 +29,17 @@ class RGofuncr(RPackage): homepage = "https://bioconductor.org/packages/GOfuncR" git = "https://git.bioconductor.org/packages/GOfuncR.git" + version('1.10.0', commit='51b01a2b9afa03fde2e1628036096cbeafaa2ef4') version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709') version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded') version('1.0.0', commit='becd4ddde085c5477042adb856e7a4f40dbd648e') + depends_on('r+X', type=('build', 'run')) 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')) + depends_on('r-annotationdbi', 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 2e997e79ac..9c5c0c7cee 100644 --- a/var/spack/repos/builtin/packages/r-gosemsim/package.py +++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py @@ -7,7 +7,7 @@ from spack import * class RGosemsim(RPackage): - """GO-terms Semantic Similarity Measures. + """GO-terms Semantic Similarity Measures The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, @@ -20,6 +20,7 @@ class RGosemsim(RPackage): homepage = "https://bioconductor.org/packages/GOSemSim" git = "https://git.bioconductor.org/packages/GOSemSim.git" + version('2.16.1', commit='92f1d567f3584fe488f434abce87c2e1950081c0') version('2.10.0', commit='5db1ecbf2f8d870430d6e587609327d05ba3ad7b') version('2.8.0', commit='c8c985b2a814cc2365c7f05b2509205e1b6b7f58') version('2.6.2', commit='2ffe78e89276e804306554965fc0799318ec56ed') @@ -27,8 +28,8 @@ class RGosemsim(RPackage): version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52') depends_on('r@3.3.2:', type=('build', 'run')) + depends_on('r@3.4.0:', when='@2.8.0:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@2.16.1:', 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 82d200ebb3..56139b3caf 100644 --- a/var/spack/repos/builtin/packages/r-goseq/package.py +++ b/var/spack/repos/builtin/packages/r-goseq/package.py @@ -7,7 +7,7 @@ from spack import * class RGoseq(RPackage): - """Gene Ontology analyser for RNA-seq and other length biased data. + """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""" @@ -15,6 +15,7 @@ class RGoseq(RPackage): homepage = "https://bioconductor.org/packages/goseq" git = "https://git.bioconductor.org/packages/goseq.git" + version('1.42.0', commit='8164b90e7505bbc1035105fdc15219c764ef8b8d') version('1.36.0', commit='26c9f7de18889afeee1b571ca1c4ab4d2877ab80') version('1.34.1', commit='bad217b42cc34423698fbcf701d4e3591aac4474') version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36') diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py index b346844189..e14654376d 100644 --- a/var/spack/repos/builtin/packages/r-gostats/package.py +++ b/var/spack/repos/builtin/packages/r-gostats/package.py @@ -7,7 +7,7 @@ from spack import * class RGostats(RPackage): - """Tools for manipulating GO and microarrays. + """Tools for manipulating GO and microarrays A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple @@ -16,22 +16,23 @@ class RGostats(RPackage): homepage = "https://bioconductor.org/packages/GOstats" git = "https://git.bioconductor.org/packages/GOstats.git" + version('2.56.0', commit='8f988c3b4b1ce7e05626aae8956004c7bbdd6f3a') 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+X', 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-category@2.43.2:', when='@2.44.0:', type=('build', 'run')) depends_on('r-graph@1.15.15:', when='@2.42.0', type=('build', 'run')) + depends_on('r-graph', when='@2.44.0:', 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@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 327baac6cd..e13346800e 100644 --- a/var/spack/repos/builtin/packages/r-graph/package.py +++ b/var/spack/repos/builtin/packages/r-graph/package.py @@ -7,13 +7,14 @@ from spack import * class RGraph(RPackage): - """graph: A package to handle graph data structures. + """graph: A package to handle graph data structures A package that implements some simple graph handling capabilities.""" homepage = "https://bioconductor.org/packages/graph" git = "https://git.bioconductor.org/packages/graph.git" + version('1.68.0', commit='03ad9ed088095605e317510b8234501318994e94') version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3') version('1.60.0', commit='e2aecb0a862f32091b16e0036f53367d3edf4c1d') version('1.58.2', commit='6455d8e7a5a45dc733915942cb71005c1016b6a0') diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index b8e688983f..97c7dc3ac8 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -7,7 +7,7 @@ from spack import * class RGseabase(RPackage): - """Gene set enrichment data structures and methods. + """Gene set enrichment data structures and methods This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).""" @@ -15,6 +15,7 @@ class RGseabase(RPackage): homepage = "https://bioconductor.org/packages/GSEABase" git = "https://git.bioconductor.org/packages/GSEABase.git" + version('1.52.1', commit='257dfccbc5b507d82099fac6b06bb03825e995e8') version('1.46.0', commit='edce83a9256a0c03206c2bce7c90ada0d90f6622') version('1.44.0', commit='7042ff64a98b05b9572231ee1b4f3ae4fc9c768e') version('1.42.0', commit='5e40ce0fdd4dc0cff7601b169bbf6aa1430ae33e') diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py index 2aa71f9430..7493244f6f 100644 --- a/var/spack/repos/builtin/packages/r-gtrellis/package.py +++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py @@ -7,7 +7,7 @@ from spack import * class RGtrellis(RPackage): - """Genome Level Trellis Layout. + """Genome Level Trellis Layout Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, @@ -19,6 +19,7 @@ class RGtrellis(RPackage): homepage = "https://bioconductor.org/packages/gtrellis" git = "https://git.bioconductor.org/packages/gtrellis.git" + version('1.22.0', commit='c071c5631f3dedda212aed87d9c02954b5ed6611') version('1.16.1', commit='a9003ededc8f2a48c78d4545e2f214023c13a7da') version('1.14.0', commit='93935fb34211d12b250e22291712e18a31b0208d') version('1.12.1', commit='7f3941adddbbfa17f4cf474b703568678a38272d') @@ -29,6 +30,5 @@ class RGtrellis(RPackage): depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-circlize@0.3.3:', type=('build', 'run')) - depends_on('r-getoptlong', type=('build', 'run')) - depends_on('r-circlize@0.4.8:', when='@1.16.1', type=('build', 'run')) + depends_on('r-getoptlong', 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 09cf6fc39e..3e2ac772b4 100644 --- a/var/spack/repos/builtin/packages/r-gviz/package.py +++ b/var/spack/repos/builtin/packages/r-gviz/package.py @@ -7,7 +7,7 @@ from spack import * class RGviz(RPackage): - """Plotting data and annotation information along genomic coordinates. + """Plotting data and annotation information along genomic coordinates Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the @@ -19,6 +19,7 @@ class RGviz(RPackage): homepage = "https://bioconductor.org/packages/Gviz" git = "https://git.bioconductor.org/packages/Gviz.git" + version('1.34.0', commit='445fadff2aedd8734580fa908aa47ff1216a8182') version('1.28.3', commit='20b9825af144cfc888629c34aa980b5bbd65bf86') version('1.26.5', commit='430310b9d2e098f9757a71d26a2f69871071f30c') version('1.24.0', commit='3ee1eec97a56653c07c434a97f82cfe3c4281841') @@ -26,6 +27,7 @@ class RGviz(RPackage): version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c') depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r@4.0:', when='@1.34.0:', 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')) @@ -37,6 +39,7 @@ class RGviz(RPackage): 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-ensembldb@2.11.3:', when='@1.34.0:', 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')) diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py index c7d6458e63..7c2400d9a6 100644 --- a/var/spack/repos/builtin/packages/r-hdf5array/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -7,7 +7,7 @@ from spack import * class RHdf5array(RPackage): - """HDF5 backend for DelayedArray objects. + """HDF5 backend for DelayedArray objects Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of @@ -21,6 +21,7 @@ class RHdf5array(RPackage): homepage = "https://bioconductor.org/packages/HDF5Array" git = "https://git.bioconductor.org/packages/HDF5Array.git" + version('1.18.0', commit='d5bd55d170cb384fdebdf60751e1e28483782caa') version('1.12.3', commit='21c6077f3f789748a18f2e579110576c5522e975') version('1.10.1', commit='0b8ae1dfb56e4203dd8e14781850370df46a5e2c') version('1.8.1', commit='3c9aa23d117bf489b6341708dc80c943bd1af11a') @@ -29,21 +30,21 @@ class RHdf5array(RPackage): 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-delayedarray@0.15.16:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-rhdf5', type=('build', 'run')) + depends_on('r-rhdf5@2.25.6:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-rhdf5@2.31.6:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-matrix', when='@1.18.0:', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.31.5:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-s4vectors@0.21.6:', when='@1.12.3:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.13:', when='@1.18.0:', type=('build', 'run')) + depends_on('r-iranges', 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 3c325756c7..5296cde4c8 100644 --- a/var/spack/repos/builtin/packages/r-hypergraph/package.py +++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py @@ -7,7 +7,7 @@ from spack import * class RHypergraph(RPackage): - """A package providing hypergraph data structures. + """A package providing hypergraph data structures A package that implements some simple capabilities for representing and manipulating hypergraphs.""" @@ -15,6 +15,7 @@ class RHypergraph(RPackage): homepage = "https://bioconductor.org/packages/hypergraph" git = "https://git.bioconductor.org/packages/hypergraph.git" + version('1.62.0', commit='a286bbb70289e9f3cdf41407d52e5976bd6ed11e') version('1.56.0', commit='f8b977fe068f15ecea49d30e77a871a35afcb97b') version('1.54.0', commit='cf134b9221e9b5f6329a6786a366f57426c49e7c') version('1.52.0', commit='3e28d8e8ab4c3facb79857b4e4cfffd65e064aca') diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py index c240f7f28b..e99aa99d8e 100644 --- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py @@ -7,7 +7,9 @@ from spack import * class RIlluminahumanmethylation450kannoIlmn12Hg19(RPackage): - """Manifests and annotation for Illumina's 450k array data.""" + """Annotation for Illumina's 450k methylation arrays + + Manifests and annotation for Illumina's 450k array data.""" # This package is available via bioconductor but there is no available git # repository. diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py index f0d5cfd8dd..0d2d87cfab 100644 --- a/var/spack/repos/builtin/packages/r-illuminaio/package.py +++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py @@ -7,13 +7,14 @@ from spack import * class RIlluminaio(RPackage): - """Parsing Illumina Microarray Output Files. + """Parsing Illumina Microarray Output Files 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('0.32.0', commit='e1322c781dd475a5e8ff6c0422bebb3deb47fa80') version('0.26.0', commit='40c2f94df2ea64d745d25aadd2bfb33ac3e02f81') version('0.24.0', commit='47953c77713c2da00a610f39308f86c5b44f6c59') version('0.22.0', commit='dbd842340999569975ea593f47d70a729b3f68f2') diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py index 3e1c749481..7629e3e406 100644 --- a/var/spack/repos/builtin/packages/r-impute/package.py +++ b/var/spack/repos/builtin/packages/r-impute/package.py @@ -7,13 +7,14 @@ from spack import * class RImpute(RPackage): - """impute: Imputation for microarray data. + """impute: Imputation for microarray data Imputation for microarray data (currently KNN only)""" homepage = "https://bioconductor.org/packages/impute" git = "https://git.bioconductor.org/packages/impute.git" + version('1.64.0', commit='31a5636f4dfbb1fd61386738786a0de048a620c2') version('1.58.0', commit='dc17173df08d965a0d0aac9fa4ad519bd99d127e') version('1.56.0', commit='6c037ed4dffabafceae684265f86f2a18751b559') version('1.54.0', commit='efc61f5197e8c4baf4ae881fb556f0312beaabd8') diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py index 81468520fa..ce45cce7d1 100644 --- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py +++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py @@ -8,7 +8,7 @@ from spack import * class RInteractivedisplaybase(RPackage): """Base package for enabling powerful shiny web displays of Bioconductor - objects. + objects The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor @@ -17,6 +17,7 @@ class RInteractivedisplaybase(RPackage): homepage = "https://bioconductor.org/packages/interactiveDisplayBase" git = "https://git.bioconductor.org/packages/interactiveDisplayBase.git" + version('1.28.0', commit='a74c02c971c4f9c7086e14abd23f1a4190da4599') version('1.22.0', commit='4ce3cde1dabc01375c153ad614d77a5e28b96916') version('1.20.0', commit='f40912c8af7afbaaf68c003a6e148d81cbe84df6') version('1.18.0', commit='d07ea72a595877f27bf054f664f23e8f0304def8') @@ -26,3 +27,4 @@ class RInteractivedisplaybase(RPackage): 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-dt', when='@1.28.