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update bioconductor packages to bioconductor 3.14 (#28900)

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This commit is contained in:
Glenn Johnson 2022-02-21 16:38:27 -06:00 committed by GitHub
parent 1953d986ae
commit 51488dbff5
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221 changed files with 1682 additions and 1124 deletions
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6
var/spack/repos/builtin/packages/r-a4/package.py
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@ -7,14 +7,14 @@
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"
bioc = "a4"
version('1.42.0', commit='fc26809e2bce7cd50d99d6f6dd5f85c38342fdea')
version('1.38.0', commit='5b7a9087bab10c55e24707e96e48046995236c94')
version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712')
version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d')

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var/spack/repos/builtin/packages/r-a4base/package.py
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@ -7,14 +7,14 @@
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"
bioc = "a4Base"
version('1.42.0', commit='d7296e2792020e9c5b1c19101104326ee8bebfe6')
version('1.38.0', commit='4add242fa9c62795aca5b0dfca34a43484c5aa82')
version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7')
version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229')
@ -32,4 +32,5 @@ class RA4base(RPackage):
depends_on('r-multtest', type=('build', 'run'))
depends_on('r-glmnet', type=('build', 'run'))
depends_on('r-gplots', type=('build', 'run'))
depends_on('r-annotationdbi', when='@:1.32.0', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.32.0')

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var/spack/repos/builtin/packages/r-a4classif/package.py
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@ -7,15 +7,15 @@
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"
bioc = "a4Classif"
version('1.42.0', commit='820854a7ca9ed0c295479a25b7e3375c6d01d0b5')
version('1.38.0', commit='c4d058813efb835774813b2d69c52912162f8e75')
version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88')
version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3')
@ -25,9 +25,10 @@ class RA4classif(RPackage):
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-biobase', when='@1.38.0:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'), when='@1.38.0:')
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'))
depends_on('r-mlinterfaces', type=('build', 'run'), when='@:1.32.0')

6
var/spack/repos/builtin/packages/r-a4core/package.py
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@ -7,14 +7,14 @@
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"
bioc = "a4Core"
version('1.42.0', commit='6985950b72c2a0f20ec44fe2067d8864e004bfaa')
version('1.38.0', commit='a027dcd3486c64950815ec7c7271f1f65ba3d8a1')
version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce')
version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141')

13
var/spack/repos/builtin/packages/r-a4preproc/package.py
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@ -7,14 +7,14 @@
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"
bioc = "a4Preproc"
version('1.42.0', commit='773a91e884d2ada16fe9cf57d5ed53c0155e3fa2')
version('1.38.0', commit='c93c223bd531bff090531a109b51f8dcd710d0cb')
version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558')
version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978')
@ -22,6 +22,7 @@ class RA4preproc(RPackage):
version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea')
version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
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'))
depends_on('r-biocgenerics', type=('build', 'run'), when='@1.38.0:')
depends_on('r-biobase', type=('build', 'run'), when='@1.38.0:')
depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.32.0')

9
var/spack/repos/builtin/packages/r-a4reporting/package.py
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@ -7,14 +7,14 @@
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"
bioc = "a4Reporting"
version('1.42.0', commit='b0d715b9cdac80bc412f0a9a6b33941c4a7582bb')
version('1.38.0', commit='cd3cf244e7a299b2485684ed15519cbbda1c590f')
version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792')
version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390')
@ -23,4 +23,5 @@ class RA4reporting(RPackage):
version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-annaffy', when='@:1.32.0', type=('build', 'run'))
depends_on('r-annaffy', type=('build', 'run'), when='@:1.32.0')

6
var/spack/repos/builtin/packages/r-abadata/package.py
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@ -7,7 +7,7 @@
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
@ -18,9 +18,9 @@ class RAbadata(RPackage):
Developing Human Brain expression data. All datasets are restricted to
protein coding genes."""
homepage = "https://bioconductor.org/packages/ABAData"
git = "https://git.bioconductor.org/packages/ABAData.git"
bioc = "ABAData"
version('1.24.0', commit='c4c42701f995ab8d5ede7f36ff06650493c82e36')
version('1.20.0', commit='c08a841ffb54d6555eb80b90a7a8afe7e48201b3')
version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd')
version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d')

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var/spack/repos/builtin/packages/r-abaenrichment/package.py
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@ -7,7 +7,7 @@
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
@ -22,9 +22,9 @@ class RAbaenrichment(RPackage):
tests are implemented, e.g. for cases when genes are ranked instead of
divided into candidate and background."""
homepage = "https://bioconductor.org/packages/ABAEnrichment"
git = "https://git.bioconductor.org/packages/ABAEnrichment.git"
bioc = "ABAEnrichment"
version('1.24.0', commit='5d20752263ae8f18ea5f5a6cfbdd5921a0f236d7')
version('1.20.0', commit='608433a0b07e6dd99915dc536a038d960f1be1d5')
version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23')
version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7')
@ -34,10 +34,10 @@ class RAbaenrichment(RPackage):
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@3.4:', type=('build', 'run'), when='@1.8.0:')
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-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'))
depends_on('r-data-table@1.10.4:', type=('build', 'run'), when='@1.8.0:')
depends_on('r-gofuncr@1.1.2:', type=('build', 'run'), when='@1.12.0:')

6
var/spack/repos/builtin/packages/r-absseq/package.py
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@ -8,16 +8,16 @@
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
moderating fold-change according to heterogeneity of dispersion across
expression level."""
homepage = "https://bioconductor.org/packages/ABSSeq"
git = "https://git.bioconductor.org/packages/ABSSeq.git"
bioc = "ABSSeq"
version('1.48.0', commit='b237c967d44d075ca306c35e92df8b66a60ce72d')
version('1.44.0', commit='c202b4a059021ed1228ccee7303c69b0aa4ca1ee')
version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce')
version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a')

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var/spack/repos/builtin/packages/r-acde/package.py
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@ -7,7 +7,7 @@
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
@ -20,9 +20,9 @@ class RAcde(RPackage):
Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo
(2015, pending publication)."""
homepage = "https://bioconductor.org/packages/acde"
git = "https://git.bioconductor.org/packages/acde.git"
bioc = "acde"
version('1.24.0', commit='0c3c4d47af7eaff37420032ea5245743a65124cf')
version('1.20.0', commit='cefb4f2e2b0ef3c5f51944c0ece7a71294020350')
version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417')
version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4')

6
var/spack/repos/builtin/packages/r-acgh/package.py
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@ -7,16 +7,16 @@
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
data. Basic methods for accessing/replacing, subsetting, printing and
plotting aCGH objects."""
homepage = "https://bioconductor.org/packages/aCGH"
git = "https://git.bioconductor.org/packages/aCGH.git"
bioc = "aCGH"
version('1.72.0', commit='b5d4022ac487125194d3913f1b8c2948db6e2792')
version('1.68.0', commit='91f41a3917ddce43eb05e11c90eb99c467ba2247')
version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f')
version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21')

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var/spack/repos/builtin/packages/r-acme/package.py
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@ -7,7 +7,7 @@
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
@ -19,9 +19,9 @@ class RAcme(RPackage):
fast and can be applied on whole-genome tiling array experiments quite
easily with enough memory."""
homepage = "https://bioconductor.org/packages/ACME"
git = "https://git.bioconductor.org/packages/ACME.git"
bioc = "ACME"
version('2.50.0', commit='d55a19a8c091e8ea5fd35041520107a7f7603e14')
version('2.46.0', commit='68f45c9f7d34c28adf6a0fc4245fdf63881109de')
version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a')
version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b')

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var/spack/repos/builtin/packages/r-adsplit/package.py
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@ -7,16 +7,16 @@
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
annotated to, splits into two subclasses are computed and a significance
of the supporting gene set is determined."""
homepage = "https://bioconductor.org/packages/adSplit"
git = "https://git.bioconductor.org/packages/adSplit.git"
bioc = "adSplit"
version('1.64.0', commit='32f150eb51c66b867301dceeb527de5b97f9f490')
version('1.60.0', commit='de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd')
version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652')
version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19')
@ -29,5 +29,7 @@ class RAdsplit(RPackage):
depends_on('r-biobase@1.5.12:', type=('build', 'run'))
depends_on('r-cluster@1.9.1:', type=('build', 'run'))
depends_on('r-go-db@1.8.1:', type=('build', 'run'))
depends_on('r-kegg-db@1.8.1:', type=('build', 'run'))
depends_on('r-keggrest@1.30.1:', type=('build', 'run'), when='@1.62.0:')
depends_on('r-multtest@1.6.0:', type=('build', 'run'))
depends_on('r-kegg-db@1.8.1:', type=('build', 'run'), when='@:1.60.0')

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var/spack/repos/builtin/packages/r-affxparser/package.py
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@ -7,7 +7,7 @@
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
@ -18,9 +18,9 @@ class RAffxparser(RPackage):
probesets can be extracted very quickly from a set of CEL files into a
convenient list structure."""
homepage = "https://bioconductor.org/packages/affxparser"
git = "https://git.bioconductor.org/packages/affxparser.git"
bioc = "affxparser"
version('1.66.0', commit='2ea72d4c924ac14bdd807b23563c8501c226ce3a')
version('1.62.0', commit='b3e988e5c136c3f1a064e1da13730b403c8704c0')
version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056')
version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f')

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var/spack/repos/builtin/packages/r-affy/package.py
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@ -7,15 +7,15 @@
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
functions. 'affy' is fully functional without it."""
homepage = "https://bioconductor.org/packages/affy"
git = "https://git.bioconductor.org/packages/affy.git"
bioc = "affy"
version('1.72.0', commit='3750b4eb8e5224b19100f6c881b67e568d8968a2')
version('1.68.0', commit='1664399610c9aa519399445a2ef8bb9ea2233eac')
version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605')
version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206')
@ -24,10 +24,12 @@ class RAffy(RPackage):
version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
depends_on('r@2.8.0:4.0', type=('build', 'run'), when='@:1.68.0')
depends_on('r@:4.0', type=('build', 'run'), when='@:1.68.0')
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-biocmanager', when='@1.60.0:', type=('build', 'run'))
depends_on('r-biocmanager', type=('build', 'run'), when='@1.60.0:')
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'), when='@1.54.0:1.58.0')

