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Update the Spack R BioConductor packages to Bioconductor-3.12 (#21575)

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This commit is contained in:
Glenn Johnson 2021-02-09 15:35:30 -06:00 committed by GitHub
parent e341a76543
commit f7a9fbc688
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193 changed files with 1203 additions and 661 deletions
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6
var/spack/repos/builtin/packages/r-a4/package.py
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@ -7,11 +7,15 @@
class RA4(RPackage):
"""Automated Affymetrix Array Analysis Umbrella Package."""
"""Automated Affymetrix Array Analysis Umbrella Package
Umbrella package is available for the entire Automated Affymetrix Array
Analysis suite of package."""
homepage = "https://bioconductor.org/packages/a4"
git = "https://git.bioconductor.org/packages/a4.git"
version('1.38.0', commit='5b7a9087bab10c55e24707e96e48046995236c94')
version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712')
version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d')
version('1.28.0', commit='e81a8c15e1062ed9433e2d4d333f0484bc0e8bfb')

12
var/spack/repos/builtin/packages/r-a4base/package.py
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@ -7,25 +7,29 @@
class RA4base(RPackage):
"""Automated Affymetrix Array Analysis Base Package."""
"""Automated Affymetrix Array Analysis Base Package
Base utility functions are available for the Automated Affymetrix Array
Analysis set of packages."""
homepage = "https://bioconductor.org/packages/a4Base"
git = "https://git.bioconductor.org/packages/a4Base.git"
version('1.38.0', commit='4add242fa9c62795aca5b0dfca34a43484c5aa82')
version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7')
version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229')
version('1.28.0', commit='3918a9ebafa065027c29620ee4d83789cb02f932')
version('1.26.0', commit='9b8ee4a8be90f5035a4b105ecebb8bb5b50cd0d9')
version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annaffy', type=('build', 'run'))
depends_on('r-mpm', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-multtest', type=('build', 'run'))
depends_on('r-glmnet', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-gplots', type=('build', 'run'))
depends_on('r-annotationdbi', when='@:1.32.0', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-a4classif/package.py
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@ -7,11 +7,16 @@
class RA4classif(RPackage):
"""Automated Affymetrix Array Analysis Classification Package."""
"""Automated Affymetrix Array Analysis Classification Package
Functionalities for classification of Affymetrix microarray data,
integrating within the Automated Affymetrix Array Analysis set of
packages."""
homepage = "https://bioconductor.org/packages/a4Classif"
git = "https://git.bioconductor.org/packages/a4Classif.git"
version('1.38.0', commit='c4d058813efb835774813b2d69c52912162f8e75')
version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88')
version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3')
version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7')
@ -20,8 +25,9 @@ class RA4classif(RPackage):
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-mlinterfaces', type=('build', 'run'))
depends_on('r-biobase', when='@1.38.0:', type=('build', 'run'))
depends_on('r-rocr', type=('build', 'run'))
depends_on('r-pamr', type=('build', 'run'))
depends_on('r-glmnet', type=('build', 'run'))
depends_on('r-varselrf', type=('build', 'run'))
depends_on('r-mlinterfaces', when='@:1.32.0', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-a4core/package.py
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@ -7,11 +7,15 @@
class RA4core(RPackage):
"""Automated Affymetrix Array Analysis Core Package."""
"""Automated Affymetrix Array Analysis Core Package
Utility functions for the Automated Affymetrix Array Analysis set of
packages."""
homepage = "https://bioconductor.org/packages/a4Core"
git = "https://git.bioconductor.org/packages/a4Core.git"
version('1.38.0', commit='a027dcd3486c64950815ec7c7271f1f65ba3d8a1')
version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce')
version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141')
version('1.28.0', commit='39b6ee29bc2f2fdc5733438c14dc02f8abc6460b')