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index 6d896c7f11..3c600ed71b 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -7,7 +7,7 @@ from spack import * class RIranges(RPackage): - """Foundation of integer range manipulation in Bioconductor. + """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. @@ -19,6 +19,7 @@ class RIranges(RPackage): homepage = "https://bioconductor.org/packages/IRanges" git = "https://git.bioconductor.org/packages/IRanges.git" + version('2.24.1', commit='6c61fddf4c5830f69a0f7f108888c67cd0a12b19') version('2.22.2', commit='8c5e991') version('2.18.3', commit='c98a7ba074e72f2e5ec98252dffe9d3392711972') version('2.16.0', commit='26834c6868d7c279dd8ac1bb9daa16e6fef273c2') @@ -27,17 +28,15 @@ class RIranges(RPackage): version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614') depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r@4.0.0:', when='@2.24.1:', 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-biocgenerics@0.36.0:', when='@2.24.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.13.17:', type=('build', 'run')) + depends_on('r-s4vectors@0.15.5:', when='@2.12.0:', 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')) - depends_on('r-s4vectors@0.25.14:', when='@2.22.2:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@2.24.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py index 6833dd7bc2..4b3bf9695b 100644 --- a/var/spack/repos/builtin/packages/r-kegg-db/package.py +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -7,10 +7,21 @@ from spack import * class RKeggDb(RPackage): - """A set of annotation maps for KEGG assembled using data from KEGG.""" + """A set of annotation maps for KEGG + + A set of annotation maps for KEGG assembled using data from KEGG.""" + + # NOTE: The KEGG.db package is deprecated homepage = "https://www.bioconductor.org/packages/KEGG.db/" url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" - version('3.2.3', sha256='02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963') - depends_on('r-annotationdbi', type=('build', 'run')) + version('3.2.4', + sha256='2e60d1b664cbd1491cc00ed13a22904706c5a4651150f70daca04bf3ba9ead88', + url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/KEGG.db_3.2.4.tar.gz') + version('3.2.3', + sha256='02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963', + url='https://bioconductor.org/packages/3.10/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz') + + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.34.3:', 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 a56a91abef..21f7c27ed3 100644 --- a/var/spack/repos/builtin/packages/r-kegggraph/package.py +++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py @@ -7,7 +7,7 @@ from spack import * class RKegggraph(RPackage): - """KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor. + """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. @@ -19,6 +19,7 @@ class RKegggraph(RPackage): homepage = "https://bioconductor.org/packages/KEGGgraph" git = "https://git.bioconductor.org/packages/KEGGgraph.git" + version('1.50.0', commit='3335e85cdba264c04e6e36378578cf6c83a30eb8') version('1.44.0', commit='2c24e8ec53fe34c72ea65f34e3c09905ab2e5c62') version('1.42.0', commit='7d907e22a3ad7b4829a7cbaba5a8f8dc8013a609') version('1.40.0', commit='6351a1637276f71697b01a994ebda0d3d1cf6d7a') @@ -28,5 +29,4 @@ class RKegggraph(RPackage): 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-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 a30ac6e7a7..d2ff44714b 100644 --- a/var/spack/repos/builtin/packages/r-keggrest/package.py +++ b/var/spack/repos/builtin/packages/r-keggrest/package.py @@ -7,7 +7,7 @@ from spack import * class RKeggrest(RPackage): - """Client-side REST access to KEGG. + """Client-side REST access to KEGG 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 @@ -16,12 +16,14 @@ class RKeggrest(RPackage): homepage = "https://bioconductor.org/packages/KEGGREST" git = "https://git.bioconductor.org/packages/KEGGREST.git" + version('1.30.1', commit='fd9970ea9df117d625257b8c6351cf85098cfbc1') 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@3.5.0:', when='@1.30.1:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-biostrings', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py index af1b0a2231..f0fe8822f4 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -7,7 +7,7 @@ from spack import * class RLimma(RPackage): - """Linear Models for Microarray Data. + """Linear Models for Microarray Data Data analysis, linear models and differential expression for microarray data.""" @@ -15,6 +15,7 @@ class RLimma(RPackage): homepage = "https://bioconductor.org/packages/limma" git = "https://git.bioconductor.org/packages/limma.git" + version('3.46.0', commit='ff03542231827f39ebde6464cdbba0110e24364e') version('3.40.6', commit='3ae0767ecf7a764030e7b7d0b1d0f292c0b24055') version('3.38.3', commit='77b292eb150cdedaa1db704bcfb01f0bb29e9849') version('3.36.5', commit='3148d1cb7eea9c6bdd60351d51abcfd665332d44') @@ -22,5 +23,4 @@ class RLimma(RPackage): version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60') 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-limsolve/package.py b/var/spack/repos/builtin/packages/r-limsolve/package.py new file mode 100644 index 0000000000..f7b6208dd0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-limsolve/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2021 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 RLimsolve(RPackage): + """Solving Linear Inverse Models + + Functions that (1) find the minimum/maximum of a linear or quadratic + function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) + subject to equality constraints Ex=f and/or inequality constraints Gx>=h, + (2) sample an underdetermined- or overdetermined system Ex=f subject to + Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the + unknown x. It includes banded and tridiagonal linear systems.""" + + homepage = "https://cloud.r-project.org/package=limSolve" + url = "https://cloud.r-project.org/src/contrib/limSolve_1.5.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/limSolve" + + version('1.5.6', sha256='b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-quadprog', type=('build', 'run')) + depends_on('r-lpsolve', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py index ce4869a6b4..d12eb1de9a 100644 --- a/var/spack/repos/builtin/packages/r-lumi/package.py +++ b/var/spack/repos/builtin/packages/r-lumi/package.py @@ -7,7 +7,10 @@ from spack import * class RLumi(RPackage): - """The lumi package provides an integrated solution for the Illumina + """BeadArray Specific Methods for Illumina Methylation and Expression + Microarrays + + The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It @@ -17,6 +20,7 @@ class RLumi(RPackage): homepage = "https://bioconductor.org/packages/release/bioc/html/lumi.html" git = "https://git.bioconductor.org/packages/lumi" + version('2.42.0', commit='a643b3ba46fee951b8566ddd8216af7e6c92f6f6') version('2.38.0', commit='321d480d44ce9a0c02ce5af1bddc1f549abdea59') depends_on('r@2.10:', 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 b6f72903db..1d3b968b8c 100644 --- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py +++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py @@ -7,7 +7,7 @@ from spack import * class RMakecdfenv(RPackage): - """CDF Environment Maker. + """CDF Environment Maker This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the @@ -17,6 +17,7 @@ class RMakecdfenv(RPackage): homepage = "https://bioconductor.org/packages/makecdfenv" git = "https://git.bioconductor.org/packages/makecdfenv.git" + version('1.66.0', commit='02aa975d543089f5495cb3b4e8edbcf0ff05148a') version('1.60.0', commit='900ece3ecd7a0ade9f8a0374e5a03def4e079cb3') version('1.58.0', commit='6f513e39c4920a6da10d22718fc3bf278fe5ffe2') version('1.56.0', commit='f6b48e9a9f18598653d05bc0bdffeae7fefbb327') diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py new file mode 100644 index 0000000000..daf207f782 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2021 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 RMatrixgenerics(RPackage): + """S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects + + S4 generic functions modeled after the 'matrixStats' API for alternative + matrix implementations. Packages with alternative matrix implementation can + depend on this package and implement the generic functions that are defined + here for a useful set of row and column summary statistics. Other package + developers can import this package and handle a different matrix + implementations without worrying about incompatibilities.""" + + homepage = "https://bioconductor.org/packages/MatrixGenerics" + git = "https://git.bioconductor.org/packages/MatrixGenerics" + + version('1.2.1', commit='abcc9ca0504e0b915cd7933a3169a8e9e5bd2fe9') + + depends_on('r-matrixstats@0.57.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index 4430c2d08e..8559edd0f4 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -19,6 +19,7 @@ class RMatrixstats(RPackage): url = "https://cloud.r-project.org/src/contrib/matrixStats_0.52.2.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/matrixStats" + version('0.58.0', sha256='8367b4b98cd24b6e40022cb2b11e907aa0bcf5ee5b2f89fefb186f53661f4b49') version('0.57.0', sha256='f9681887cd3b121762c83f55f189cae26cb8443efce91fcd212ac714fde9f343') version('0.55.0', sha256='16d6bd90eee4cee8df4c15687de0f9b72730c03e56603c2998007d4533e8db19') version('0.54.0', sha256='8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f') diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py index a4dd724e07..9f01e66279 100644 --- a/var/spack/repos/builtin/packages/r-methylumi/package.py +++ b/var/spack/repos/builtin/packages/r-methylumi/package.py @@ -7,7 +7,9 @@ from spack import * class RMethylumi(RPackage): - """This package provides classes for holding and manipulating Illumina + """Handle Illumina methylation data + + This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files @@ -19,6 +21,7 @@ class RMethylumi(RPackage): homepage = "https://bioconductor.org/packages/release/bioc/html/methylumi.html" git = "https://git.bioconductor.org/packages/methylumi" + version('2.36.0', commit='5fb0b609f9c9181ac99f902745958774e5489606') version('2.32.0', commit='e2a29c1b214c0d43c7325d176f9ce41dcf8e2f9d') depends_on('r@2.13:', type=('build', 'run')) @@ -30,6 +33,7 @@ class RMethylumi(RPackage): depends_on('r-fdb-infiniummethylation-hg19@2.2.0:', type=('build', 'run')) depends_on('r-minfi', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', when='@2.36.0:', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py index e88fd5c866..da82288422 100644 --- a/var/spack/repos/builtin/packages/r-minfi/package.py +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -7,13 +7,14 @@ from spack import * class RMinfi(RPackage): - """Analyze Illumina Infinium DNA methylation arrays. + """Analyze Illumina Infinium DNA methylation arrays Tools to analyze & visualize Illumina Infinium methylation arrays.""" homepage = "https://bioconductor.org/packages/minfi" git = "https://git.bioconductor.org/packages/minfi.git" + version('1.36.0', commit='94301da343226be7cd878c2a6c1bb529564785d6') version('1.30.0', commit='a4c28e9388fe3b35e7d21a9669e39250ed6dcbcd') version('1.28.4', commit='b5125b2f3e05d37d519eeb6fd44a60efdad388e7') version('1.26.2', commit='ebb07b728b2453998d46e4e53d4fbf873e8e81fc') @@ -37,7 +38,9 @@ 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@0.50.0:', type=('build', 'run')) + depends_on('r-illuminaio@0.23.2:', when='@1.28.4:', type=('build', 'run')) + depends_on('r-delayedmatrixstats', when='@1.26.2:', type=('build', 'run')) + depends_on('r-delayedmatrixstats@1.3.4:', when='@1.28.4:', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) depends_on('r-genefilter', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) @@ -46,14 +49,10 @@ 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-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')) + depends_on('r-delayedarray@0.15.16:', when='@1.36.0:', 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-matrixstats@0.50.0:', 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 c697594a69..67465eb4b8 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -8,7 +8,7 @@ from spack import * class RMlinterfaces(RPackage): """Uniform interfaces to R machine learning procedures for data in - Bioconductor containers. + Bioconductor containers This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.""" @@ -16,6 +16,7 @@ class RMlinterfaces(RPackage): homepage = "https://bioconductor.org/packages/MLInterfaces" git = "https://git.bioconductor.org/packages/MLInterfaces.git" + version('1.70.0', commit='7b076c3e85314dd5fd5bd8a98e8123d08d9acd3b') version('1.64.1', commit='0b081112d87771248bc33b3b82d5ca4685f986a1') version('1.62.1', commit='6cf59a90b14779cf57a0b36f1087304082ae50fe') version('1.60.1', commit='019e9ed44923e5d845a4800246aa044ddd59d548') @@ -23,6 +24,8 @@ class RMlinterfaces(RPackage): version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f') depends_on('r@2.9:', type=('build', 'run')) + depends_on('r@3.5:', when='@1.60.1:', type=('build', 'run')) + depends_on('r-rcpp', when='@1.70.0:', 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')) @@ -32,7 +35,6 @@ class RMlinterfaces(RPackage): 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')) depends_on('r-ggvis', type=('build', 'run')) @@ -42,5 +44,4 @@ class RMlinterfaces(RPackage): depends_on('r-hwriter', 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')) + depends_on('r-rda', when='@:1.64.1', 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 adaf259f0e..ea3330b9c1 100644 --- a/var/spack/repos/builtin/packages/r-msnbase/package.py +++ b/var/spack/repos/builtin/packages/r-msnbase/package.py @@ -7,7 +7,7 @@ from spack import * class RMsnbase(RPackage): - """Base Functions and Classes for Mass Spectrometry and Proteomics. + """Base Functions and Classes for Mass Spectrometry and Proteomics MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw @@ -16,6 +16,7 @@ class RMsnbase(RPackage): homepage = "https://bioconductor.org/packages/MSnbase" git = "https://git.bioconductor.org/packages/MSnbase.git" + version('2.16.1', commit='4d88b4edd1af59474462b1b06ad0ec5831f3a878') version('2.10.1', commit='4d5899bc9c714f0b1a70cddd537cd4621b2b53b0') version('2.8.3', commit='ef883752c5e92d445647bc5b5d23d5df320db415') version('2.6.4', commit='46836860ce0281eef135303f2e2948303d67f68c') @@ -23,35 +24,33 @@ class RMsnbase(RPackage): version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197') depends_on('r@3.1:', type=('build', 'run')) + depends_on('r@3.5:', when='@2.16.1:', 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-mzr@2.11.11:', when='@2.4.2:', type=('build', 'run')) + depends_on('r-mzr@2.13.6:', 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')) + depends_on('r-mzr@2.19.6:', when='@2.16.1:', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-protgenerics@1.5.1:', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r-protgenerics@1.19.3:', when='@2.16.1:', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) + depends_on('r-iranges@2.13.28:', when='@2.6.4:', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) depends_on('r-preprocesscore', type=('build', 'run')) depends_on('r-vsn', type=('build', 'run')) 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@1.5.2:', type=('build', 'run')) depends_on('r-maldiquant@1.16:', type=('build', 'run')) + depends_on('r-mzid@1.5.2:', 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-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')) + depends_on('r-rcpp', 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 2502a67da9..87a021d35b 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -7,7 +7,7 @@ from spack import * class RMulttest(RPackage): - """Resampling-based multiple hypothesis testing. + """Resampling-based multiple hypothesis testing Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling @@ -30,6 +30,7 @@ class RMulttest(RPackage): homepage = "https://bioconductor.org/packages/multtest" git = "https://git.bioconductor.org/packages/multtest.git" + version('2.46.0', commit='c4dd27b333c80313a88668b59d0299988c6478a2') version('2.40.0', commit='5f00017c2d3a31e05e1cfe06d9f7afdee19f8473') version('2.38.0', commit='4dfe71cecfb298a94521088fb7bd83c5498d2915') version('2.36.0', commit='babb15e8d110eb72300ad59cf7e53386237a4198') diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py index 5aef4f93a4..a96b5803b3 100644 --- a/var/spack/repos/builtin/packages/r-mzid/package.py +++ b/var/spack/repos/builtin/packages/r-mzid/package.py @@ -7,7 +7,7 @@ from spack import * class RMzid(RPackage): - """An mzIdentML parser for R. + """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 @@ -18,6 +18,7 @@ class RMzid(RPackage): homepage = "https://bioconductor.org/packages/mzID" git = "https://git.bioconductor.org/packages/mzID.git" + version('1.28.0', commit='cd006631c8222ce5b4af0577a7401b39cc58fd9c') version('1.22.0', commit='382d9cf11f0cba996911a9d79e193d28f3ac6042') version('1.20.1', commit='819582646944440ddd9ed3724ae964841573e54c') version('1.18.0', commit='7d8924ae95585eb8cf472d21619a7603d291d652') diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 8f9121126d..75aad10526 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -8,7 +8,7 @@ from spack import * class RMzr(RPackage): """parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass - spectrometry data). + 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 @@ -20,6 +20,7 @@ class RMzr(RPackage): homepage = "https://bioconductor.org/packages/mzR" git = "https://git.bioconductor.org/packages/mzR.git" + version('2.24.1', commit='e1d4de8761e6729fd45320d842691c8fe9116b7b') version('2.18.1', commit='13f9f9b1149859c3e29cfce941d958cc4f680546') version('2.16.2', commit='22d7dad98f46b5bed7f6f7b3a703dcdf5997f709') version('2.14.0', commit='bf1154bc45101d95b5a67c66980856a779b84bd4') @@ -30,11 +31,9 @@ class RMzr(RPackage): depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics@0.13.6:', type=('build', 'run')) depends_on('r-protgenerics', type=('build', 'run')) - depends_on('r-zlibbioc', type=('build', 'run')) - 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-protgenerics@1.17.3:', when='@2.24.1:', type=('build', 'run')) depends_on('r-ncdf4', when='@2.16.2:', type=('build', 'run')) - + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('r-rhdf5lib@1.1.4:', when='@2.14.0:', type=('build', 'run')) depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-nada/package.py b/var/spack/repos/builtin/packages/r-nada/package.py new file mode 100644 index 0000000000..0aa6aad73f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nada/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2021 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 RNada(RPackage): + """Nondetects and Data Analysis for Environmental Data + + Contains methods described by Dennis Helsel in his book "Nondetects And + Data Analysis: Statistics for Censored Environmental Data".""" + + homepage = "https://cloud.r-project.org/package=NADA" + url = "https://cloud.r-project.org/src/contrib/NADA_1.6-1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/NADA" + + version('1.6-1.1', sha256='670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py index add9def3e1..7c24b1333a 100644 --- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py +++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py @@ -7,7 +7,7 @@ from spack import * class ROligoclasses(RPackage): - """Classes for high-throughput arrays supported by oligo and crlmm. + """Classes for high-throughput arrays supported by oligo and crlmm This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm @@ -16,6 +16,7 @@ class ROligoclasses(RPackage): homepage = "https://bioconductor.org/packages/oligoClasses" git = "https://git.bioconductor.org/packages/oligoClasses.git" + version('1.52.0', commit='7995efbd2d26b8fa950830d62db92bdaf5cbeeea') version('1.46.0', commit='325684f66fc92f778098f24bcfbef0ce3da9717c') version('1.44.0', commit='d3e1134cdbea5f95b83215dc66e5f7b6a1cd0638') version('1.42.0', commit='ef125700d487b470281a9c1e985390633c4dd2bd') @@ -24,19 +25,17 @@ class ROligoclasses(RPackage): depends_on('r@2.14:', type=('build', 'run')) depends_on('r-biocgenerics@0.3.2:', type=('build', 'run')) + depends_on('r-biocgenerics@0.27.1:', when='@1.44.0:', 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@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', when='@1.38.0:1.42.0', type=('build', 'run')) + depends_on('r-biocmanager', when='@1.44.0:', 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')) + depends_on('r-ff', type=('build', 'run')) + depends_on('r-biocinstaller', when='@:1.42.0', 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 03e38dc8cb..c2668dc61b 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 @@ -7,17 +7,25 @@ from spack import * class ROrgHsEgDb(RPackage): - """Genome wide annotation for Human, primarily based on mapping - using Entrez Gene identifiers.""" + """Genome wide annotation for Human + + Genome wide annotation for Human, primarily based on mapping 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', + version('3.12.0', + sha256='48a1ab5347ec7a8602c555d9aba233102b61ffa2765826e5c8890ff0003249bb', + url='https://www.bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.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@2.7.0:', when='@3.4.1:', type=('build', 'run')) + version('3.4.1', + sha256='0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00', + url='https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz') - depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run')) + depends_on('r@2.7.0:', type=('build', 'run')) + depends_on('r-annotationdbi@1.37.4:', type=('build', 'run')) depends_on('r-annotationdbi@1.43.1:', when='@3.8.2:', type=('build', 'run')) + depends_on('r-annotationdbi@1.51.3:', when='@3.12.0:', 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 ec91f6b166..db674d3889 100644 --- a/var/spack/repos/builtin/packages/r-organismdbi/package.py +++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py @@ -8,7 +8,7 @@ from spack import * class ROrganismdbi(RPackage): """Software to enable the smooth interfacing of different database - packages. + packages The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the @@ -17,6 +17,7 @@ class ROrganismdbi(RPackage): homepage = "https://bioconductor.org/packages/OrganismDbi" git = "https://git.bioconductor.org/packages/OrganismDbi.git" + version('1.32.0', commit='c8100c4fea17bf1b10d4efacc73a7e2866d649e3') version('1.26.0', commit='495b4a8f8264d06d827537d43b3c6cc705244bb5') version('1.24.0', commit='3428952dc0f267a01e256a1c0873656cfbfde7f8') version('1.22.0', commit='24e953eb3847222d8018103b79b9fc72483cc513') @@ -27,15 +28,14 @@ class ROrganismdbi(RPackage): 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-genomicfeatures@1.39.4:', when='@1.32.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-biocinstaller', when='@1.18.1:1.22.0', type=('build', 'run')) + depends_on('r-biocmanager', when='@1.24.