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var/spack/repos/builtin/packages/r-affycomp/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/affycomp"
git = "https://git.bioconductor.org/packages/affycomp.git"
bioc = "affycomp"
version('1.70.0', commit='487f6775975092475581a6c02ddb27590559cf07')
version('1.66.0', commit='388d01af8b1e6ab11051407f77d0206512df8424')
version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c')
version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef')

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var/spack/repos/builtin/packages/r-affycompatible/package.py
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@ -7,7 +7,7 @@
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
@ -16,9 +16,9 @@ class RAffycompatible(RPackage):
(GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation
files."""
homepage = "https://bioconductor.org/packages/AffyCompatible"
git = "https://git.bioconductor.org/packages/AffyCompatible.git"
bioc = "AffyCompatible"
version('1.54.0', commit='fde7d86ccdb03c13c4838c18ac25477ffe6e0fe5')
version('1.50.0', commit='3b12d12bd6d1a9f0d45e012817231d137d47089e')
version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476')
version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8')

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var/spack/repos/builtin/packages/r-affycontam/package.py
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@ -7,14 +7,14 @@
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"""
homepage = "https://bioconductor.org/packages/affyContam"
git = "https://git.bioconductor.org/packages/affyContam.git"
bioc = "affyContam"
version('1.52.0', commit='47c1d86da330f157d3ece0e26b0657d66a5ca0c9')
version('1.48.0', commit='88387a2ad4be4234d36710c65f2ca3a5b06b67da')
version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe')
version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614')

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var/spack/repos/builtin/packages/r-affycoretools/package.py
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@ -8,14 +8,14 @@
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."""
homepage = "https://bioconductor.org/packages/affycoretools"
git = "https://git.bioconductor.org/packages/affycoretools.git"
bioc = "affycoretools"
version('1.66.0', commit='6bf769d70e196634097f465ed2fa85cce5312a6d')
version('1.62.0', commit='c9779e4da648fd174c9bd575c6020be1c03047c4')
version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898')
version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845')
@ -41,5 +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'))
depends_on('r-dbi', type=('build', 'run'), when='@1.50.6:')
depends_on('r-glimma', type=('build', 'run'), when='@1.62.0:')

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var/spack/repos/builtin/packages/r-affydata/package.py
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@ -7,15 +7,15 @@
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
affy."""
homepage = "https://bioconductor.org/packages/affydata"
git = "https://git.bioconductor.org/packages/affydata.git"
bioc = "affydata"
version('1.42.0', commit='4b54c1206bedd27ff9be32affc999a279f4e96f0')
version('1.38.0', commit='b5e843b2514789d0d87bea44d762c89a95314ee7')
version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd')
version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea')

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var/spack/repos/builtin/packages/r-affyexpress/package.py
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@ -7,14 +7,13 @@
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
genes in the Affymetrix gene expression data."""
homepage = "https://bioconductor.org/packages/AffyExpress"
git = "https://git.bioconductor.org/packages/AffyExpress.git"
bioc = "AffyExpress"
version('1.56.0', commit='e07085833de2bbf81537410cad526d39f8a82478')
version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96')

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var/spack/repos/builtin/packages/r-affyilm/package.py
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@ -7,16 +7,16 @@
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
first background subtract intensities before calculating concentrations
on behalf of the Langmuir model."""
homepage = "https://bioconductor.org/packages/affyILM"
git = "https://git.bioconductor.org/packages/affyILM.git"
bioc = "affyILM"
version('1.46.0', commit='67ffbfa6c881ed83d15604bf4463fe5dba81036b')
version('1.42.0', commit='b97b29786b866de38802ebbb995169be91e90942')
version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132')
version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564')

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var/spack/repos/builtin/packages/r-affyio/package.py
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@ -7,15 +7,15 @@
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
formats."""
homepage = "https://bioconductor.org/packages/affyio"
git = "https://git.bioconductor.org/packages/affyio.git"
bioc = "affyio"
version('1.64.0', commit='aa7ce48f3f4110431f6f488d45961fde4019ffb0')
version('1.60.0', commit='ee20528b32700e99768da48143d6d45c9a7bbe91')
version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f')
version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963')

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var/spack/repos/builtin/packages/r-affypdnn/package.py
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@ -12,8 +12,7 @@ class RAffypdnn(RPackage):
The package contains functions to perform the PDNN method described by
Li Zhang et al."""
homepage = "https://bioconductor.org/packages/affypdnn"
git = "https://git.bioconductor.org/packages/affypdnn.git"
bioc = "affypdnn"
version('1.58.0', commit='83d8b6b0d9606845bd77dbf7164dd5b160f32ccf')
version('1.56.0', commit='5fd9c5265fb895a1f646cf72e8d5169669d979f2')

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var/spack/repos/builtin/packages/r-affyplm/package.py
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@ -7,7 +7,7 @@
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.
@ -15,9 +15,9 @@ class RAffyplm(RPackage):
models and tools using these models. PLM based quality assessment
tools."""
homepage = "https://bioconductor.org/packages/affyPLM"
git = "https://git.bioconductor.org/packages/affyPLM.git"
bioc = "affyPLM"
version('1.70.0', commit='64abfec92b347aa340b54a8c7b2fbd524fe9c312')
version('1.66.0', commit='f0780c3d0e9dccaff83861b98beb5c1d324c4399')
version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d')
version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8')

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var/spack/repos/builtin/packages/r-affyqcreport/package.py
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@ -7,14 +7,13 @@
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
arrays in an AffyBatch object."""
homepage = "https://bioconductor.org/packages/affyQCReport"
git = "https://git.bioconductor.org/packages/affyQCReport.git"
bioc = "affyQCReport"
version('1.68.0', commit='34b42a16f87a90a595146f4a1802ed04f6bfccca')
version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4')
@ -27,7 +26,7 @@ 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-biobase', type=('build', 'run'), when='@1.68.0:')
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-simpleaffy', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
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@ -8,7 +8,7 @@
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
@ -16,9 +16,9 @@ class RAffyrnadegradation(RPackage):
probe positional bias, and thus improves comparability of samples that
are affected by RNA degradation."""
homepage = "https://bioconductor.org/packages/AffyRNADegradation"
git = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
bioc = "AffyRNADegradation"
version('1.40.0', commit='8539a91ee464d692a267bb17c91dc1ef9a231f41')
version('1.36.0', commit='89662b93076659db2967a526899184c12c156bc5')
version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1')
version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24')

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var/spack/repos/builtin/packages/r-agdex/package.py
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@ -7,14 +7,14 @@
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"""
homepage = "https://bioconductor.org/packages/AGDEX"
git = "https://git.bioconductor.org/packages/AGDEX.git"
bioc = "AGDEX"
version('1.42.0', commit='175cf1b384b0942103d841b1feb9e4f7d141ba06')
version('1.38.0', commit='7e2c1f5f27ccbea6a7157f5122212e40408b74da')
version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf')
version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b')

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var/spack/repos/builtin/packages/r-agilp/package.py
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@ -7,13 +7,13 @@
class RAgilp(RPackage):
"""Agilent expression array processing package
"""Agilent expression array processing package.
More about what it does (maybe more than one line)."""
homepage = "https://bioconductor.org/packages/agilp"
git = "https://git.bioconductor.org/packages/agilp.git"
bioc = "agilp"
version('3.26.0', commit='3170fe2b1cc459d5e2ca7f61a127aac17cd66a96')
version('3.22.0', commit='7d089d576752e0526f15a1007e94436089954313')
version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47')
version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61')

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var/spack/repos/builtin/packages/r-agimicrorna/package.py
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@ -8,13 +8,13 @@
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"
bioc = "AgiMicroRna"
version('2.44.0', commit='8b308baa3b1b0afc0855ea263630a288689e3864')
version('2.40.0', commit='cfa4acb2215da44767ab3a45845bcd587c309e74')
version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a')
version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8')

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var/spack/repos/builtin/packages/r-aims/package.py
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@ -7,7 +7,7 @@
class RAims(RPackage):
"""AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
"""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,
@ -15,9 +15,9 @@ class RAims(RPackage):
done on individual samples as well as on dataset of gene expression
data."""
homepage = "https://bioconductor.org/packages/AIMS"
git = "https://git.bioconductor.org/packages/AIMS.git"
bioc = "AIMS"
version('1.26.0', commit='5dcf60eb4cdcf563ea848482c9c488f465c27bbd')
version('1.22.0', commit='34a38978b24377abb864eff7683bb36344ff171d')
version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84')
version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f')

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var/spack/repos/builtin/packages/r-aldex2/package.py
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@ -7,7 +7,7 @@
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-
@ -21,9 +21,9 @@ class RAldex2(RPackage):
aldex.glm), or a correlation test (via aldex.corr). All tests report
p-values and Benjamini-Hochberg corrected p-values."""
homepage = "https://bioconductor.org/packages/ALDEx2"
git = "https://git.bioconductor.org/packages/ALDEx2.git"
bioc = "ALDEx2"
version('1.26.0', commit='0876a2eac08d3f1c01df7414d97d391c80182ada')
version('1.22.0', commit='ac7f0ab3f094ec52713da7620a27058b14c7181d')
version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f')
version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8')
@ -31,10 +31,11 @@ class RAldex2(RPackage):
version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a')
version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
depends_on('r-zcompositions', when='@1.22.0:', type=('build', 'run'))
depends_on('r-zcompositions', type=('build', 'run'), when='@1.22.0:')
depends_on('r-rfast', type=('build', 'run'), when='@1.26.0:')
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-multtest', when='@1.10.0:', type=('build', 'run'))
depends_on('r-multtest', type=('build', 'run'), when='@1.10.0:')