10
var/spack/repos/builtin/packages/r-a4preproc/package.py
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@ -7,15 +7,21 @@
class RA4preproc(RPackage):
"""Automated Affymetrix Array Analysis Preprocessing Package."""
"""Automated Affymetrix Array Analysis Preprocessing Package
Utility functions to pre-process data for the Automated Affymetrix Array
Analysis set of packages."""
homepage = "https://bioconductor.org/packages/a4Preproc"
git = "https://git.bioconductor.org/packages/a4Preproc.git"
version('1.38.0', commit='c93c223bd531bff090531a109b51f8dcd710d0cb')
version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558')
version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978')
version('1.28.0', commit='435d66727f1187020d034a1beaf4cd8bd4f76981')
version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea')
version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.38.0:', type=('build', 'run'))
depends_on('r-biobase', when='@1.38.0:', type=('build', 'run'))
depends_on('r-annotationdbi', when='@:1.32.0', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-a4reporting/package.py
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@ -7,16 +7,20 @@
class RA4reporting(RPackage):
"""Automated Affymetrix Array Analysis Reporting Package."""
"""Automated Affymetrix Array Analysis Reporting Package
Utility functions to facilitate the reporting of the Automated Affymetrix
Array Analysis Reporting set of packages."""
homepage = "https://bioconductor.org/packages/a4Reporting"
git = "https://git.bioconductor.org/packages/a4Reporting.git"
version('1.38.0', commit='cd3cf244e7a299b2485684ed15519cbbda1c590f')
version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792')
version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390')
version('1.28.0', commit='0fe72f48374353c39479a45e5516d0709f8c9ef7')
version('1.26.0', commit='cce201502e2d3b28fd2823b66d9f81b034dc7eaa')
version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
depends_on('r-annaffy', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-annaffy', when='@:1.32.0', type=('build', 'run'))

3
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
@ -21,6 +21,7 @@ class RAbadata(RPackage):
homepage = "https://bioconductor.org/packages/ABAData"
git = "https://git.bioconductor.org/packages/ABAData.git"
version('1.20.0', commit='c08a841ffb54d6555eb80b90a7a8afe7e48201b3')
version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd')
version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d')
version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a')

8
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
@ -25,19 +25,19 @@ class RAbaenrichment(RPackage):
homepage = "https://bioconductor.org/packages/ABAEnrichment"
git = "https://git.bioconductor.org/packages/ABAEnrichment.git"
version('1.20.0', commit='608433a0b07e6dd99915dc536a038d960f1be1d5')
version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23')
version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7')
version('1.10.0', commit='15f33ccb694a91d2d2067c937682c4bc952def6c')
version('1.8.0', commit='cb8155ee9a04fb55b2a2e8c23df7c0be15bb2624')
version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run'))
depends_on('r-rcpp@0.11.5:', type=('build', 'run'))
depends_on('r-gplots@2.14.2:', type=('build', 'run'))
depends_on('r-gtools@3.5.0:', type=('build', 'run'))
depends_on('r-abadata@0.99.2:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run'))
depends_on('r-data-table@1.10.4:', when='@1.8.0:', type=('build', 'run'))
depends_on('r-gofuncr@1.1.2:', when='@1.12.0:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-absseq/package.py
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@ -8,7 +8,7 @@
class RAbsseq(RPackage):
"""ABSSeq: a new RNA-Seq analysis method based on modelling absolute
expression differences.
expression differences
Inferring differential expression genes by absolute counts difference
between two groups, utilizing Negative binomial distribution and
@ -18,6 +18,7 @@ class RAbsseq(RPackage):
homepage = "https://bioconductor.org/packages/ABSSeq"
git = "https://git.bioconductor.org/packages/ABSSeq.git"
version('1.44.0', commit='c202b4a059021ed1228ccee7303c69b0aa4ca1ee')
version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce')
version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a')
version('1.34.1', commit='0c3a2514ef644c6e0de3714bc91959a302c9e006')

3
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
@ -23,6 +23,7 @@ class RAcde(RPackage):
homepage = "https://bioconductor.org/packages/acde"
git = "https://git.bioconductor.org/packages/acde.git"
version('1.20.0', commit='cefb4f2e2b0ef3c5f51944c0ece7a71294020350')
version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417')
version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4')
version('1.10.0', commit='2c303dec45f3c70bf333a6eacae568a08d5ca010')

3
var/spack/repos/builtin/packages/r-acgh/package.py
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@ -7,7 +7,7 @@
class RAcgh(RPackage):
"""Classes and functions for Array Comparative Genomic Hybridization data..
"""Classes and functions for Array Comparative Genomic Hybridization data
Functions for reading aCGH data from image analysis output files and
clone information files, creation of aCGH S3 objects for storing these
@ -17,6 +17,7 @@ class RAcgh(RPackage):
homepage = "https://bioconductor.org/packages/aCGH"
git = "https://git.bioconductor.org/packages/aCGH.git"
version('1.68.0', commit='91f41a3917ddce43eb05e11c90eb99c467ba2247')
version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f')
version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21')
version('1.58.0', commit='2decc79a21bff5a14d708cdc654e351515b20d3e')