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-genomicranges@1.31.13:', when='@1.22.0:', 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@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')) + depends_on('r-biocinstaller', when='@:1.22.0', 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 f6b5067df4..177171627d 100644 --- a/var/spack/repos/builtin/packages/r-pathview/package.py +++ b/var/spack/repos/builtin/packages/r-pathview/package.py @@ -7,7 +7,7 @@ from spack import * class RPathview(RPackage): - """a tool set for pathway based data integration and visualization. + """a tool set for pathway based data integration and visualization Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on @@ -21,18 +21,20 @@ class RPathview(RPackage): homepage = "https://bioconductor.org/packages/pathview" git = "https://git.bioconductor.org/packages/pathview.git" + version('1.30.1', commit='a6a32395db408798cb076894678e90148bae6bf4') 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+X', 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-org-hs-eg-db', type=('build', 'run')) 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 09a5ecfe93..7da7698eee 100644 --- a/var/spack/repos/builtin/packages/r-pcamethods/package.py +++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py @@ -7,7 +7,7 @@ from spack import * class RPcamethods(RPackage): - """A collection of PCA methods. + """A collection of PCA methods Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing @@ -22,6 +22,7 @@ class RPcamethods(RPackage): homepage = "https://bioconductor.org/packages/pcaMethods" git = "https://git.bioconductor.org/packages/pcaMethods.git" + version('1.82.0', commit='d500b3363308f1f8ca70625c5cd10cce59b27641') version('1.76.0', commit='5db995330ced37dfd5ddad6ad1d90b4815d3127a') version('1.74.0', commit='1b8f0a5cdfe3664119d0d7e926a2e0fe7320133c') version('1.72.0', commit='1bb8c7d056645e62ee5179f6bb30b6594ebf3bfd') 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 09fbbdc2f0..a0c945fc94 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -7,16 +7,25 @@ from spack import * class RPfamDb(RPackage): - """A set of protein ID mappings for PFAM assembled using data from + """A set of protein ID mappings for PFAM + + A set of protein ID mappings for PFAM assembled using data from public repositories.""" 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') + version('3.12.0', + sha256='ec42d067522baf2d7d3ca78d4f8cc0dac08a4b98f1d890f52424e5d5b16f2fe9', + url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/PFAM.db_3.12.0.tar.gz') + version('3.10.0', + sha256='038888f95ce69230ac0e0b08aa3bcb09965682415520d437a7fb0a031eefe158', + url='https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PFAM.db_3.10.0.tar.gz') + version('3.4.1', + sha256='fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f', + url='https://bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz') 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')) + depends_on('r-annotationdbi@1.51.3:', when='@3.12.0:', 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 de498cdc23..05a380d6bf 100644 --- a/var/spack/repos/builtin/packages/r-phyloseq/package.py +++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py @@ -7,7 +7,7 @@ from spack import * class RPhyloseq(RPackage): - """Handling and analysis of high-throughput microbiome census data. + """Handling and analysis of high-throughput microbiome census data phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.""" @@ -15,6 +15,7 @@ class RPhyloseq(RPackage): homepage = "https://bioconductor.org/packages/phyloseq" git = "https://git.bioconductor.org/packages/phyloseq.git" + version('1.34.0', commit='cbed93ead5528fe9024d646c597dab9fc95952d3') version('1.28.0', commit='a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d') version('1.26.1', commit='a084072bc9e057b90adfbd59e27db2a1ecee151c') version('1.24.2', commit='829992f88c79de48bb8749678624e2bbd3b66645') @@ -22,13 +23,19 @@ class RPhyloseq(RPackage): version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0') depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r-biocgenerics@0.18.0:', type=('build', 'run')) + depends_on('r@3.4.0:', when='@1.22.3', 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-ape@5.0:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biobase', type=('build', 'run')) + depends_on('r-biobase@2.36.2:', when='@1.22.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.18.0:', type=('build', 'run')) + depends_on('r-biocgenerics@0.22.0:', when='@1.22.3:', 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-data-table@1.10.4:', when='@1.22.3:', 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')) @@ -37,13 +44,5 @@ class RPhyloseq(RPackage): 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-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py index db453721d6..2391db4cea 100644 --- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py +++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py @@ -7,13 +7,14 @@ from spack import * class RPreprocesscore(RPackage): - """A collection of pre-processing functions. + """A collection of pre-processing functions A library of core preprocessing routines.""" homepage = "https://bioconductor.org/packages/preprocessCore" git = "https://git.bioconductor.org/packages/preprocessCore.git" + version('1.52.1', commit='91de4ab67315dc2af68554ae3c48823f4b1ea8ac') version('1.46.0', commit='8cfc3938c1b08424587f437ed6cd2ec43512500e') version('1.44.0', commit='dc1dc61fc562aaff3fd9b11ab0d48c2d6b3a5b81') version('1.42.0', commit='2e3a8baeacfaa1526d51252642772ea951015bba') diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py index 93aea27fec..c439f381b6 100644 --- a/var/spack/repos/builtin/packages/r-protgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py @@ -7,13 +7,14 @@ from spack import * class RProtgenerics(RPackage): - """S4 generic functions for Bioconductor proteomics infrastructure. + """S4 generic functions for Bioconductor proteomics infrastructure S4 generic functions needed by Bioconductor proteomics packages.""" homepage = "https://bioconductor.org/packages/ProtGenerics" git = "https://git.bioconductor.org/packages/ProtGenerics.git" + version('1.22.0', commit='2bb3011fb0d79536e1c50251084a7057004449c6') version('1.16.0', commit='960a5fdc586898513b5ae9c48fffba5c5d703723') version('1.14.0', commit='c85940b70a16ad69275c4facb3ef673d20a1c998') version('1.12.0', commit='e84382a4b1730409f572fb681b5070017d00d30d') diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py index e67d68911c..26cdd7dc00 100644 --- a/var/spack/repos/builtin/packages/r-quantro/package.py +++ b/var/spack/repos/builtin/packages/r-quantro/package.py @@ -7,7 +7,7 @@ from spack import * class RQuantro(RPackage): - """A test for when to use quantile normalization. + """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, @@ -19,6 +19,7 @@ class RQuantro(RPackage): homepage = "https://bioconductor.org/packages/quantro" git = "https://git.bioconductor.org/packages/quantro.git" + version('1.24.0', commit='c7c0180292156a01722d91b353da44324e72d68f') version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359') version('1.16.0', commit='cfc2e853bdc3cc90fd35e153fe243892d50d61c6') version('1.14.0', commit='2d43264b2a95ae8ca51a69d7768fe43b9f1b77bb') @@ -26,6 +27,7 @@ class RQuantro(RPackage): version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9') depends_on('r@3.1.3:', type=('build', 'run')) + depends_on('r@4.0:', when='@1.24.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-minfi', type=('build', 'run')) depends_on('r-doparallel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py index bec062977c..600f210281 100644 --- a/var/spack/repos/builtin/packages/r-qvalue/package.py +++ b/var/spack/repos/builtin/packages/r-qvalue/package.py @@ -7,7 +7,7 @@ from spack import * class RQvalue(RPackage): - """Q-value estimation for false discovery rate control. + """Q-value estimation for false discovery rate control This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR @@ -24,6 +24,7 @@ class RQvalue(RPackage): homepage = "https://bioconductor.org/packages/qvalue" git = "https://git.bioconductor.org/packages/qvalue.git" + version('2.22.0', commit='b4bde8198252737b287fd7f9a4ed697f57fad92c') version('2.16.0', commit='5efbe20ef522a45a7a04b681f72bb9a12e2747ae') version('2.14.1', commit='b694e4b264f25250eb1d1115e70c07f65767c20e') version('2.12.0', commit='7df64ebfcbe69dcbf8b88cb6ef0068bf16979673') diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py index 54174e89a9..d9fadb4732 100644 --- a/var/spack/repos/builtin/packages/r-rbgl/package.py +++ b/var/spack/repos/builtin/packages/r-rbgl/package.py @@ -7,7 +7,7 @@ from spack import * class RRbgl(RPackage): - """An interface to the BOOST graph library. + """An interface to the BOOST graph library A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.""" @@ -15,6 +15,7 @@ class RRbgl(RPackage): homepage = "https://bioconductor.org/packages/RBGL" git = "https://git.bioconductor.org/packages/RBGL.git" + version('1.66.0', commit='bf0c111dbc231de6d3423c28e115b54fb010e1ea') version('1.60.0', commit='ef24c17c411659b8f030602bd9781c534d6ec93b') version('1.58.2', commit='086ad0c6bab7be29311b6ae14fd39df7a21331a6') version('1.56.0', commit='a1fa9d89c6a3401892c5dd1493df6a14031f0912') @@ -22,5 +23,4 @@ class RRbgl(RPackage): version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0') 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-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index e497fe7414..251f6e3e21 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -7,7 +7,7 @@ from spack import * class RReportingtools(RPackage): - """Tools for making reports in various formats. + """Tools for making reports in various formats The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray @@ -24,12 +24,14 @@ class RReportingtools(RPackage): homepage = "https://bioconductor.org/packages/ReportingTools" git = "https://git.bioconductor.org/packages/ReportingTools.git" + version('2.30.0', commit='fb9aee416f38cfd308d6d7264ccbcda0467642a7') 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+X', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-hwriter', 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 b960f85421..69264ccbea 100644 --- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py +++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py @@ -7,7 +7,7 @@ from spack import * class RRgraphviz(RPackage): - """Provides plotting capabilities for R graph objects. + """Provides plotting capabilities for R graph objects Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.""" @@ -15,13 +15,14 @@ class RRgraphviz(RPackage): homepage = "https://bioconductor.org/packages/Rgraphviz" git = "https://git.bioconductor.org/packages/Rgraphviz.git" + version('2.34.0', commit='9746623211be794226258631992dfcccccfd7487') 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+X', type=('build', 'run')) 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 661714f5cc..f3312f9019 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py @@ -7,7 +7,7 @@ from spack import * class RRhdf5(RPackage): - """R Interface to HDF5. + """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 @@ -20,17 +20,17 @@ class RRhdf5(RPackage): homepage = "https://bioconductor.org/packages/rhdf5" git = "https://git.bioconductor.org/packages/rhdf5.git" + version('2.34.0', commit='ec861b81fc6962e844bf56b7549ba565a7e4c69c') 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-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', when='@2.24.0:', type=('build', 'run')) depends_on('r-rhdf5lib@1.3.2:', when='@2.26.2:', type=('build', 'run')) - + depends_on('r-rhdf5lib@1.11.0:', when='@2.34.0:', type=('build', 'run')) + depends_on('r-rhdf5filters', when='@2.34.0:', type=('build', 'run')) + depends_on('r-zlibbioc', when='@:2.28.1', type=('build', 'run')) depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py new file mode 100644 index 0000000000..b6f8037f04 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2021 