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var/spack/repos/builtin/packages/r-allelicimbalance/package.py
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@ -7,14 +7,14 @@
class RAllelicimbalance(RPackage):
"""Investigates Allele Specific Expression
"""Investigates Allele Specific Expression.
Provides a framework for allelic specific expression investigation using
RNA-seq data."""
homepage = "https://bioconductor.org/packages/AllelicImbalance"
git = "https://git.bioconductor.org/packages/AllelicImbalance.git"
bioc = "AllelicImbalance"
version('1.32.0', commit='428ab8c96bb15fab45e4084da25f98b01b9d60b6')
version('1.28.0', commit='ac5d13c9ee0935bf9500ee542792644e752a1fde')
version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3')
@ -23,29 +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@4.0.0:', type=('build', 'run'), when='@1.28.0:')
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.18.0:')
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-genomicalignments@1.15.6:', type=('build', 'run'), when='@1.18.0:')
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-bsgenome@1.47.3:', type=('build', 'run'), when='@1.18.0:')
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-variantannotation@1.25.11:', type=('build', 'run'), when='@1.18.0:')
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.18.0:')
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-s4vectors@0.17.25:', type=('build', 'run'), when='@1.18.0:')
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.18.0:')
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-rsamtools@1.31.2:', type=('build', 'run'), when='@1.18.0:')
depends_on('r-rsamtools@1.99.3:', type=('build', 'run'), when='@1.22.0:')
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.31.3:', type=('build', 'run'), when='@1.18.0:')
depends_on('r-gviz', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-latticeextra', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-alpine/package.py
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@ -7,14 +7,14 @@
class RAlpine(RPackage):
"""alpine
"""alpine.
Fragment sequence bias modeling and correction for RNA-seq transcript
abundance estimation."""
homepage = "https://bioconductor.org/packages/alpine"
git = "https://git.bioconductor.org/packages/alpine.git"
bioc = "alpine"
version('1.20.0', commit='9348ef14128aa6be10cca1987736ddbc385df7e9')
version('1.16.0', commit='aee397774ac6cd17ad45dc05be14c526647f3c13')
version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c')
version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4')

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var/spack/repos/builtin/packages/r-alsace/package.py
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@ -7,7 +7,7 @@
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
@ -16,9 +16,9 @@ class RAlsace(RPackage):
functionality for high-throughput analysis, including definition of time
windows, clustering of profiles, retention time correction, etcetera."""
homepage = "https://bioconductor.org/packages/alsace"
git = "https://git.bioconductor.org/packages/alsace.git"
bioc = "alsace"
version('1.30.0', commit='d0e09b283da2b4869d5d6e6801399676246bc5bc')
version('1.26.0', commit='40a76404acb1466723a78a55d87c67eec3e6f306')
version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389')
version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191')

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var/spack/repos/builtin/packages/r-altcdfenvs/package.py
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@ -7,13 +7,13 @@
class RAltcdfenvs(RPackage):
"""alternative CDF environments (aka probeset mappings)
"""alternative CDF environments (aka probeset mappings).
Convenience data structures and functions to handle cdfenvs."""
homepage = "https://bioconductor.org/packages/altcdfenvs"
git = "https://git.bioconductor.org/packages/altcdfenvs.git"
bioc = "altcdfenvs"
version('2.56.0', commit='941e00b97a33662a8230991e387070324b2e76bf')
version('2.52.0', commit='21329abf82eae26f84b7c0270e81c8e089c548ce')
version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b')
version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133')

3
var/spack/repos/builtin/packages/r-ampliqueso/package.py
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@ -12,8 +12,7 @@ class RAmpliqueso(RPackage):
The package provides tools and reports for the analysis of amplicon
sequencing panels, such as AmpliSeq"""
homepage = "https://bioconductor.org/packages/3.8/bioc/html/ampliQueso.html"
git = "https://git.bioconductor.org/packages/ampliQueso.git"
bioc = "ampliQueso"
version('1.21.0', commit='ed99c5194a452ee299a93e981da2224e4dab5bdd')
version('1.20.0', commit='ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8')

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var/spack/repos/builtin/packages/r-analysispageserver/package.py
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@ -13,8 +13,7 @@ class RAnalysispageserver(RPackage):
AnalysisPageServer is a modular system that enables sharing of
customizable R analyses via the web."""
homepage = "https://bioconductor.org/packages/AnalysisPageServer"
git = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
bioc = "AnalysisPageServer"
version('1.18.1', commit='08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630')
version('1.16.0', commit='67b063523f80e2af1d26262367ff50f34e195174')

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var/spack/repos/builtin/packages/r-anaquin/package.py
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@ -7,7 +7,7 @@
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
@ -15,9 +15,9 @@ class RAnaquin(RPackage):
source library for quantitative analysis, modelling and visualization of
spike-in controls."""
homepage = "https://bioconductor.org/packages/Anaquin"
git = "https://git.bioconductor.org/packages/Anaquin.git"
bioc = "Anaquin"
version('2.18.0', commit='c8e3df3e299c32daac0dda23cea59a18673d886b')
version('2.14.0', commit='d0a34c931a0e72080bff91dacb37dbbe26b45386')
version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601')
version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6')

14
var/spack/repos/builtin/packages/r-aneufinder/package.py
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@ -7,15 +7,15 @@
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
genome sequencing and strand-seq data."""
homepage = "https://bioconductor.org/packages/AneuFinder"
git = "https://git.bioconductor.org/packages/AneuFinder.git"
bioc = "AneuFinder"
version('1.22.0', commit='ea0beb3d827c2dd4bc56708a839a93c55304918b')
version('1.18.0', commit='76ec9af947f97212084ca478e8e82f9e0eb79de9')
version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e')
version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd')
@ -24,22 +24,22 @@ 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@3.5:', type=('build', 'run'), when='@1.10.2:')
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-biocgenerics', type=('build', 'run'), when='@1.4.0:1.6.0')
depends_on('r-biocgenerics@0.31.6:', type=('build', 'run'), when='@1.18.0:')
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-ecp', type=('build', 'run'), when='@1.8.0:')
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-aneufinderdata/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/AneuFinderData"
git = "https://git.bioconductor.org/packages/AneuFinderData.git"
bioc = "AneuFinderData"
version('1.22.0', commit='ae8eec3b0afdc351dc447aad2024df5b2c75e56b')
version('1.18.0', commit='1bf1657b28fc8c1425e611980a692da952ce3d1e')
version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1')
version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035')

10
var/spack/repos/builtin/packages/r-annaffy/package.py
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@ -7,16 +7,16 @@
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
data and URL links to many online databases. Allows searching biological
metadata using various criteria."""
homepage = "https://bioconductor.org/packages/annaffy"
git = "https://git.bioconductor.org/packages/annaffy.git"
bioc = "annaffy"
version('1.66.0', commit='aa1afa1509754128d27508228c1f39f51a8da043')
version('1.62.0', commit='ad9c37e0e7e45e0f35c208ce528ba48000b37432')
version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233')
version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484')
@ -26,7 +26,9 @@ class RAnnaffy(RPackage):
depends_on('r@2.5.0:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocmanager', type=('build', 'run'), when='@1.64.2:')
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-kegg-db', type=('build', 'run'))
depends_on('r-annotationdbi@0.1.15:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-kegg-db', type=('build', 'run'), when='@:1.62.0')

11
var/spack/repos/builtin/packages/r-annotate/package.py
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@ -7,13 +7,13 @@
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"
bioc = "annotate"
version('1.72.0', commit='67ac76a9ff6d60dc1620763d3aa98aef39443110')
version('1.68.0', commit='98cdb12c612b3f3fc06329a89a1ffb0a92b555c0')
version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd')
version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16')
@ -28,5 +28,6 @@ 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-httr', when='@1.68.0:', type=('build', 'run'))
depends_on('r-rcurl', when='@:1.62.0', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'), when='@1.68.0:')
depends_on('r-rcurl', type=('build', 'run'), when='@:1.62.0')

11
var/spack/repos/builtin/packages/r-annotationdbi/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/AnnotationDbi"
git = "https://git.bioconductor.org/packages/AnnotationDbi.git"
bioc = "AnnotationDbi"
version('1.56.2', commit='13fdc4a93852199ca6ec120a2fe1078f9f445f67')
version('1.52.0', commit='c4e0ca9bd65362ae9cad6a98d90f54267b0ae838')
version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9')
version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac')
@ -24,10 +24,11 @@ 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-biocgenerics@0.23.1:', type=('build', 'run'), when='@1.40.0:')
depends_on('r-biocgenerics@0.29.2:', type=('build', 'run'), when='@1.46.1:')
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-keggrest', type=('build', 'run'), when='@1.56.2:')

6
var/spack/repos/builtin/packages/r-annotationfilter/package.py
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@ -7,15 +7,15 @@
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
will be used by ensembldb, Organism.dplyr, and other packages."""
homepage = "https://bioconductor.org/packages/AnnotationFilter"
git = "https://git.bioconductor.org/packages/AnnotationFilter.git"
bioc = "AnnotationFilter"
version('1.18.0', commit='60a9b666d7362d7ed5c357fd4a5d2744d8598c20')
version('1.14.0', commit='6ee3a13ed93a535ed452cbc8c118151a2cbb732c')
version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed')
version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3')

6
var/spack/repos/builtin/packages/r-annotationforge/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/AnnotationForge"
git = "https://git.bioconductor.org/packages/AnnotationForge.git"
bioc = "AnnotationForge"
version('1.36.0', commit='523b5f0c3ffb77e59e1568e5f36a5a470bfeeae5')
version('1.32.0', commit='3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7')
version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e')
version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d')

21
var/spack/repos/builtin/packages/r-annotationhub/package.py
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@ -7,7 +7,7 @@
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
@ -18,9 +18,9 @@ class RAnnotationhub(RPackage):
cache of files retrieved by the user, helping with quick and
reproducible access."""
homepage = "https://bioconductor.org/packages/AnnotationHub"
git = "https://git.bioconductor.org/packages/AnnotationHub.git"
bioc = "AnnotationHub"
version('3.2.1', commit='ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa')
version('2.22.0', commit='3ab7dceebbc31ac14ca931f66c662cf9538b7d0a')
version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed')
version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12')
@ -29,16 +29,17 @@ 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-biocfilecache@1.5.1:', type=('build', 'run'), when='@2.16.1:')
depends_on('r-rsqlite', 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-biocmanager', type=('build', 'run'), when='@2.14.5:')
depends_on('r-biocversion', type=('build', 'run'), when='@2.22.0:')
depends_on('r-curl', type=('build', 'run'), when='@2.10.1:')
depends_on('r-rappdirs', type=('build', 'run'), when='@2.16.1:')
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-dplyr', when='@2.16.1:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@:2.16.1', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'), when='@2.16.1:')
depends_on('r-biocinstaller', type=('build', 'run'), when='@:2.16.1')