3
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
@ -22,6 +22,7 @@ class RAcme(RPackage):
homepage = "https://bioconductor.org/packages/ACME"
git = "https://git.bioconductor.org/packages/ACME.git"
version('2.46.0', commit='68f45c9f7d34c28adf6a0fc4245fdf63881109de')
version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a')
version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b')
version('2.36.0', commit='39e056435b9775d35e7f7fc5446c2c3cafe15670')

3
var/spack/repos/builtin/packages/r-adsplit/package.py
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@ -7,7 +7,7 @@
class RAdsplit(RPackage):
"""Annotation-Driven Clustering.
"""Annotation-Driven Clustering
This package implements clustering of microarray gene expression
profiles according to functional annotations. For each term genes are
@ -17,6 +17,7 @@ class RAdsplit(RPackage):
homepage = "https://bioconductor.org/packages/adSplit"
git = "https://git.bioconductor.org/packages/adSplit.git"
version('1.60.0', commit='de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd')
version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652')
version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19')
version('1.50.0', commit='a02e2c994e78ececd5a248575109c5ed36c969db')

3
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
@ -21,6 +21,7 @@ class RAffxparser(RPackage):
homepage = "https://bioconductor.org/packages/affxparser"
git = "https://git.bioconductor.org/packages/affxparser.git"
version('1.62.0', commit='b3e988e5c136c3f1a064e1da13730b403c8704c0')
version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056')
version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f')
version('1.52.0', commit='8e0c4b89ee1cb4ff95f58a5dd947249dc718bc58')

8
var/spack/repos/builtin/packages/r-affy/package.py
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@ -7,7 +7,7 @@
class RAffy(RPackage):
"""Methods for Affymetrix Oligonucleotide Arrays.
"""Methods for Affymetrix Oligonucleotide Arrays
The package contains functions for exploratory oligonucleotide array
analysis. The dependence on tkWidgets only concerns few convenience
@ -16,6 +16,7 @@ class RAffy(RPackage):
homepage = "https://bioconductor.org/packages/affy"
git = "https://git.bioconductor.org/packages/affy.git"
version('1.68.0', commit='1664399610c9aa519399445a2ef8bb9ea2233eac')
version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605')
version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206')
version('1.58.0', commit='4698231f45f225228f56c0708cd477ad450b4ee6')
@ -26,8 +27,7 @@ class RAffy(RPackage):
depends_on('r-biocgenerics@0.1.12:', type=('build', 'run'))
depends_on('r-biobase@2.5.5:', type=('build', 'run'))
depends_on('r-affyio@1.13.3:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run'))
depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-affycomp/package.py
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@ -7,7 +7,7 @@
class RAffycomp(RPackage):
"""Graphics Toolbox for Assessment of Affymetrix Expression Measures.
"""Graphics Toolbox for Assessment of Affymetrix Expression Measures
The package contains functions that can be used to compare expression
measures for Affymetrix Oligonucleotide Arrays."""
@ -15,6 +15,7 @@ class RAffycomp(RPackage):
homepage = "https://bioconductor.org/packages/affycomp"
git = "https://git.bioconductor.org/packages/affycomp.git"
version('1.66.0', commit='388d01af8b1e6ab11051407f77d0206512df8424')
version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c')
version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef')
version('1.56.0', commit='b0994da338be19396e647c680059fd35341b50a2')

3
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
@ -19,6 +19,7 @@ class RAffycompatible(RPackage):
homepage = "https://bioconductor.org/packages/AffyCompatible"
git = "https://git.bioconductor.org/packages/AffyCompatible.git"
version('1.50.0', commit='3b12d12bd6d1a9f0d45e012817231d137d47089e')
version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476')
version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8')
version('1.40.0', commit='44838bdb5e8c26afbd898c49ed327ddd1a1d0301')