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 RRhdf5filters(RPackage): + """HDF5 Compression Filters + + Provides a collection of compression filters for use with HDF5 datasets.""" + + homepage = "https://github.com/grimbough/rhdf5filters" + git = "https://git.bioconductor.org/packages/rhdf5filters" + + version('1.2.0', commit='25af0180f926b4b3ea11b30ec9277d26ad3d56b3') + + depends_on('r-rhdf5lib', 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 index a4c878bae0..bcee3cd524 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py @@ -7,16 +7,18 @@ from spack import * class RRhdf5lib(RPackage): - """hdf5 library as an R package. + """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('1.12.1', commit='cf464f40fd95274d0d351cf28b586c49307c4f0b') 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('r@3.3.0:', when='@1.12.1:', type='build') 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 f7134bc3a1..76b95ae557 100644 --- a/var/spack/repos/builtin/packages/r-rhtslib/package.py +++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py @@ -7,7 +7,7 @@ from spack import * class RRhtslib(RPackage): - """HTSlib high-throughput sequencing library as an R package. + """HTSlib high-throughput sequencing library as an R package This package provides version 1.7 of the 'HTSlib' C library for high- throughput sequence analysis. The package is primarily useful to @@ -18,6 +18,7 @@ class RRhtslib(RPackage): homepage = "https://bioconductor.org/packages/Rhtslib" git = "https://git.bioconductor.org/packages/Rhtslib.git" + version('1.22.0', commit='899b79faa54d42c7c9b9a2bc49972109637d367f') version('1.18.1', commit='751a2ebaed43b7991204b27bd6c7870645001d82') version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4') version('1.14.1', commit='4be260720f845a34d0ac838278fce1363f645230') @@ -26,7 +27,6 @@ class RRhtslib(RPackage): version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79') depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('bzip2', type=('build', 'link', 'run')) depends_on('xz', type=('build', 'link', 'run')) depends_on('curl', type=('build', 'link', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py index 7d9a06bf11..73472bbda8 100644 --- a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py +++ b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py @@ -7,7 +7,7 @@ from spack import * class RRnaseqmap(RPackage): - """rnaSeq secondary analyses. + """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 @@ -16,6 +16,7 @@ class RRnaseqmap(RPackage): homepage = "https://bioconductor.org/packages/rnaSeqMap" git = "https://git.bioconductor.org/packages/rnaSeqMap.git" + version('2.48.0', commit='a8c515e518cebf571d1524c3a8a986ba7d1557db') version('2.42.0', commit='3a3a1030cc38d79d04536e0ab16114e4fa6721cf') version('2.40.1', commit='c122d645b3503fb1a061f5515e4f8cf2863b3ba3') version('2.38.0', commit='5eb9583bfacd375161739a8ae6057204487f8b9e') diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py index ddd008419f..023683a28a 100644 --- a/var/spack/repos/builtin/packages/r-roc/package.py +++ b/var/spack/repos/builtin/packages/r-roc/package.py @@ -7,11 +7,14 @@ from spack import * class RRoc(RPackage): - """Provide utilities for ROC, with microarray focus.""" + """utilities for ROC, with microarray focus + + Provide utilities for ROC, with microarray focus.""" homepage = "https://bioconductor.org/packages/release/bioc/html/ROC.html" git = "https://git.bioconductor.org/packages/ROC" + version('1.66.0', commit='62701ee41f48f99d15344127384fa032db69486f') version('1.62.0', commit='60250fdb091f6a938709b8a2cffe6442ee22a9a2') depends_on('r@1.9.0:', 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 8758aaabab..57063ce900 100644 --- a/var/spack/repos/builtin/packages/r-rots/package.py +++ b/var/spack/repos/builtin/packages/r-rots/package.py @@ -7,7 +7,7 @@ from spack import * class RRots(RPackage): - """Reproducibility-Optimized Test Statistic. + """Reproducibility-Optimized Test Statistic Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.""" @@ -15,6 +15,7 @@ class RRots(RPackage): homepage = "https://bioconductor.org/packages/ROTS" git = "https://git.bioconductor.org/packages/ROTS.git" + version('1.18.0', commit='1d4e206a8ce68d5a1417ff51c26174ed9d0ba7d2') version('1.12.0', commit='7e2c96fd8fd36710321498745f24cc6b59ac02f0') version('1.10.1', commit='1733d3f868cef4d81af6edfc102221d80793937b') version('1.8.0', commit='02e3c6455bb1afe7c4cc59ad6d4d8bae7b01428b') diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py index 2497a8dc88..b444102992 100644 --- a/var/spack/repos/builtin/packages/r-rsamtools/package.py +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -8,7 +8,7 @@ from spack import * class RRsamtools(RPackage): """Binary alignment (BAM), FASTA, variant call (BCF), and tabix file - import. + import This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), @@ -18,6 +18,7 @@ class RRsamtools(RPackage): homepage = "https://bioconductor.org/packages/Rsamtools" git = "https://git.bioconductor.org/packages/Rsamtools.git" + version('2.6.0', commit='f2aea061517c5a55e314c039251ece9831c7fad2') version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30') version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70') version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c') @@ -27,25 +28,22 @@ class RRsamtools(RPackage): depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run')) depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.32.3:', type=('build', 'run')) depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run')) depends_on('r-biocgenerics@0.1.3:', type=('build', 'run')) + depends_on('r-biocgenerics@0.25.1:', when='@1.32.3:', type=('build', 'run')) depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.32.3:', type=('build', 'run')) depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run')) depends_on('r-xvector@0.15.1:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.32.3:', 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-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('r-rhtslib@1.17.7:', when='@2.2.1:', type=('build', 'run')) - depends_on('gmake', type='build') # this is not a listed dependency but is needed diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py index 85dc4d6e0c..fa0c07dea1 100644 --- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py +++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py @@ -7,7 +7,7 @@ from spack import * class RRtracklayer(RPackage): - """R interface to genome annotation files and the UCSC genome browser. + """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 @@ -19,6 +19,7 @@ class RRtracklayer(RPackage): homepage = "https://bioconductor.org/packages/rtracklayer" git = "https://git.bioconductor.org/packages/rtracklayer.git" + version('1.50.0', commit='d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6') version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3') version('1.42.2', commit='76702f671faea736807d54aeecfbadcd152d94c5') version('1.40.6', commit='ba9a6e711504a702147383bc7abfcc36eb304df7') @@ -27,28 +28,27 @@ class RRtracklayer(RPackage): depends_on('r@3.3:', type=('build', 'run')) depends_on('r-genomicranges@1.21.20:', type=('build', 'run')) + depends_on('r-genomicranges@1.37.2:', when='@1.50.0:', 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-biocgenerics@0.25.1:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-biocgenerics@0.35.3:', when='@1.50.0:', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.40.6:', type=('build', 'run')) + depends_on('r-s4vectors@0.19.22:', when='@1.42.2:', type=('build', 'run')) + depends_on('r-s4vectors@0.23.18:', when='@1.50.0:', type=('build', 'run')) depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-iranges@2.11.12:', when='@1.38.3:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.40.6:', type=('build', 'run')) depends_on('r-xvector@0.9.4:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.40.6:', type=('build', 'run')) depends_on('r-genomeinfodb@1.3.14:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.40.6:', type=('build', 'run')) depends_on('r-biostrings@2.43.7:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.40.6:', type=('build', 'run')) depends_on('r-zlibbioc', 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@1.5.4:', 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 7b365d6ccb..b15c954cfa 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -7,7 +7,7 @@ from spack import * class RS4vectors(RPackage): - """Foundation of vector-like and list-like containers in Bioconductor. + """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 @@ -21,6 +21,7 @@ class RS4vectors(RPackage): homepage = "https://bioconductor.org/packages/S4Vectors" git = "https://git.bioconductor.org/packages/S4Vectors.git" + version('0.28.1', commit='994cb7ef830e76f8b43169cc72b553869fafb2ed') version('0.26.1', commit='935769c') version('0.22.1', commit='d25e517b48ca4184a4c2ee1f8223c148a55a8b8a') version('0.20.1', commit='1878b2909086941e556c5ea953c6fd86aebe9b02') @@ -29,7 +30,8 @@ class RS4vectors(RPackage): version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23') depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@4.0.0:', when='@0.28.1:', type=('build', 'run')) depends_on('r-biocgenerics@0.21.1:', type=('build', 'run')) - depends_on('r-biocgenerics@0.23.3:', when='@0.16.0:0.22.1', type=('build', 'run')) depends_on('r-biocgenerics@0.31.1:', when='@0.26.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.36.0:', when='@0.28.1:', 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 index 21cab7f15a..eb0dfab9a1 100644 --- a/var/spack/repos/builtin/packages/r-scater/package.py +++ b/var/spack/repos/builtin/packages/r-scater/package.py @@ -7,7 +7,7 @@ from spack import * class RScater(RPackage): - """Single-Cell Analysis Toolkit for Gene Expression Data in R. + """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 @@ -16,6 +16,7 @@ class RScater(RPackage): homepage = "https://bioconductor.org/packages/scater" git = "https://git.bioconductor.org/packages/scater.git" + version('1.18.3', commit='a94e7f413bf0f5f527b41b0b34e7a8e5c947ae37') version('1.12.2', commit='1518dc27a87c79181c34107d639e95fe55e55092') version('1.10.1', commit='2e6694af2929092f263c2b0830d48b3f9632e70c') version('1.8.4', commit='d560a9a378541d53d17990d2aa2cd28874df3dcd') @@ -23,16 +24,31 @@ class RScater(RPackage): 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@3.4:', when='@1.6.3', type=('build', 'run')) + depends_on('r@3.5:', when='@1.8.4', type=('build', 'run')) + depends_on('r@3.6:', when='@1.12.2', type=('build', 'run')) + depends_on('r-singlecellexperiment', when='@1.6.3:', 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-gridextra', when='@1.18.3:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', when='@1.6.3:', type=('build', 'run')) + depends_on('r-summarizedexperiment', when='@1.6.3:', type=('build', 'run')) + depends_on('r-delayedarray', when='@1.8.4:', type=('build', 'run')) + depends_on('r-delayedmatrixstats', when='@1.8.4:', 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')) + depends_on('r-biocparallel', when='@1.10.1:', type=('build', 'run')) + depends_on('r-scuttle', when='@1.18.3:', type=('build', 'run')) + depends_on('r-rlang', when='@1.18.3:', type=('build', 'run')) + depends_on('r-ggbeeswarm', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) + depends_on('r-biobase', when='@1.4.0:1.8.4', type=('build', 'run')) + depends_on('r-biomart', when='@1.4.0:1.6.3', 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')) @@ -41,23 +57,7 @@ class RScater(RPackage): 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-rcpp', when='@1.6.3:1.12.2', type=('build', 'run')) + depends_on('r-rcpp@0.12.14:', when='@1.8.4:1.12.2', 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')) + depends_on('r-beachmat', when='@1.6.3:1.12.2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterpie/package.py b/var/spack/repos/builtin/packages/r-scatterpie/package.py new file mode 100644 index 0000000000..5b19e86cb4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scatterpie/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2021 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 RScatterpie(RPackage): + """Scatter Pie Plot + + Creates scatterpie plots, especially useful for plotting pies on a map.""" + + homepage = "https://cloud.r-project.org/package=scatterpie" + url = "https://cloud.r-project.org/src/contrib/scatterpie_0.1.