28
var/spack/repos/builtin/packages/r-aplot/package.py Normal file
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@ -0,0 +1,28 @@
# Copyright 2013-2022 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 RAplot(RPackage):
"""Decorate a 'ggplot' with Associated Information.
For many times, we are not just aligning plots as what 'cowplot' and
'patchwork' did. Users would like to align associated information that
requires axes to be exactly matched in subplots, e.g. hierarchical
clustering with a heatmap. This package provides utilities to aligns
associated subplots to a main plot at different sides (left, right, top and
bottom) with axes exactly matched."""
cran = "aplot"
version('0.1.2', sha256='899c4d101ddcedb1eba9803d78cf02288b63de25e2879add8add1165167509f0')
depends_on('r-ggfun@0.0.4:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-ggplotify', type=('build', 'run'))
depends_on('r-patchwork', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-yulab-utils', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-aroma-light/package.py
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@ -8,22 +8,22 @@
class RAromaLight(RPackage):
"""Light-Weight Methods for Normalization and Visualization of Microarray
Data using Only Basic R Data Types
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"
bioc = "aroma.light"
version('3.24.0', commit='3ff48b8f546acc9803b3c652363cac78d3b81ae5')
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-oo@1.23.0:', type=('build', 'run'), when='@3.20.0:')
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'))
depends_on('r-matrixstats@0.55.0:', type=('build', 'run'), when='@3.20.0:')

12
var/spack/repos/builtin/packages/r-bamsignals/package.py
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@ -7,16 +7,16 @@
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
computes reads profiles and coverage profiles. It also handles paired-
end data."""
homepage = "https://bioconductor.org/packages/bamsignals"
git = "https://git.bioconductor.org/packages/bamsignals.git"
bioc = "bamsignals"
version('1.26.0', commit='d57643441d04f77db0907637dc9e7cd5bed5842f')
version('1.22.0', commit='5f533969c84212406bcb3ebf725ebb6d77e9947a')
version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657')
version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d')
@ -31,9 +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('r-rhtslib@1.12.1:', type=('build', 'run'), when='@1.12.1:')
depends_on('r-rhtslib@1.13.1:', type=('build', 'run'), when='@1.14.0:')
depends_on('gmake', type='build')
# this is no listed but is needed
# this is not listed but is needed
depends_on('curl')

34
var/spack/repos/builtin/packages/r-beachmat/package.py
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@ -7,7 +7,7 @@
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
@ -15,9 +15,9 @@ class RBeachmat(RPackage):
S4 classes may be supported by external linkage, while all other
matrices are handled by DelayedArray block processing."""
homepage = "https://bioconductor.org/packages/beachmat"
git = "https://git.bioconductor.org/packages/beachmat.git"
bioc = "beachmat"
version('2.10.0', commit='b7cc532d4a5b26d9073135cc9945258ea08e5079')
version('2.6.4', commit='7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb')
version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab')
version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a')
@ -25,17 +25,19 @@ class RBeachmat(RPackage):
version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run'))
depends_on('r@3.5:', type=('build', 'run'), when='@1.2.1:1.4.0')
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-delayedarray@0.5.30:', when='@1.2.1', 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'))
depends_on('r-delayedarray@0.5.30:', type=('build', 'run'), when='@1.2.1')
depends_on('r-delayedarray@0.7.38:', type=('build', 'run'), when='@1.4.0')
depends_on('r-delayedarray@0.15.14:', type=('build', 'run'), when='@2.6.4')
depends_on('r-biocgenerics', type=('build', 'run'), when='@1.4.0:')
depends_on('r-matrix', type=('build', 'run'), when='@2.6.4:')
depends_on('r-rcpp@0.12.14:', type=('build', 'run'), when='@1.0.2:1.4.0')
depends_on('r-rcpp', type=('build', 'run'), when='@2.10.0:')
depends_on('r-rhdf5lib', type=('build', 'run'), when='@1.0.2:1.4.0')
depends_on('r-rhdf5lib@1.1.4:', type=('build', 'run'), when='@1.2.1')
depends_on('r-hdf5array', type=('build', 'run'), when='@1.0.2:1.4.0')
depends_on('r-hdf5array@1.7.3:', type=('build', 'run'), when='@1.2.1')
depends_on('r-hdf5array@1.9.5:', type=('build', 'run'), when='@1.4.0')
depends_on('r-rhdf5', type=('build', 'run'), when='@1.0.2:1.4.0')

8
var/spack/repos/builtin/packages/r-biobase/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/Biobase"
git = "https://git.bioconductor.org/packages/Biobase.git"
bioc = "Biobase"
version('2.54.0', commit='8215d76ce44899e6d10fe8a2f503821a94ef6b40')
version('2.50.0', commit='9927f90d0676382f2f99e099d8d2c8e2e6f1b4de')
version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3')
version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d')
@ -24,4 +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'))
depends_on('r-biocgenerics@0.27.1:', type=('build', 'run'), when='@2.42.0:')

11
var/spack/repos/builtin/packages/r-biocfilecache/package.py
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@ -7,16 +7,16 @@
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
as custom Txdb objects) that are costly or difficult to create, web
resources, and data files used across sessions."""
homepage = "https://bioconductor.org/packages/BiocFileCache"
git = "https://git.bioconductor.org/packages/BiocFileCache.git"
bioc = "BiocFileCache"
version('2.2.1', commit='cc912123408803193bf37395f4d18baa8dcd6f47')
version('1.14.0', commit='cdcde4b59ae73dda12aa225948dbd0a058d9be6d')
version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0')
version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba')
@ -26,9 +26,10 @@ class RBiocfilecache(RPackage):
depends_on('r@3.4.0:', 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-dbplyr@1.0.0:', type=('build', 'run'), when='@1.2.3:')
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rappdirs', type=('build', 'run'))
depends_on('r-curl', when='@1.6.0:', type=('build', 'run'))
depends_on('r-filelock', type=('build', 'run'), when='@2.2.1:')
depends_on('r-curl', type=('build', 'run'), when='@1.6.0:')
depends_on('r-httr', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-biocgenerics/package.py
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@ -7,13 +7,13 @@
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"
bioc = "BiocGenerics"
version('0.40.0', commit='0bc1e0ed4d20c7101cd782a14f6373e27478acfc')
version('0.36.0', commit='0d5d169d7d64d648a22f9043837c93bc784e71ed')
version('0.34.0', commit='f7c2020')
version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8')
@ -22,5 +22,5 @@ class RBiocgenerics(RPackage):
version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
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'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@0.30.0:')
depends_on('r@4.0.0:', type=('build', 'run'), when='@0.36.0:')

6
var/spack/repos/builtin/packages/r-biocinstaller/package.py
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@ -12,8 +12,7 @@ class RBiocinstaller(RPackage):
This package is used to install and update Bioconductor, CRAN, and
(some) github packages."""
homepage = "https://bioconductor.org/packages/3.8/bioc/html/BiocInstaller.html"
git = "https://git.bioconductor.org/packages/BiocInstaller.git"
bioc = "BiocInstaller"
version('1.33.1', commit='6193f31c18e7e64d91e0e15ed0ba6924eda1416f')
version('1.32.1', commit='4c2a39e1cae470af3a5cf1491715f272b70f4bb4')
@ -22,5 +21,4 @@ class RBiocinstaller(RPackage):
version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.30.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.30.0:')

29
var/spack/repos/builtin/packages/r-biocio/package.py Normal file
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@ -0,0 +1,29 @@
# Copyright 2013-2022 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 RBiocio(RPackage):
"""Standard Input and Output for Bioconductor Packages.
Implements `import()` and `export()` standard generics for importing and
exporting biological data formats. `import()` supports whole-file as well
as chunk-wise iterative import. The `import()` interface optionally
provides a standard mechanism for 'lazy' access via `filter()` (on row or
element-like components of the file resource), `select()` (on column-like
components of the file resource) and `collect()`. The `import()` interface
optionally provides transparent access to remote (e.g. via https) as well
as local access. Developers can register a file extension, e.g., `.loom`
for dispatch from character-based URIs to specific `import()` / `export()`
methods based on classes representing file types, e.g., `LoomFile()`."""
bioc = "BiocIO"
version('1.4.0', commit='c335932526a38c75dbfa4970c1d90b8a21466d37')
depends_on('r@4.0.0:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))

17
var/spack/repos/builtin/packages/r-biocneighbors/package.py
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@ -7,7 +7,7 @@
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
@ -19,18 +19,19 @@ class RBiocneighbors(RPackage):
BiocParallel. Functions are also provided to search for all neighbors
within a given distance."""
homepage = "https://bioconductor.org/packages/BiocNeighbors"
git = "https://git.bioconductor.org/packages/BiocNeighbors.git"
bioc = "BiocNeighbors"
version('1.12.0', commit='3c8a290f75adc944b408e6e77a36f3a0c1509c4c')
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@3.5:', type=('build', 'run'), when='@1.0.0')
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-s4vectors', 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'))
depends_on('r-matrix', type=('build', 'run'), when='@1.8.2:')
depends_on('r-rcpphnsw', type=('build', 'run'), when='@1.2.0:')
depends_on('r-rcppannoy', type=('build', 'run'), when='@:1.2.0')
depends_on('r-biocgenerics', type=('build', 'run'), when='@1.2.0')

9
var/spack/repos/builtin/packages/r-biocparallel/package.py
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@ -7,15 +7,15 @@
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
objects."""
homepage = "https://bioconductor.org/packages/BiocParallel"
git = "https://git.bioconductor.org/packages/BiocParallel.git"
bioc = "BiocParallel"
version('1.28.3', commit='2f9d88ad83659939e7911d49c2d24d2cd599c7cc')
version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f')
version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e')
version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4')
@ -23,6 +23,7 @@ class RBiocparallel(RPackage):
version('1.12.0', commit='2143a9addceed0151a27b95c70aadd2add5cbace')
version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.28.3:')
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'))
depends_on('r-bh', type=('build', 'run'), when='@1.12.0:')

7
var/spack/repos/builtin/packages/r-biocsingular/package.py
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@ -7,7 +7,7 @@
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
@ -15,9 +15,9 @@ class RBiocsingular(RPackage):
workflows. Where possible, parallelization is achieved using the
BiocParallel framework."""
homepage = "https://bioconductor.org/packages/BiocSingular"
git = "https://git.bioconductor.org/packages/BiocSingular.git"
bioc = "BiocSingular"
version('1.10.0', commit='6615ae8cb124aba6507447c1081bd2eba655e57d')
version('1.6.0', commit='11baf1080d6f791439cd5d97357589d6451643d9')
version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833')
@ -26,6 +26,7 @@ class RBiocsingular(RPackage):
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-scaledmatrix', type=('build', 'run'), when='@1.10.0:')
depends_on('r-irlba', type=('build', 'run'))
depends_on('r-rsvd', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-biocstyle/package.py
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@ -7,14 +7,14 @@
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."""
homepage = "https://bioconductor.org/packages/BiocStyle"
git = "https://git.bioconductor.org/packages/BiocStyle.git"
bioc = "BiocStyle"
version('2.22.0', commit='86250b637afa3a3463fac939b99c0402b47876ea')
version('2.18.1', commit='956f0654e8e18882ba09305742401128c9c7d47d')
version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498')
version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70')
@ -25,7 +25,7 @@ class RBiocstyle(RPackage):
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-knitr@1.30:', type=('build', 'run'), when='@2.18.1:')
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'))
depends_on('r-biocmanager', type=('build', 'run'), when='@2.10.0:')

7
var/spack/repos/builtin/packages/r-biocversion/package.py
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@ -7,14 +7,15 @@
class RBiocversion(RPackage):
"""Set the appropriate version of Bioconductor packages
"""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"
bioc = "BiocVersion"
version('3.14.0', commit='aa56d93d0ea5dcdbf301f120502981740fd91e1e')
version('3.12.0', commit='23b971963c6b73550a7e330dab5a046d58ce0223')
depends_on('r@4.0.0:', type=('build', 'run'))
depends_on('r@4.1.0:', type=('build', 'run'), when='@3.14.0:')

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var/spack/repos/builtin/packages/r-biomart/package.py
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@ -7,7 +7,7 @@
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
@ -22,9 +22,9 @@ class RBiomart(RPackage):
range of powerful online queries from gene annotation to database
mining."""
homepage = "https://bioconductor.org/packages/biomaRt"
git = "https://git.bioconductor.org/packages/biomaRt.git"
bioc = "biomaRt"
version('2.50.3', commit='83a519ac13d73dc545cb6aafde5f4b5001e9e08f')
version('2.46.2', commit='90d6abfdfa04259006f7b47efb10271ada76aec1')
version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68')
version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658')
@ -34,11 +34,13 @@ class RBiomart(RPackage):
depends_on('r-xml', 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'))
depends_on('r-progress', type=('build', 'run'), when='@2.34.2:')
depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:')
depends_on('r-httr', type=('build', 'run'), when='@2.34.2:')
depends_on('r-digest', type=('build', 'run'), when='@2.50.3:')
depends_on('r-biocfilecache', type=('build', 'run'), when='@2.46.2:')
depends_on('r-rappdirs', type=('build', 'run'), when='@2.46.2:')
depends_on('r-xml2', type=('build', 'run'), when='@2.46.2:')
depends_on('r-rcurl', type=('build', 'run'), when='@:2.40.5')
depends_on('r-openssl', type=('build', 'run'), when='@2.46.2')

6
var/spack/repos/builtin/packages/r-biomformat/package.py
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@ -7,7 +7,7 @@
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
@ -19,9 +19,9 @@ class RBiomformat(RPackage):
includes S4 classes and methods, as well as extensions of common core
functions/methods."""
homepage = "https://bioconductor.org/packages/biomformat"
git = "https://git.bioconductor.org/packages/biomformat.git"
bioc = "biomformat"
version('1.22.0', commit='ab7c6411a038fec010baa72e663f362fd972cb34')
version('1.18.0', commit='dc18859c139f4d76805adb6f01e199573cdd5a8b')
version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a')
version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09')

35
var/spack/repos/builtin/packages/r-biostrings/package.py
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@ -7,15 +7,15 @@
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
sets of sequences."""
homepage = "https://bioconductor.org/packages/Biostrings"
git = "https://git.bioconductor.org/packages/Biostrings.git"
bioc = "Biostrings"
version('2.62.0', commit='53ed287e03d16fa523789af3131c60375ccf587f')
version('2.58.0', commit='0ec1a5455d5e9eebd14b26228906bb04e2abb197')
version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5')
version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2')
@ -24,19 +24,22 @@ 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@3.5.0:', type=('build', 'run'), when='@2.50.2:')
depends_on('r@4.0.0:', type=('build', 'run'), when='@2.62.0:')
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-biocgenerics@0.31.5:', type=('build', 'run'), when='@2.58.0:')
depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@2.62.0:')
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', 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-s4vectors@0.17.25:', type=('build', 'run'), when='@2.48.0:')
depends_on('r-s4vectors@0.21.13:', type=('build', 'run'), when='@2.52.0:')
depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@2.58.0:')
depends_on('r-iranges@2.9.18:', type=('build', 'run'), when='@2.44.2:')
depends_on('r-iranges@2.13.24:', type=('build', 'run'), when='@2.48.0:')
depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@2.58.0:')
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-xvector@0.21.4:', when='@2.50.2:', 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'))
depends_on('r-xvector@0.19.8:', type=('build', 'run'), when='@2.48.0:')
depends_on('r-xvector@0.21.4:', type=('build', 'run'), when='@2.50.2:')
depends_on('r-xvector@0.23.2:', type=('build', 'run'), when='@2.52.0:')
depends_on('r-xvector@0.29.2:', type=('build', 'run'), when='@2.58.0:')
depends_on('r-genomeinfodb', type=('build', 'run'), when='@2.62.0:')
depends_on('r-crayon', type=('build', 'run'), when='@2.58.0:')

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var/spack/repos/builtin/packages/r-biovizbase/package.py
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@ -14,9 +14,9 @@ class RBiovizbase(RPackage):
various high-level packages for biological data visualization. This
saves development effort and encourages consistency."""
homepage = "https://bioconductor.org/packages/biovizBase"
git = "https://git.bioconductor.org/packages/biovizBase.git"
bioc = "biovizBase"
version('1.42.0', commit='f1627b2b567471837daca6e763acfc3e13937461')
version('1.38.0', commit='d0f3362e0ad0e90b4b1d3e47b13ed57907d03403')
version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82')
@ -25,14 +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@3.5.0:', type=('build', 'run'), when='@1.38.0:')
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-s4vectors@0.23.19:', type=('build', 'run'), when='@1.38.0:')
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'))
@ -45,4 +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'))
depends_on('r-rlang', type=('build', 'run'), when='@1.28.2:')

8
var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
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@ -8,14 +8,14 @@
class RBsgenomeHsapiensUcscHg19(RPackage):
"""Full genome sequences for Homo sapiens (UCSC version hg19, based on
GRCh37.p13)
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 = "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"
bioc = "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('1.4.3',
sha256='5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a',
@ -25,4 +25,4 @@ class RBsgenomeHsapiensUcscHg19(RPackage):
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'))
depends_on('r-bsgenome@1.54.0:', type=('build', 'run'), when='@1.4.3:')

30
var/spack/repos/builtin/packages/r-bsgenome/package.py
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@ -8,13 +8,13 @@
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"
bioc = "BSgenome"
version('1.62.0', commit='9b1859e11ffa082833f035a45274af6e4e83e863')
version('1.58.0', commit='3a4926e03a7a1d7140a10c1b2bf6090808470145')
version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b')
version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9')
@ -25,22 +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-s4vectors@0.17.28:', type=('build', 'run'), when='@1.48.0:')
depends_on('r-iranges@2.1.33:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.16:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0:')
depends_on('r-iranges@2.13.16:', type=('build', 'run'), when='@1.48.0:')
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-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0:')
depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.48.0:')
depends_on('r-genomeinfodb@1.25.6:', type=('build', 'run'), when='@1.58.0:')
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-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0:')
depends_on('r-genomicranges@1.31.10:', type=('build', 'run'), when='@1.48.0:')
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-biostrings@2.47.6:', type=('build', 'run'), when='@1.48.0:')
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-rtracklayer@1.39.7:', type=('build', 'run'), when='@1.48.0:')
depends_on('r-matrixstats', type=('build', 'run'), when='@1.58.0:')
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.29.3:', when='@1.58.0:', type=('build', 'run'))
depends_on('r-xvector@0.29.3:', type=('build', 'run'), when='@1.58.0:')
depends_on('r-rsamtools', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-bsseq/package.py
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@ -7,31 +7,31 @@
class RBsseq(RPackage):
"""Analyze, manage and store bisulfite sequencing data
"""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"
bioc = "bsseq"
version('1.30.0', commit='7eb5223e9ee02fd08a52be56eaa9316a67c0d66b')
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@4.0:', type=('build', 'run'), when='@1.26.0:')
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-genomicranges@1.33.6:', type=('build', 'run'), when='@1.24.4:')
depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.26.0:')
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-summarizedexperiment@1.17.4:', type=('build', 'run'), when='@1.24.4:')
depends_on('r-summarizedexperiment@1.19.5:', type=('build', 'run'), when='@1.26.0:')
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-iranges@2.22.2:', type=('build', 'run'), when='@1.24.4:')
depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
@ -39,20 +39,21 @@ class RBsseq(RPackage):
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@0.27.12:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.23.11:', type=('build', 'run'), when='@1.22.0:')
depends_on('r-s4vectors@0.25.14:', type=('build', 'run'), when='@1.24.4:')
depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.26.0:')
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-delayedarray@0.15.16:', type=('build', 'run'), when='@1.26.0:')
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-hdf5array@1.15.19:', type=('build', 'run'), when='@1.26.0:')
depends_on('r-hdf5array@1.19.11:', type=('build', 'run'), when='@1.30.0:')
depends_on('r-rhdf5', type=('build', 'run'))
depends_on('r-beachmat', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-bumphunter/package.py
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@ -7,13 +7,13 @@
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"
bioc = "bumphunter"
version('1.36.0', commit='db50fcf7798c2eddfe48fd510d081dda82f2ee4e')
version('1.32.0', commit='b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0')
version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa')
version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b')
@ -22,8 +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@3.4:', type=('build', 'run'), when='@1.20.0:')
depends_on('r@3.5:', type=('build', 'run'), when='@1.24.5:')
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'))