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/scatterpie" + + version('0.1.5', sha256='e13237b7effc302acafc1c9b520b4904e55875f4a3b804f653eed2940ca08840') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggforce', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-rvcheck', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py new file mode 100644 index 0000000000..5646ad08f2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scuttle/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2021 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 RScuttle(RPackage): + """Single-Cell RNA-Seq Analysis Utilities + + Provides basic utility functions for performing single-cell analyses, + focusing on simple normalization, quality control and data transformations. + Also provides some helper functions to assist development of other + packages.""" + + homepage = "https://bioconductor.org/packages/scuttle/" + git = "https://git.bioconductor.org/packages/scuttle" + + version('1.0.4', commit='a827e2759d80e6c3510e2f8fd4bd680274206d9f') + + depends_on('r-singlecellexperiment', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-biocgenerics', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run')) + depends_on('r-biocparallel', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-delayedarray', type=('build', 'run')) + depends_on('r-delayedmatrixstats', type=('build', 'run')) + depends_on('r-beachmat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py index 7852354a2b..bf1ec4c915 100644 --- a/var/spack/repos/builtin/packages/r-seqlogo/package.py +++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py @@ -7,7 +7,7 @@ from spack import * class RSeqlogo(RPackage): - """Sequence logos for DNA sequence alignments. + """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 @@ -16,6 +16,7 @@ class RSeqlogo(RPackage): homepage = "https://bioconductor.org/packages/seqLogo" git = "https://git.bioconductor.org/packages/seqLogo.git" + version('1.56.0', commit='169260c43fc58dc75becb3b7842cac3d0038a8d5') version('1.50.0', commit='57986221c90c3920f9829756c4b3ee566dc1e14d') version('1.48.0', commit='dde85582e7fd0c08c5b8bc73f9aed8f23b727d9d') version('1.46.0', commit='e78be03db5f6a516138aeea6aa9512685633a4a2') diff --git a/var/spack/repos/builtin/packages/r-shadowtext/package.py b/var/spack/repos/builtin/packages/r-shadowtext/package.py new file mode 100644 index 0000000000..d93ed78a7e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shadowtext/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2021 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 RShadowtext(RPackage): + """Shadow Text Grob and Layer + + Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for + 'ggplot2'. These functions create/draw text grob with background shadow.""" + + homepage = "https://github.com/GuangchuangYu/shadowtext/" + url = "https://cloud.r-project.org/src/contrib/shadowtext_0.0.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/shadowtext" + + version('0.0.7', sha256='6e32b1dfd3d4816803848b876666185258b888286ec3d3e8500499ec3eba31e8') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py index 3b8681eeb8..b67583c9d4 100644 --- a/var/spack/repos/builtin/packages/r-shortread/package.py +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -7,7 +7,7 @@ from spack import * class RShortread(RPackage): - """FASTQ input and manipulation. + """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 @@ -19,6 +19,7 @@ class RShortread(RPackage): homepage = "https://bioconductor.org/packages/ShortRead" git = "https://git.bioconductor.org/packages/ShortRead.git" + version('1.48.0', commit='ba44cd2517bc0e6f46d2cfcfce393f86eec814d0') version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908') version('1.40.0', commit='0cbe4b62b0be4c5f2e2670da17493423446e008f') version('1.38.0', commit='e9498f04b7b4bf0212bbb10ec7e3de2d7699f4bf') @@ -26,27 +27,26 @@ class RShortread(RPackage): version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd') depends_on('r-biocgenerics@0.22.1:', type=('build', 'run')) + depends_on('r-biocgenerics@0.23.3:', when='@1.36.1:', type=('build', 'run')) depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-biostrings@2.37.1:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.38.0:', type=('build', 'run')) depends_on('r-rsamtools@1.21.4:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', when='@1.38.0:', type=('build', 'run')) depends_on('r-genomicalignments@1.5.4:', type=('build', 'run')) + depends_on('r-genomicalignments@1.15.6:', when='@1.38.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-s4vectors@0.13.8:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.25:', when='@1.38.0:', type=('build', 'run')) depends_on('r-iranges@2.3.7:', type=('build', 'run')) + depends_on('r-iranges@2.13.12:', when='@1.38.0:', type=('build', 'run')) depends_on('r-genomeinfodb@1.1.19:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.38.0:', type=('build', 'run')) depends_on('r-genomicranges@1.21.6:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.38.0:', 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')) + depends_on('r-rhtslib', when='@1.48.0:', 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 3332a6fd5d..003e190b9f 100644 --- a/var/spack/repos/builtin/packages/r-siggenes/package.py +++ b/var/spack/repos/builtin/packages/r-siggenes/package.py @@ -7,7 +7,7 @@ from spack import * class RSiggenes(RPackage): - """Multiple Testing using SAM and Efron's Empirical Bayes Approaches. + """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 @@ -17,6 +17,7 @@ class RSiggenes(RPackage): homepage = "https://bioconductor.org/packages/siggenes" git = "https://git.bioconductor.org/packages/siggenes.git" + version('1.64.0', commit='3b528d37c16fc41bbc5c98165f606394313aa050') version('1.58.0', commit='69500158d69942cf7c62f583830933cf8baf89a1') version('1.56.0', commit='3e929feaa76311be07ff51ad807e657b0b521f6f') version('1.54.0', commit='1630e42652192e3e4e48e9e78e53665a120cfc7f') @@ -25,5 +26,4 @@ class RSiggenes(RPackage): depends_on('r-biobase', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) - 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 6dc2b70528..5910be33b9 100644 --- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py +++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py @@ -7,7 +7,7 @@ from spack import * class RSimpleaffy(RPackage): - """Very simple high level analysis of Affymetrix data. + """Very simple high level analysis of Affymetrix data Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold @@ -18,6 +18,7 @@ class RSimpleaffy(RPackage): homepage = "https://bioconductor.org/packages/simpleaffy" git = "https://git.bioconductor.org/packages/simpleaffy.git" + version('2.66.0', commit='902db69e4ea4b6d306f0c744d3be600f1418ebc9') version('2.60.0', commit='b32b5e7d5c65e43c10f98ab8684a1086a06d04f9') version('2.58.0', commit='70cf1199bad620f60eaa288279632110bb571200') version('2.56.0', commit='a05d768180b8713ad9e1dc46d491b7ef389b299d') diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py index 70686003e7..67851cf21a 100644 --- a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py @@ -7,7 +7,7 @@ from spack import * class RSinglecellexperiment(RPackage): - """S4 Classes for Single Cell Data. + """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, @@ -17,14 +17,14 @@ class RSinglecellexperiment(RPackage): homepage = "https://bioconductor.org/packages/SingleCellExperiment" git = "https://git.bioconductor.org/packages/SingleCellExperiment.git" + version('1.12.0', commit='66063b74c8b0bd0fd1277c7ad425ad11823ab356') 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@3.5:', when='@1.2.0:1.6.0', 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 e5048597cd..e59bfe0ca8 100644 --- a/var/spack/repos/builtin/packages/r-snprelate/package.py +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -8,7 +8,7 @@ from spack import * class RSnprelate(RPackage): """Parallel Computing Toolset for Relatedness and Principal Component - Analysis of SNP Data. + 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 @@ -30,6 +30,7 @@ class RSnprelate(RPackage): homepage = "https://bioconductor.org/packages/SNPRelate" git = "https://git.bioconductor.org/packages/SNPRelate.git" + version('1.24.0', commit='419b13b761ea39a8b1b9bc73097fb0359c59f1c2') version('1.18.1', commit='81c581bf76392efdc8ba237ca2e42ca1dba788ca') version('1.16.0', commit='0e38e8df4af87dff6c27a23af2867661998c0d85') version('1.14.0', commit='9501cbfc411aa320e58654a865fda2e9077977af') diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py index cac4915c64..dde1f1bc30 100644 --- a/var/spack/repos/builtin/packages/r-snpstats/package.py +++ b/var/spack/repos/builtin/packages/r-snpstats/package.py @@ -7,7 +7,7 @@ from spack import * class RSnpstats(RPackage): - """SnpMatrix and XSnpMatrix classes and methods. + """SnpMatrix and XSnpMatrix classes and methods Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in @@ -16,6 +16,7 @@ class RSnpstats(RPackage): homepage = "https://bioconductor.org/packages/snpStats" git = "https://git.bioconductor.org/packages/snpStats.git" + version('1.40.0', commit='5fcac6f3b4bb6f45c19dff8f3089b693b74a56ce') version('1.34.0', commit='e31cdfb18a9e12d70d6a3e8e6fbf7cf8faa3ea5b') version('1.32.0', commit='7c31158183b4e39da6dc30c7da275acc36b2e32f') version('1.30.0', commit='0dc1e4246f015feaf2579d60268b10ab5149ce09') diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py index bc678e161a..fb01e47dc7 100644 --- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -7,7 +7,7 @@ from spack import * class RSomaticsignatures(RPackage): - """Somatic Signatures. + """Somatic Signatures The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the @@ -17,6 +17,7 @@ class RSomaticsignatures(RPackage): homepage = "https://bioconductor.org/packages/SomaticSignatures" git = "https://git.bioconductor.org/packages/SomaticSignatures.git" + version('2.26.0', commit='9d4bed6e118ac76755ffb7abd058b09bac58a9d7') version('2.20.0', commit='dbedc30d92b600b3a17de596ebe38d15982c70c6') version('2.18.0', commit='facccd67eee5202fcbe6ad32e667546546e7ccff') version('2.16.0', commit='4ae348d9fa096c0ec307df95149991edf6044977') @@ -34,6 +35,7 @@ class RSomaticsignatures(RPackage): depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggbio', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-nmf', when='@2.26.0:', type=('build', 'run')) depends_on('r-pcamethods', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py new file mode 100644 index 0000000000..8a1c35b339 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2021 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 RSparsematrixstats(RPackage): + """Summary Statistics for Rows and Columns of Sparse Matrices + + High performance functions for row and column operations on sparse + matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars + etc. Currently, the optimizations are limited to data in the column sparse + format. This package is inspired by the matrixStats package by Henrik + Bengtsson.""" + + homepage = "https://bioconductor.org/packages/sparseMatrixStats/" + git = "https://git.bioconductor.org/packages/sparseMatrixStats" + + version('1.2.1', commit='9726f3d5e0f03b50c332d85d5e4c339c18b0494c') + + depends_on('r-matrixgenerics', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-matrixstats', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py index 610e646f67..376c5993c3 100644 --- a/var/spack/repos/builtin/packages/r-spem/package.py +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -7,7 +7,7 @@ from spack import * class RSpem(RPackage): - """S-system parameter estimation method. + """S-system parameter estimation method