23
var/spack/repos/builtin/packages/r-bwstest/package.py Normal file
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@ -0,0 +1,23 @@
# Copyright 2013-2022 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 RBwstest(RPackage):
"""Baumgartner Weiss Schindler Test of Equal Distributions.
Performs the 'Baumgartner-Weiss-Schindler' two-sample test of equal
probability distributions, <doi:10.2307/2533862>. Also performs similar
rank-based tests for equal probability distributions due to Neuhauser
<doi:10.1080/10485250108832874> and Murakami
<doi:10.1080/00949655.2010.551516>."""
cran = "BWStest"
version('0.2.2', sha256='faff1dd698f1673a6befacb94d14281077d4c19be035a0a3bf85d77c1dfd5509')
depends_on('r-memoise', type=('build', 'run'))
depends_on('r-rcpp@0.12.3:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-category/package.py
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@ -7,14 +7,14 @@
class RCategory(RPackage):
"""Category Analysis
"""Category Analysis.
A collection of tools for performing category (gene set enrichment)
analysis."""
homepage = "https://bioconductor.org/packages/Category"
git = "https://git.bioconductor.org/packages/Category.git"
bioc = "Category"
version('2.60.0', commit='55210d8c539474954d18cf913a219dce883eac2e')
version('2.56.0', commit='ad478caa9d693dbc2770608e79dd852375b9a223')
version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9')
version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5')

5
var/spack/repos/builtin/packages/r-champ/package.py
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@ -8,14 +8,15 @@
class RChamp(RPackage):
"""Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and
EPIC:
EPIC.
The package includes quality control metrics, a selection of
normalization methods and novel methods to identify differentially
methylated regions and to highlight copy number alterations."""
bioc = "ChAMP"
bioc = "ChAMP"
version('2.24.0', commit='7ba19da74b61e1c40ced162ba753f0f9b9c7647a')
version('2.20.1', commit='99ea0463bce59f5b06bcc91f479dcd4065074896')
depends_on('r@3.3:', type=('build', 'run'))

5
var/spack/repos/builtin/packages/r-champdata/package.py
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@ -7,13 +7,14 @@
class RChampdata(RPackage):
"""Packages for ChAMP package:
"""Packages for ChAMP package.
Provides datasets needed for ChAMP including a test dataset and blood
controls for CNA analysis."""
bioc = "ChAMPdata"
bioc = "ChAMPdata"
version('2.26.0', commit='ea7882707921af33eefab5133a1ccd4a409f045d')
version('2.22.0', commit='eeedd4c477fac79f00743da8ff7da064221c5f3d')
depends_on('r@3.3:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-chipseq/package.py
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@ -7,15 +7,15 @@
class RChipseq(RPackage):
"""A package for analyzing chipseq data
"""A package for analyzing chipseq data,
Tools for helping process short read data for chipseq experiments"""
homepage = "https://bioconductor.org/packages/release/bioc/html/chipseq.html"
git = "https://git.bioconductor.org/packages/chipseq"
bioc = "chipseq"
maintainers = ['dorton21']
version('1.44.0', commit='b64d0d28e9fcf0fdab9a7f9c521baf729426a594')
version('1.40.0', commit='84bcbc0b7ad732730b5989a308f1624a6a358df1')
depends_on('r@2.10:', type=('build', 'run'))

33
var/spack/repos/builtin/packages/r-clusterprofiler/package.py
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@ -8,14 +8,14 @@
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."""
homepage = "https://bioconductor.org/packages/clusterProfiler"
git = "https://git.bioconductor.org/packages/clusterProfiler.git"
bioc = "clusterProfiler"
version('4.2.2', commit='4ebb9de8e03eedc971f54a57cf5bf1b250ed43d5')
version('3.18.0', commit='064a6e612ce27e260e33af78b907bee4065ff821')
version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c')
@ -24,23 +24,26 @@ class RClusterprofiler(RPackage):
version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
depends_on('r@3.3.1:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
depends_on('r@3.4.0:', type=('build', 'run'), when='@3.8.1:')
depends_on('r@3.5.0:', type=('build', 'run'), when='@4.2.2:')
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-downloader', when='@3.18.0:', type=('build', 'run'))
depends_on('r-downloader', type=('build', 'run'), when='@3.18.0:')
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-dose@3.3.2:', type=('build', 'run'), when='@3.6.0:')
depends_on('r-dose@3.5.1:', type=('build', 'run'), when='@3.8.1:')
depends_on('r-dose@3.13.1:', type=('build', 'run'), when='@3.18.0:')
depends_on('r-dplyr', type=('build', 'run'), when='@3.18.0:')
depends_on('r-enrichplot@0.99.7:', type=('build', 'run'), when='@3.8.1:')
depends_on('r-enrichplot@1.9.3:', type=('build', 'run'), when='@3.18.0:')
depends_on('r-go-db', 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-gosemsim@2.0.0:', type=('build', 'run'), when='@3.4.4:3.6.0')
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-rlang', type=('build', 'run'), when='@3.18.0:')
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-ggplot2', when='@:3.12.0', type=('build', 'run'))
depends_on('r-yulab-utils', type=('build', 'run'), when='@4.2.2:')
depends_on('r-ggplot2', type=('build', 'run'), when='@:3.12.0')
depends_on('r-rvcheck', type=('build', 'run'), when='@:3.18.0')

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var/spack/repos/builtin/packages/r-cner/package.py
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@ -7,14 +7,14 @@
class RCner(RPackage):
"""CNE Detection and Visualization
"""CNE Detection and Visualization.
Large-scale identification and advanced visualization of sets of
conserved noncoding elements."""
homepage = "https://bioconductor.org/packages/CNEr"
git = "https://git.bioconductor.org/packages/CNEr.git"
bioc = "CNEr"
version('1.30.0', commit='e682f2a7c8ebb561c872cf51a58ba36eed341187')
version('1.26.0', commit='e5e582da6feeae0618c4460f16ece724215e3b20')
version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5')
version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606')
@ -23,10 +23,10 @@ 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@3.4:', type=('build', 'run'), when='@1.14.0:')
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-dbi@0.7:', type=('build', 'run'), when='@1.14.0:')
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'))

6
var/spack/repos/builtin/packages/r-codex/package.py
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@ -8,7 +8,7 @@
class RCodex(RPackage):
"""A Normalization and Copy Number Variation Detection Method for Whole
Exome Sequencing
Exome Sequencing.
A normalization and copy number variation calling procedure for whole
exome DNA sequencing data. CODEX relies on the availability of multiple
@ -20,9 +20,9 @@ class RCodex(RPackage):
segmentation procedure that explicitly models the count-based exome
sequencing data."""
homepage = "https://www.bioconductor.org/packages/release/bioc/html/CODEX.html"
git = "https://git.bioconductor.org/packages/CODEX"
bioc = "CODEX"
version('1.26.0', commit='729fd10bd42d12edcedd65b5a8fb1579e5949718')
version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb')
version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')

32
var/spack/repos/builtin/packages/r-complexheatmap/package.py
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@ -7,16 +7,16 @@
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
ComplexHeatmap package provides a highly flexible way to arrange
multiple heatmaps and supports various annotation graphics."""
homepage = "https://bioconductor.org/packages/ComplexHeatmap"
git = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
bioc = "ComplexHeatmap"
version('2.10.0', commit='170df82a1568e879e4019e0ff6feb0047851684f')
version('2.6.2', commit='0383bada2c76dc3dde71cf6a625016b619aec4d3')
version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4')
version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f')
@ -25,19 +25,23 @@ class RComplexheatmap(RPackage):
version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
depends_on('r@3.1.2:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@2.10.0:')
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-circlize@0.4.1:', type=('build', 'run'), when='@1.17.1:')
depends_on('r-circlize@0.4.5:', type=('build', 'run'), when='@2.0.0:')
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-clue', type=('build', 'run'), when='@2.0.0:')
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-globaloptions@0.0.10:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', 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'))
depends_on('r-globaloptions@0.1.0:', type=('build', 'run'), when='@1.20.0:')
depends_on('r-png', type=('build', 'run'), when='@2.0.0:')
depends_on('r-digest', type=('build', 'run'), when='@2.6.2:')
depends_on('r-iranges', type=('build', 'run'), when='@2.6.2:')
depends_on('r-matrixstats', type=('build', 'run'), when='@2.6.2:')
depends_on('r-foreach', type=('build', 'run'), when='@2.10.0:')
depends_on('r-doparallel', type=('build', 'run'), when='@2.10.0:')
depends_on('r-dendextend@1.0.1:', type=('build', 'run'), when='@1.14.0:1.17.1')
depends_on('r-s4vectors@0.26.1:', type=('build', 'run'), when='@2.6.2')
depends_on('r-cairo', type=('build', 'run'), when='@2.6.2')

4
var/spack/repos/builtin/packages/r-ctc/package.py
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@ -12,9 +12,9 @@ class RCtc(RPackage):
Tools for export and import classification trees and clusters to other
programs"""
homepage = "https://bioconductor.org/packages/ctc"
git = "https://git.bioconductor.org/packages/ctc.git"
bioc = "ctc"
version('1.68.0', commit='c2733534ef9d948e07ea654d1998a67ed8f7a98a')
version('1.64.0', commit='35dbe620a21056b8f69890e6f9a7c320528d8621')
version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb')
version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f')

9
var/spack/repos/builtin/packages/r-decipher/package.py
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@ -7,13 +7,13 @@
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"
bioc = "DECIPHER"
version('2.22.0', commit='45da5cab5869d83af797aa82b08ebcd24f5bdab3')
version('2.18.1', commit='6a708421550e6705d05e2fb50a0f5ab4f9041cb0')
version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f')
version('2.10.2', commit='db7b017c9050a7ec1d4daa15352994890095e9c3')
@ -22,8 +22,9 @@ 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@3.5.0:', type=('build', 'run'), when='@2.18.1:')
depends_on('r-biostrings@2.35.12:', type=('build', 'run'))
depends_on('r-biostrings@2.59.1:', type=('build', 'run'), when='@2.22.0:')
depends_on('r-rsqlite@1.1:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))

37
var/spack/repos/builtin/packages/r-delayedarray/package.py
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@ -8,7 +8,7 @@
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
@ -18,9 +18,9 @@ class RDelayedarray(RPackage):
on in-memory array-like objects like DataFrame objects (typically with
Rle columns), Matrix objects, and ordinary arrays and data frames."""
homepage = "https://bioconductor.org/packages/DelayedArray"
git = "https://git.bioconductor.org/packages/DelayedArray.git"
bioc = "DelayedArray"
version('0.20.0', commit='829b52916ec54bb4f1a3c6f06c9955f3e28b3592')
version('0.16.1', commit='c95eba771ad3fee1b49ec38c51cd8fd1486feadc')
version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a')
version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f')
@ -29,20 +29,23 @@ 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@4.0.0:', type=('build', 'run'), when='@0.20.0:')
depends_on('r-matrix', type=('build', 'run'), when='@0.10.0:')
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-biocgenerics@0.25.1:', type=('build', 'run'), when='@0.6.6:')
depends_on('r-biocgenerics@0.27.1:', type=('build', 'run'), when='@0.8.0:')
depends_on('r-biocgenerics@0.31.5:', type=('build', 'run'), when='@0.16.1:')
depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@0.20.1:')
depends_on('r-matrixgenerics@1.1.3:', type=('build', 'run'), when='@0.16.1:')
depends_on('r-s4vectors@0.14.3:', type=('build', 'run'))
depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', 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-s4vectors@0.15.3:', type=('build', 'run'), when='@0.4.1:')
depends_on('r-s4vectors@0.17.43:', type=('build', 'run'), when='@0.6.6:')
depends_on('r-s4vectors@0.19.15:', type=('build', 'run'), when='@0.8.0:')
depends_on('r-s4vectors@0.21.7:', type=('build', 'run'), when='@0.10.0:')
depends_on('r-s4vectors@0.27.2:', type=('build', 'run'), when='@0.16.1:')
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-matrixstats', when='@:0.10.0', type=('build', 'run'))
depends_on('r-biocparallel', when='@0.6.6:0.10.0', type=('build', 'run'))
depends_on('r-iranges@2.11.17:', type=('build', 'run'), when='@0.4.1:')
depends_on('r-iranges@2.17.3:', type=('build', 'run'), when='@0.10.0:')
depends_on('r-matrixstats', type=('build', 'run'), when='@:0.10.0')
depends_on('r-biocparallel', type=('build', 'run'), when='@0.6.6:0.10.0')

35
var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
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@ -7,7 +7,7 @@
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
@ -16,29 +16,34 @@ class RDelayedmatrixstats(RPackage):
for subsetted calculations such that both memory usage and processing
time is minimized."""
homepage = "https://github.com/PeteHaitch/DelayedMatrixStats"
git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git"
bioc = "DelayedMatrixStats"
version('1.16.0', commit='d44a3d765769cb022193428a77af25bf19916be7')
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-matrixgenerics', type=('build', 'run'), when='@1.12.2:')
depends_on('r-matrixgenerics@1.5.3:', type=('build', 'run'), when='@1.16.0:')
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-delayedarray@0.5.27:', type=('build', 'run'), when='@1.2.0:')
depends_on('r-delayedarray@0.7.37:', type=('build', 'run'), when='@1.4.0:')
depends_on('r-delayedarray@0.9.8:', type=('build', 'run'), when='@1.6.1:')
depends_on('r-delayedarray@0.15.3:', type=('build', 'run'), when='@1.12.2:')
depends_on('r-delayedarray@0.17.6:', type=('build', 'run'), when='@1.16.0:')
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-matrixstats@0.55.0:', type=('build', 'run'), when='@1.6.1:')
depends_on('r-matrixstats@0.56.0:', type=('build', 'run'), when='@1.12.2:')
depends_on('r-matrixstats@0.60.0:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-sparsematrixstats', type=('build', 'run'), when='@1.12.2:')
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.5:', type=('build', 'run'), when='@1.2.0:')
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-iranges@2.25.10:', type=('build', 'run'), when='@1.16.0:')
depends_on('r-hdf5array@1.7.10:', type=('build', 'run'), when='@1.4.0:1.12.3')
depends_on('r-hdf5array@1.17.2:', type=('build', 'run'), when='@1.12.2:1.12.3')
depends_on('r-biocparallel', type=('build', 'run'), when='@1.4.0:1.12.3')

5
var/spack/repos/builtin/packages/r-deseq/package.py
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@ -8,14 +8,13 @@
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
using the negative binomial distribution"""
homepage = "https://bioconductor.org/packages/DESeq"
git = "https://git.bioconductor.org/packages/DESeq.git"
bioc = "DESeq"
version('1.42.0', commit='da76bc64e8c4073b58eaf1c93aa4e89bec5c4e50')
version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e')

8
var/spack/repos/builtin/packages/r-deseq2/package.py
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@ -8,7 +8,7 @@
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('1.34.0', commit='25d4f74be59548122ccfbe8687d30c0bae5cf49a')
version('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77')
version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce')
@ -25,7 +26,7 @@ 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-s4vectors@0.23.18:', type=('build', 'run'), when='@1.30.0:')
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run'))
@ -36,6 +37,7 @@ class RDeseq2(RPackage):
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-geneplotter', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
depends_on('r-rcpparmadillo', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'), when='@:1.30.0')

19
var/spack/repos/builtin/packages/r-dexseq/package.py
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@ -7,7 +7,7 @@
class RDexseq(RPackage):
"""Inference of differential exon usage in RNA-Seq
"""Inference of differential exon usage in RNA-Seq.
The package is focused on finding differential exon usage using RNA-seq
exon counts between samples with different experimental designs. It
@ -21,16 +21,9 @@ class RDexseq(RPackage):
maintainers = ['dorton21']
version('1.40.0', commit='7d2d639b3a157e443058fc557132cd2629bb36f3')
version('1.36.0', commit='f0a361af6954fcc2abb2db801c26e303570669b2')
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-geneplotter', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biomart', type=('build', 'run'))
depends_on('r-hwriter', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-statmod', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
@ -40,3 +33,11 @@ class RDexseq(RPackage):
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-s4vectors@0.23.18:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biomart', type=('build', 'run'))
depends_on('r-hwriter', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-statmod', type=('build', 'run'))
depends_on('r-geneplotter', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
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@ -8,7 +8,7 @@
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
@ -16,9 +16,9 @@ class RDirichletmultinomial(RPackage):
7(2): 1-15, as discussed further in the man page for this package,
?DirichletMultinomial."""
homepage = "https://bioconductor.org/packages/DirichletMultinomial"
git = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
bioc = "DirichletMultinomial"
version('1.36.0', commit='926baff6c75cb498945c5895f25cc143c907a357')
version('1.32.0', commit='6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16')
version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f')
version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35')

10
var/spack/repos/builtin/packages/r-dmrcate/package.py
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@ -7,7 +7,7 @@
class RDmrcate(RPackage):
"""Methylation array and sequencing spatial analysis methods:
"""Methylation array and sequencing spatial analysis methods.
De novo identification and extraction of differentially methylated regions
(DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS)
@ -15,22 +15,24 @@ class RDmrcate(RPackage):
for filtering probes possibly confounded by SNPs and cross-hybridisation.
Includes GRanges generation and plotting functions."""
bioc = "DMRcate"
bioc = "DMRcate"
version('2.8.5', commit='c65dc79a33a047c10932a98b3383709a6bcb8903')
version('2.4.1', commit='bc6242a0291a9b997872f575a4417d38550c9550')
depends_on('r@3.6.0:', type=('build', 'run'))
depends_on('r-minfi', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r@4.0.0:', type=('build', 'run'), when='@2.8.5:')
depends_on('r-experimenthub', type=('build', 'run'))
depends_on('r-bsseq', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-edger', type=('build', 'run'))
depends_on('r-dss', type=('build', 'run'))
depends_on('r-minfi', type=('build', 'run'))
depends_on('r-missmethyl', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-gviz', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-dnacopy/package.py
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@ -7,15 +7,15 @@
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
number."""
homepage = "https://bioconductor.org/packages/DNAcopy"
git = "https://git.bioconductor.org/packages/DNAcopy.git"
bioc = "DNAcopy"
version('1.68.0', commit='08f039f58bc2f5ed2cc3117ae817dbac333002a6')
version('1.64.0', commit='01650266ea7a4e5c600de545fe70a1103e79b2d8')
version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23')
version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a')

5
var/spack/repos/builtin/packages/r-do-db/package.py
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@ -7,15 +7,16 @@
class RDoDb(RPackage):
"""A set of annotation maps describing the entire Disease Ontology
"""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."""
# There is no git repository for this package.
homepage = "https://bioconductor.org/packages/DO.db/"
url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz"
version('2.9', sha256='762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881')
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationdbi@1.9.7:', type=('build', 'run'))