This package can optimize the parameter in S-system models given time series data""" @@ -15,6 +15,7 @@ class RSpem(RPackage): homepage = "https://bioconductor.org/packages/SPEM" git = "https://git.bioconductor.org/packages/SPEM.git" + version('1.30.0', commit='6b2eb64bfe6287846b1408297dd46dc772431031') version('1.24.0', commit='537ed19e466008f2972a246479b327c95177a99e') version('1.22.0', commit='fddb7cd1f81e47eae603724ea149c2adca5b3eb4') version('1.20.0', commit='b0e1049c61a35da00882d21026f4c1eb03b17517') diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py index 734d8d072a..9eea513302 100644 --- a/var/spack/repos/builtin/packages/r-sseq/package.py +++ b/var/spack/repos/builtin/packages/r-sseq/package.py @@ -8,7 +8,7 @@ from spack import * class RSseq(RPackage): """Shrinkage estimation of dispersion in Negative Binomial models for RNA- - seq experiments with small sample size. + seq experiments with small sample size The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. @@ -24,6 +24,7 @@ class RSseq(RPackage): homepage = "https://bioconductor.org/packages/sSeq" git = "https://git.bioconductor.org/packages/sSeq.git" + version('1.28.0', commit='401f6805628bdf6579cc0e643b7ed54319f024be') version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc') version('1.20.1', commit='91f31440323612cb04beb44404ab0a1bcb3ad87d') version('1.18.0', commit='1f65e5a55ce0d51672b785450031872e6db5ca0f') diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py index e3f92dfb07..846e042884 100644 --- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py @@ -7,7 +7,7 @@ from spack import * class RSummarizedexperiment(RPackage): - """SummarizedExperiment container. + """SummarizedExperiment container The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows @@ -17,6 +17,7 @@ class RSummarizedexperiment(RPackage): homepage = "https://bioconductor.org/packages/SummarizedExperiment" git = "https://git.bioconductor.org/packages/SummarizedExperiment.git" + version('1.20.0', commit='874aa87a481e4076a0ec3369f55c9c0a1ab8025e') version('1.18.2', commit='e22fafe') version('1.14.1', commit='2c68d99e11c7345e5ed388370822ea48395c64a4') version('1.12.0', commit='5f8416864636add121ec1d6737ebb89a42227fd7') @@ -25,22 +26,24 @@ class RSummarizedexperiment(RPackage): version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0') depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-matrixgenerics@1.1.3:', type=('build', 'run')) depends_on('r-genomicranges@1.27.22:', 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='@1.10.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.33.6:', when='@1.12.0:', type=('build', 'run')) + depends_on('r-genomicranges@1.41.5:', when='@1.20.0:', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) - depends_on('r-delayedarray@0.1.9:', type=('build', 'run')) depends_on('r-matrix', 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@0.17.25:', when='@1.10.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@1.20.0:', 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')) + depends_on('r-iranges@2.23.9:', when='@1.20.0:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.13.1:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.1.9:', type=('build', 'run')) + depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run')) + depends_on('r-delayedarray@0.15.10:', when='@1.20.0:', 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 c702a51757..2c3b51e302 100644 --- a/var/spack/repos/builtin/packages/r-sva/package.py +++ b/var/spack/repos/builtin/packages/r-sva/package.py @@ -7,7 +7,7 @@ from spack import * class RSva(RPackage): - """Surrogate Variable Analysis. + """Surrogate Variable Analysis The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva @@ -31,6 +31,7 @@ class RSva(RPackage): homepage = "https://bioconductor.org/packages/sva" git = "https://git.bioconductor.org/packages/sva.git" + version('3.38.0', commit='5ded8ba649200ec4829051f86a59e1a2548a7ab8') version('3.32.1', commit='1b8286734d00533b49d9f1456b6523cc778bb744') version('3.30.1', commit='fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c') version('3.28.0', commit='dd4937229dbccd2f383a04d5237fe147a884728d') @@ -43,3 +44,4 @@ class RSva(RPackage): depends_on('r-biocparallel', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) + depends_on('r-edger', when='@3.38.0:', 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 935e1bd97a..d9100a3af2 100644 --- a/var/spack/repos/builtin/packages/r-tfbstools/package.py +++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py @@ -7,7 +7,7 @@ from spack import * class RTfbstools(RPackage): - """Software Package for Transcription Factor Binding Site (TFBS) Analysis. + """Software Package for Transcription Factor Binding Site (TFBS) Analysis TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion @@ -19,6 +19,7 @@ class RTfbstools(RPackage): homepage = "https://bioconductor.org/packages/TFBSTools" git = "https://git.bioconductor.org/packages/TFBSTools.git" + version('1.28.0', commit='15e7cf76f39ee3280a27284d58f7adef1c33f193') version('1.22.0', commit='613d3567fd662b65269bd200c5aa5f87ac6a4612') version('1.20.0', commit='74035fc6beb1af82f171c11ef2b0a8817714c5bc') version('1.18.0', commit='17e12b9f3dcb9059d414307ec0bc23ed1ee33294') diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py index 4dd838418a..227a4c9e33 100644 --- a/var/spack/repos/builtin/packages/r-tmixclust/package.py +++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py @@ -8,7 +8,7 @@ from spack import * class RTmixclust(RPackage): """Time Series Clustering of Gene Expression with Gaussian Mixed-Effects - Models and Smoothing Splines. + Models and Smoothing Splines Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non- @@ -19,6 +19,7 @@ class RTmixclust(RPackage): homepage = "https://bioconductor.org/packages/TMixClust" git = "https://git.bioconductor.org/packages/TMixClust.git" + version('1.12.0', commit='982b31bd7e22a3dc638bbda0336546220444f0c2') version('1.6.0', commit='9f5f78e52538d15f402c8f6e4c60f7212c7bc548') version('1.4.0', commit='a52fcae6e7a5dd41e7afbe128f35397e8bc8cb12') version('1.2.0', commit='0250c0b238f08077b5b9ff17c2f3b7633c67dc3c') diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py index 20f18e7f1f..d14d35f573 100644 --- a/var/spack/repos/builtin/packages/r-topgo/package.py +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -7,7 +7,7 @@ from spack import * class RTopgo(RPackage): - """Enrichment Analysis for Gene Ontology. + """Enrichment Analysis for Gene Ontology topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different @@ -17,6 +17,7 @@ class RTopgo(RPackage): homepage = "https://bioconductor.org/packages/topGO" git = "https://git.bioconductor.org/packages/topGO.git" + version('2.42.0', commit='3a33cf53883de45bda506953303e1809ab982adc') version('2.36.0', commit='c2f6c187b41c4aa44cc92ac781fdd878491a4019') version('2.34.0', commit='44cb5eaba515b365b7b2a8c22df0a45883db6b4d') version('2.32.0', commit='78ce3068fc06ae38d55219759fa177e2fcb3f596') diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py index aa8fd2a1dd..ddb96a7c6b 100644 --- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py @@ -7,7 +7,9 @@ from spack import * class RTxdbHsapiensUcscHg18Knowngene(RPackage): - """Exposes an annotation databases generated from UCSC by exposing these as + """Annotation package for TxDb object(s) + + Exposes an annotation databases generated from UCSC by exposing these as TxDb objects""" # This is a bioconductor package but ther is no available git repo diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py index 6786afc563..9892bdd2bb 100644 --- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py @@ -7,7 +7,9 @@ from spack import * class RTxdbHsapiensUcscHg19Knowngene(RPackage): - """Exposes an annotation databases generated from UCSC by exposing these as + """Annotation package for TxDb object(s) + + Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.""" # This is a bioconductor package but there is no available git repo. diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py index 0b87308735..ad77f1f07b 100644 --- a/var/spack/repos/builtin/packages/r-tximport/package.py +++ b/var/spack/repos/builtin/packages/r-tximport/package.py @@ -8,7 +8,7 @@ from spack import * class RTximport(RPackage): """Import and summarize transcript-level estimates for transcript- and - gene-level analysis. + gene-level analysis Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level @@ -20,6 +20,7 @@ class RTximport(RPackage): homepage = "https://bioconductor.org/packages/tximport" git = "https://git.bioconductor.org/packages/tximport.git" + version('1.18.0', commit='58b20cbc566648586b6990b30ebc70bef308cb05') version('1.12.3', commit='acbdead961471c3b910d720f73bd0af1b7a07c57') version('1.10.1', commit='cd8f81cf7140f61d4a4f25f89451fb49e2cd4bd3') version('1.8.0', commit='cc91b8389ca4c16b0f588bdeb63d051a11e8a705') diff --git a/var/spack/repos/builtin/packages/r-tximportdata/package.py b/var/spack/repos/builtin/packages/r-tximportdata/package.py index a85befb5f6..2ebf3b531c 100644 --- a/var/spack/repos/builtin/packages/r-tximportdata/package.py +++ b/var/spack/repos/builtin/packages/r-tximportdata/package.py @@ -7,10 +7,16 @@ from spack import * class RTximportdata(RPackage): - """This packages provides the output of running various transcript abundance - quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project""" + """Import and summarize transcript-level estimates for transcript- and + gene-level analysis - homepage = "http://bioconductor.org/packages/release/data/experiment/html/tximportData.html" - url = "http://bioconductor.org/packages/release/data/experiment/src/contrib/tximportData_1.18.0.tar.gz" + 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.""" - version('1.18.0', sha256='4edf9fdcf5b0086fc958d5ac0249668c7cf7e2fa941cd8d413620634d0cb5971') + homepage = "https://github.com/mikelove/tximport" + git = "https://git.bioconductor.org/packages/tximportData" + + version('1.18.0', commit='24945f8dd1e4e441ad5145fb7a37a1630912f929') diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py index 56ffb6ab44..eb356adb52 100644 --- a/var/spack/repos/builtin/packages/r-variantannotation/package.py +++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py @@ -7,7 +7,7 @@ from spack import * class RVariantannotation(RPackage): - """Annotation of Genetic Variants. + """Annotation of Genetic Variants Annotate variants, compute amino acid coding changes, predict coding outcomes.""" @@ -15,6 +15,7 @@ class RVariantannotation(RPackage): homepage = "https://bioconductor.org/packages/VariantAnnotation" git = "https://git.bioconductor.org/packages/VariantAnnotation.git" + version('1.36.0', commit='9918bd19a2e6f89e5edc5fe03c8812f500bb3e19') version('1.30.1', commit='fb1ab00872570afb280522c4663e347dafc07a9e') version('1.28.13', commit='0393347b8ce2d5edf1a61589be93e6a93eda3419') version('1.26.1', commit='60ae67598cc3d7ed20ee6417920f8c209085faaf') @@ -23,37 +24,42 @@ class RVariantannotation(RPackage): depends_on('r@2.8.0:', type=('build', 'run')) depends_on('r-biocgenerics@0.15.3:', type=('build', 'run')) + depends_on('r-matrixgenerics', when='@1.36.0:', type=('build', 'run')) depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run')) + depends_on('r-genomeinfodb@1.15.2:', when='@1.26.1:', type=('build', 'run')) depends_on('r-genomicranges@1.27.6:', type=('build', 'run')) + depends_on('r-genomicranges@1.31.8:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicranges@1.41.5:', when='@1.36.0:', type=('build', 'run')) depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run')) + depends_on('r-summarizedexperiment@1.19.5:', when='@1.36.0:', type=('build', 'run')) depends_on('r-rsamtools@1.23.10:', type=('build', 'run')) + depends_on('r-rsamtools@1.31.2:', 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-dbi', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-s4vectors@0.13.13:', type=('build', 'run')) + depends_on('r-s4vectors@0.17.24:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-s4vectors@0.27.12:', when='@1.36.0:', type=('build', 