19
var/spack/repos/builtin/packages/r-dose/package.py
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@ -7,7 +7,7 @@
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
@ -16,9 +16,9 @@ class RDose(RPackage):
implemented for discovering disease associations of high-throughput
biological data."""
homepage = "https://bioconductor.org/packages/DOSE"
git = "https://git.bioconductor.org/packages/DOSE.git"
bioc = "DOSE"
version('3.20.1', commit='bf434f24d035217822cb1b0ab08a486b9a53edb4')
version('3.16.0', commit='a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd')
version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3')
version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639')
@ -27,8 +27,8 @@ 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@3.4.0:', type=('build', 'run'), when='@3.6.1:')
depends_on('r@3.5.0:', type=('build', 'run'), when='@3.16.0:')
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-do-db', type=('build', 'run'))
@ -37,7 +37,8 @@ class RDose(RPackage):
depends_on('r-gosemsim@2.0.0:', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-reshape2', 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-igraph', when='@3.2.0:3.4.0', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'), when='@:3.10.2')
depends_on('r-scales', type=('build', 'run'), when='@3.2.0:3.4.0')
depends_on('r-rvcheck', type=('build', 'run'), when='@3.4.0')
depends_on('r-igraph', type=('build', 'run'), when='@3.2.0:3.4.0')

10
var/spack/repos/builtin/packages/r-dss/package.py
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@ -7,7 +7,7 @@
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
@ -16,9 +16,9 @@ class RDss(RPackage):
shrinkage method for estimating the dispersion parameter from Gamma-Poisson
or Beta-Binomial distributions."""
homepage = "https://bioconductor.org/packages/DSS/"
git = "https://git.bioconductor.org/packages/DSS"
bioc = "DSS"
version('2.42.0', commit='33e87450fbb64bb3e321688ff613e83cd40efe48')
version('2.38.0', commit='82e65b92e6e227f1f99620362db8b03059e07e98')
version('2.36.0', commit='841c7ed')
version('2.34.0', commit='f9819c7')
@ -26,6 +26,6 @@ class RDss(RPackage):
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocparallel', when='@2.36.0:', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'), when='@2.36.0:')
depends_on('r-bsseq', type=('build', 'run'))
depends_on('r-delayedarray', when='@2.36.0:', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'), when='@2.36.0:')

14
var/spack/repos/builtin/packages/r-edger/package.py
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@ -7,7 +7,7 @@
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
@ -17,9 +17,9 @@ class REdger(RPackage):
of other types of genomic data that produce counts, including ChIP-seq,
Bisulfite-seq, SAGE and CAGE."""
homepage = "https://bioconductor.org/packages/edgeR"
git = "https://git.bioconductor.org/packages/edgeR.git"
bioc = "edgeR"
version('3.36.0', commit='c7db03addfc42138a1901834409c02da9d873026')
version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a')
version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d')
@ -28,9 +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@3.6.0:', type=('build', 'run'), when='@3.26.8:')
depends_on('r-limma', 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-limma@3.34.5:', type=('build', 'run'), when='@3.20.9:')
depends_on('r-limma@3.41.5:', type=('build', 'run'), when='@3.32.1:')
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'), when='@3.20.9:')

44
var/spack/repos/builtin/packages/r-enrichplot/package.py
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@ -7,40 +7,46 @@
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
analysis. All the visualization methods are developed based on 'ggplot2'
graphics."""
homepage = "https://bioconductor.org/packages/enrichplot"
git = "https://git.bioconductor.org/packages/enrichplot.git"
bioc = "enrichplot"
version('1.14.1', commit='ccf3a6d9b7cd9cffd8de6d6263efdffe59d2ec36')
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@3.5.0:', when='@1.10.2:', type=('build', 'run'))
depends_on('r-cowplot', 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@3.5.0:', type=('build', 'run'), when='@1.10.2:')
depends_on('r-aplot', type=('build', 'run'), when='@1.14.1:')
depends_on('r-dose@3.5.1:', type=('build', 'run'))
depends_on('r-dose@3.13.1:', type=('build', 'run'), when='@1.8.1:')
depends_on('r-dose@3.16.0:', type=('build', 'run'), when='@1.12.3:')
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-ggraph', type=('build', 'run'))
depends_on('r-igraph', 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-plyr', type=('build', 'run'), when='@1.10.2:')
depends_on('r-purrr', type=('build', 'run'), when='@1.2.0:')
depends_on('r-rcolorbrewer', type=('build', 'run'), when='@1.2.0:')
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-scatterpie', type=('build', 'run'), when='@1.10.2:')
depends_on('r-shadowtext', type=('build', 'run'), when='@1.10.2:')
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'))
depends_on('r-magrittr', type=('build', 'run'), when='@1.10.2:')
depends_on('r-ggtree', type=('build', 'run'), when='@1.14.1:')
depends_on('r-yulab-utils@0.0.4:', type=('build', 'run'), when='@1.14.1:')
depends_on('r-ggridges', type=('build', 'run'), when='@:1.4.0')
depends_on('r-upsetr', type=('build', 'run'), when='@:1.4.0')
depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.4.0')
depends_on('r-europepmc', type=('build', 'run'), when='@1.2.0:1.4.0')
depends_on('r-ggplotify', type=('build', 'run'), when='@1.2.0:1.4.0')
depends_on('r-gridextra', type=('build', 'run'), when='@1.2.0:1.4.0')
depends_on('r-cowplot', type=('build', 'run'))

25
var/spack/repos/builtin/packages/r-ensembldb/package.py
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@ -7,7 +7,7 @@
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
@ -22,9 +22,9 @@ class REnsembldb(RPackage):
encoding transcripts. Finally, ensembldb provides functions to map
between genomic, transcript and protein coordinates."""
homepage = "https://bioconductor.org/packages/ensembldb"
git = "https://git.bioconductor.org/packages/ensembldb.git"
bioc = "ensembldb"
version('2.18.3', commit='e2fcfc0c7700110df070a171d2d542b37ec098f3')
version('2.14.0', commit='c7150519ed4ef38e5eac1043209863dbc7be43a1')
version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c')
@ -34,12 +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-genomicranges@1.31.18:', type=('build', 'run'), when='@2.4.1:')
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-genomicfeatures@1.29.10:', type=('build', 'run'), when='@2.2.2:')
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-annotationfilter@1.1.9:', type=('build', 'run'), when='@2.2.2:')
depends_on('r-annotationfilter@1.5.2:', type=('build', 'run'), when='@2.6.8:')
depends_on('r-rsqlite@1.1:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
@ -47,13 +47,14 @@ 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-s4vectors@0.23.10:', when='@2.14.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.23.10:', type=('build', 'run'), when='@2.14.0:')
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@2.2.2:')
depends_on('r-iranges@2.13.24:', type=('build', 'run'), when='@2.4.1:')
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-biostrings@2.47.9:', type=('build', 'run'), when='@2.4.1:')
depends_on('r-curl', type=('build', 'run'))
depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run'))
depends_on('r-annotationhub', type=('build', 'run'), when='@2.0.4:2.2.2')

6
var/spack/repos/builtin/packages/r-exomecopy/package.py
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@ -7,7 +7,7 @@
class RExomecopy(RPackage):
"""Copy number variant detection from exome sequencing read depth
"""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
@ -15,9 +15,9 @@ class RExomecopy(RPackage):
GC-content, to simultaneously normalize and segment the samples into
regions of constant copy count."""
homepage = "https://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
git = "https://git.bioconductor.org/packages/exomeCopy"
bioc = "exomeCopy"
version('1.40.0', commit='ebde39be67baace2c326359421fd17f4a02fd4fe')
version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26')
version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')

5
var/spack/repos/builtin/packages/r-experimenthub/package.py
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@ -7,7 +7,7 @@
class RExperimenthub(RPackage):
"""Client to access ExperimentHub resources:
"""Client to access ExperimentHub resources.
This package provides a client for the Bioconductor ExperimentHub web
resource. ExperimentHub provides a central location where curated data from
@ -16,8 +16,9 @@ class RExperimenthub(RPackage):
creates and manages a local cache of files retrieved enabling quick and
reproducible access."""
bioc = "ExperimentHub"
bioc = "ExperimentHub"
version('2.2.1', commit='4e10686fa72baefef5d2990f41a7c44c527a7a7d')
version('1.16.1', commit='61d51b7ca968d6cc1befe299e0784d9a19ca51f6')
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py
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@ -7,13 +7,13 @@
class RFdbInfiniummethylationHg18(RPackage):
"""Annotation package for Illumina Infinium DNA methylation probes
"""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 = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg18.html"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"
bioc = "FDb.InfiniumMethylation.hg18"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"
version('2.2.0', sha256='4a9028ac03c11fffbab731ea750bc7f9b0884fc43c6a8dac6eb2c644e4c79f6f')

6
var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py
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@ -7,13 +7,13 @@
class RFdbInfiniummethylationHg19(RPackage):
"""Annotation package for Illumina Infinium DNA methylation probes
"""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"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"
bioc = "FDb.InfiniumMethylation.hg19"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"
version('2.2.0', sha256='605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f')

10
var/spack/repos/builtin/packages/r-fgsea/package.py
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@ -7,16 +7,16 @@
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
get more fine grained p-values, which allows to use accurate stantard
approaches to multiple hypothesis correction."""
homepage = "https://bioconductor.org/packages/fgsea"
git = "https://git.bioconductor.org/packages/fgsea.git"
bioc = "fgsea"
version('1.20.0', commit='b704f81687dc16afdaafc6d30108c62a067856b2')
version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318')
version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b')
@ -31,5 +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'))
depends_on('r-matrix', type=('build', 'run'), when='@1.6.0:')
depends_on('r-bh', type=('build', 'run'), when='@1.10.1:')

11
var/spack/repos/builtin/packages/r-gcrma/package.py
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@ -7,13 +7,13 @@
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"
bioc = "gcrma"
version('2.66.0', commit='ba134b392def89d36b5639a187e0c25a4353457b')
version('2.62.0', commit='b91bdf5bf4e875defedb4d4e3e1e75867773287a')
version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224')
version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc')
@ -27,5 +27,6 @@ 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-biocmanager', when='@2.54.0:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@:2.52.0', type=('build', 'run'))
depends_on('r-biocmanager', type=('build', 'run'), when='@2.54.0:')
depends_on('r-biocinstaller', type=('build', 'run'), when='@:2.52.0')

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