'run')) depends_on('r-iranges@2.3.25:', type=('build', 'run')) + depends_on('r-iranges@2.13.13:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-iranges@2.23.9:', when='@1.36.0:', type=('build', 'run')) depends_on('r-xvector@0.5.6:', type=('build', 'run')) + depends_on('r-xvector@0.19.7:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-xvector@0.29.2:', when='@1.36.0:', type=('build', 'run')) depends_on('r-biostrings@2.33.5:', type=('build', 'run')) + depends_on('r-biostrings@2.47.6:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-biostrings@2.57.2:', when='@1.36.0:', 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@1.37.6:', type=('build', 'run')) depends_on('r-bsgenome@1.47.3:', when='@1.26.1:', type=('build', 'run')) + depends_on('r-genomicfeatures@1.27.4:', 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') + + # Not listed but needed + depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py index 62e4b4d41f..484c296ea0 100644 --- a/var/spack/repos/builtin/packages/r-vsn/package.py +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -7,7 +7,7 @@ from spack import * class RVsn(RPackage): - """Variance stabilization and calibration for microarray data. + """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 @@ -25,6 +25,7 @@ class RVsn(RPackage): homepage = "https://bioconductor.org/packages/vsn" git = "https://git.bioconductor.org/packages/vsn.git" + version('3.58.0', commit='a451e6ae989623750feacf26d99683a7955adf85') version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe') version('3.50.0', commit='ad49fcc288c6065d0f04040acd688e7f0d7d927e') version('3.48.1', commit='d57f64112004b1d73b3be625949830209de027eb') @@ -32,11 +33,10 @@ class RVsn(RPackage): version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0') depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r@3.4.0:', when='@3.46.0:', 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', when='@3.44.0', type=('build', 'run')) - - depends_on('r@3.4.0:', when='@3.46.0:', type=('build', 'run')) + depends_on('r-hexbin', when='@3.44.0:3.52.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py index ab7dbbc638..5a69451d0d 100644 --- a/var/spack/repos/builtin/packages/r-watermelon/package.py +++ b/var/spack/repos/builtin/packages/r-watermelon/package.py @@ -7,11 +7,15 @@ from spack import * class RWatermelon(RPackage): - """Illumina 450 methylation array normalization and metrics.""" + """Illumina 450 methylation array normalization and metrics + + 15 flavours of betas and three performance metrics, with methods for + objects produced by methylumi and minfi packages.""" homepage = "https://bioconductor.org/packages/release/bioc/html/wateRmelon.html" git = "https://git.bioconductor.org/packages/wateRmelon" + version('1.34.0', commit='3fa2745535c22068a438747b41b9d793196098d4') version('1.30.0', commit='66d7579fe49206d965832288df7937c3d43ed578') depends_on('r@2.10:', 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 6eb21e9ca6..acfd509fa9 100644 --- a/var/spack/repos/builtin/packages/r-xde/package.py +++ b/var/spack/repos/builtin/packages/r-xde/package.py @@ -8,11 +8,15 @@ from spack import * class RXde(RPackage): """XDE: a Bayesian hierarchical model for cross-study analysis of - differential gene expression.""" + differential gene expression + + Multi-level model for cross-study detection of differential gene + expression.""" homepage = "https://bioconductor.org/packages/XDE" git = "https://git.bioconductor.org/packages/XDE.git" + version('2.36.0', commit='0277f9dffbd7d1880be77cb8581fc614501b3293') version('2.30.0', commit='058af6f1e431522778f970bf61f834620d3d7dd7') version('2.28.0', commit='b8cc7d0840ce1324644e8b4a750fbb964884498b') version('2.26.0', commit='7bf6368037937c53542447175061c2e2059ee3be') @@ -24,9 +28,8 @@ class RXde(RPackage): 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-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')) + depends_on('r-mergemaid', when='@:2.30.0', 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 d473f09ae9..67853d415f 100644 --- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py +++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py @@ -7,7 +7,7 @@ from spack import * class RXmapbridge(RPackage): - """Export plotting files to the xmapBridge for visualisation in X:Map. + """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.""" @@ -15,6 +15,7 @@ class RXmapbridge(RPackage): homepage = "https://bioconductor.org/packages/xmapbridge" git = "https://git.bioconductor.org/packages/xmapbridge.git" + version('1.48.0', commit='1cefe6b56c6dcb1f18028b3b7d6a67d490bc9730') version('1.42.0', commit='d79c80dfc1a0ed3fd6d3e7a7c3a4aff778537ca9') version('1.40.0', commit='00a2993863f28711e237bc937fa0ba2d05f81684') version('1.38.0', commit='08138f00385fa0c669ff4cc33d7eac3d29cd615d') diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py index 5ea822a500..7567def3f5 100644 --- a/var/spack/repos/builtin/packages/r-xvector/package.py +++ b/var/spack/repos/builtin/packages/r-xvector/package.py @@ -8,7 +8,7 @@ from spack import * class RXvector(RPackage): """Foundation of external vector representation and manipulation in - Bioconductor. + Bioconductor Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).""" @@ -16,6 +16,7 @@ class RXvector(RPackage): homepage = "https://bioconductor.org/packages/XVector" git = "https://git.bioconductor.org/packages/XVector.git" + version('0.30.0', commit='985e963e0b1c3ff004dd0b07ad7c9ff7ed853ec0') version('0.24.0', commit='e5109cb2687724b9fddddf296c07a82bae4c551d') version('0.22.0', commit='b5e107a5fd719e18374eb836eb498b529afa4473') version('0.20.0', commit='a83a7ea01f6a710f0ba7d9fb021cfa795b291cb4') @@ -25,16 +26,14 @@ class RXvector(RPackage): 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('zlib') - 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')) + depends_on('r-s4vectors@0.27.12:', when='@0.30.0:', type=('build', 'run')) + depends_on('r-iranges@2.9.18:', type=('build', 'run')) + depends_on('r-iranges@2.13.16:', when='@0.20.0:', type=('build', 'run')) + depends_on('r-iranges@2.15.12:', when='@0.22.0:', type=('build', 'run')) + depends_on('r-iranges@2.23.9:', when='@0.30.0:', type=('build', 'run')) + depends_on('r-zlibbioc', type=('build', 'run')) + depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py index ab5b3c9a22..0f646664a4 100644 --- a/var/spack/repos/builtin/packages/r-yapsa/package.py +++ b/var/spack/repos/builtin/packages/r-yapsa/package.py @@ -7,7 +7,7 @@ from spack import * class RYapsa(RPackage): - """Yet Another Package for Signature Analysis. + """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 @@ -19,6 +19,7 @@ class RYapsa(RPackage): homepage = "https://bioconductor.org/packages/YAPSA" git = "https://git.bioconductor.org/packages/YAPSA.git" + version('1.16.0', commit='f344cdb81bb886c633f9325f811912fb59d58eb1') version('1.10.0', commit='06af18e424868eb0f0be6c80e90cbab1eabf3d73') version('1.8.0', commit='402f3f7774fdf8afc7883579ad651c26df0f8fdb') version('1.6.0', commit='2455d272b076835ddb36ad21c01ef15af66abc36') @@ -26,9 +27,10 @@ class RYapsa(RPackage): version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d') depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.6.0:', when='@1.16.0:', type=('build', 'run')) depends_on('r-genomicranges', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-lsei', type=('build', 'run')) + depends_on('r-limsolve', when='@1.16.0:', type=('build', 'run')) depends_on('r-somaticsignatures', type=('build', 'run')) depends_on('r-variantannotation', type=('build', 'run')) depends_on('r-genomeinfodb', type=('build', 'run')) @@ -39,6 +41,14 @@ class RYapsa(RPackage): depends_on('r-getoptlong', type=('build', 'run')) depends_on('r-circlize', type=('build', 'run')) depends_on('r-gtrellis', type=('build', 'run')) + depends_on('r-doparallel', when='@1.16.0:', type=('build', 'run')) depends_on('r-pmcmr', type=('build', 'run')) + depends_on('r-ggbeeswarm', when='@1.16.0:', type=('build', 'run')) depends_on('r-complexheatmap', type=('build', 'run')) depends_on('r-keggrest', type=('build', 'run')) + depends_on('r-biostrings', when='@1.16.0:', type=('build', 'run')) + depends_on('r-bsgenome-hsapiens-ucsc-hg19', when='@1.16.0:', type=('build', 'run')) + depends_on('r-magrittr', when='@1.16.0:', type=('build', 'run')) + depends_on('r-pracma', when='@1.16.0:', type=('build', 'run')) + depends_on('r-dplyr', when='@1.16.0:', type=('build', 'run')) + depends_on('r-lsei', when='@:1.10.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py index b30c8b88d7..05f100f306 100644 --- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py +++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py @@ -7,7 +7,7 @@ from spack import * class RYaqcaffy(RPackage): - """Affymetrix expression data quality control and reproducibility analysis. + """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 @@ -16,6 +16,7 @@ class RYaqcaffy(RPackage): homepage = "https://bioconductor.org/packages/yaqcaffy" git = "https://git.bioconductor.org/packages/yaqcaffy.git" + version('1.50.0', commit='b32e6b947ca9c4ab7163cfddc084a1bc0a34780e') version('1.44.0', commit='00898f3ec9ac0beadbcf57bda3d3c1c99fb0c3c0') version('1.42.0', commit='a4af673774165e087499ecc35f96aab6bbfbeea1') version('1.40.0', commit='0c78f8ff8f675305f6fa4b052d2482e9aee551bb') diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py index c2302e9686..7329f7caeb 100644 --- a/var/spack/repos/builtin/packages/r-yarn/package.py +++ b/var/spack/repos/builtin/packages/r-yarn/package.py @@ -7,7 +7,7 @@ from spack import * class RYarn(RPackage): - """YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization. + """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 @@ -19,6 +19,7 @@ class RYarn(RPackage): homepage = "https://bioconductor.org/packages/yarn" git = "https://git.bioconductor.org/packages/yarn.git" + version('1.16.0', commit='ff5a18cb946ffec3cb773fe32af401c8a72d674a') version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472') version('1.8.1', commit='ee0723d4dbf082b4469ca9c22cce4f1a2ac81c04') version('1.6.0', commit='19d1b2ef275f294bd318b86e0d237c271880117d') diff --git a/var/spack/repos/builtin/packages/r-zcompositions/package.py b/var/spack/repos/builtin/packages/r-zcompositions/package.py new file mode 100644 index 0000000000..1fb90f2fc0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zcompositions/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2021 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 RZcompositions(RPackage): + """Treatment of Zeros, Left-Censored and Missing Values in Compositional + Data Sets + + Principled methods for the imputation of zeros, left-censored and missing + data in compositional data sets (Palarea-Albaladejo and Martin-Fernandez + (2015) <doi:10.1016/j.chemolab.2015.02.019>).""" + + homepage = "https://cloud.r-project.org/package=zCompositions" + url = "https://cloud.r-project.org/src/contrib/zCompositions_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/zCompositions" + + version('1.3.4', sha256='ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95') + + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-nada', type=('build', 'run')) + depends_on('r-truncnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py index 14bdb8392f..ced5ec2f16 100644 --- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py +++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py @@ -7,7 +7,7 @@ from spack import * class RZlibbioc(RPackage): - """An R packaged zlib-1.2.5. + """An R packaged zlib-1.2.5 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 @@ -17,6 +17,7 @@ class RZlibbioc(RPackage): homepage = "https://bioconductor.org/packages/zlibbioc" git = "https://git.bioconductor.org/packages/zlibbioc.git" + version('1.36.0', commit='62e888cd7fb482d512c6c31961b657e0b924e357') version('1.30.0', commit='99eae5b05968bf6abc9b54b9031afd93517381e0') version('1.28.0', commit='b825b042742ba45455fc284b988ff4cd2a33222c') version('1.26.0', commit='2e3ab097caa09a5e3ddaa3469b13e19a7224da0d') |