3
var/spack/repos/builtin/packages/r-affycontam/package.py
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@ -7,7 +7,7 @@
class RAffycontam(RPackage):
"""structured corruption of affymetrix cel file data.
"""structured corruption of affymetrix cel file data
structured corruption of cel file data to demonstrate QA
effectiveness"""
@ -15,6 +15,7 @@ class RAffycontam(RPackage):
homepage = "https://bioconductor.org/packages/affyContam"
git = "https://git.bioconductor.org/packages/affyContam.git"
version('1.48.0', commit='88387a2ad4be4234d36710c65f2ca3a5b06b67da')
version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe')
version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614')
version('1.38.0', commit='84651e8eade61619afefc83bb290047da101a5bc')

6
var/spack/repos/builtin/packages/r-affycoretools/package.py
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@ -8,7 +8,7 @@
class RAffycoretools(RPackage):
"""Functions useful for those doing repetitive analyses with Affymetrix
GeneChips.
GeneChips
Various wrapper functions that have been written to streamline the more
common analyses that a core Biostatistician might see."""
@ -16,12 +16,14 @@ class RAffycoretools(RPackage):
homepage = "https://bioconductor.org/packages/affycoretools"
git = "https://git.bioconductor.org/packages/affycoretools.git"
version('1.62.0', commit='c9779e4da648fd174c9bd575c6020be1c03047c4')
version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898')
version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845')
version('1.52.2', commit='2f98c74fad238b94c1e453b972524ab7b573b0de')
version('1.50.6', commit='4be92bcb55d7bace2a110865b7530dcfac14e76e')
version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
depends_on('r+X', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
@ -39,5 +41,5 @@ class RAffycoretools(RPackage):
depends_on('r-edger', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-dbi', when='@1.50.6:', type=('build', 'run'))
depends_on('r-glimma', when='@1.62.0:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-affydata/package.py
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@ -7,7 +7,7 @@
class RAffydata(RPackage):
"""Affymetrix Data for Demonstration Purpose.
"""Affymetrix Data for Demonstration Purpose
Example datasets of a slightly large size. They represent 'real world
examples', unlike the artificial examples included in the package
@ -16,6 +16,7 @@ class RAffydata(RPackage):
homepage = "https://bioconductor.org/packages/affydata"
git = "https://git.bioconductor.org/packages/affydata.git"
version('1.38.0', commit='b5e843b2514789d0d87bea44d762c89a95314ee7')
version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd')
version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea')
version('1.28.0', commit='a106a5514c352bf0bbc624ded58a93886d4ce96f')

3
var/spack/repos/builtin/packages/r-affyexpress/package.py
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@ -7,7 +7,7 @@
class RAffyexpress(RPackage):
"""Affymetrix Quality Assessment and Analysis Tool.
"""Affymetrix Quality Assessment and Analysis Tool
The purpose of this package is to provide a comprehensive and easy-to-
use tool for quality assessment and to identify differentially expressed
@ -16,6 +16,7 @@ class RAffyexpress(RPackage):
homepage = "https://bioconductor.org/packages/AffyExpress"
git = "https://git.bioconductor.org/packages/AffyExpress.git"
version('1.56.0', commit='e07085833de2bbf81537410cad526d39f8a82478')
version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96')
version('1.48.0', commit='dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92')
version('1.46.0', commit='2add4a4436e21aa20f1ededbfd5f1365a3d28c85')

3
var/spack/repos/builtin/packages/r-affyilm/package.py
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@ -7,7 +7,7 @@
class RAffyilm(RPackage):
"""Linear Model of background subtraction and the Langmuir isotherm.
"""Linear Model of background subtraction and the Langmuir isotherm
affyILM is a preprocessing tool which estimates gene expression levels
for Affymetrix Gene Chips. Input from physical chemistry is employed to
@ -17,6 +17,7 @@ class RAffyilm(RPackage):
homepage = "https://bioconductor.org/packages/affyILM"
git = "https://git.bioconductor.org/packages/affyILM.git"
version('1.42.0', commit='b97b29786b866de38802ebbb995169be91e90942')
version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132')
version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564')
version('1.32.0', commit='860f2ddada80435d309ba334eff3fab503817755')

3
var/spack/repos/builtin/packages/r-affyio/package.py
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@ -7,7 +7,7 @@
class RAffyio(RPackage):
"""Tools for parsing Affymetrix data files.
"""Tools for parsing Affymetrix data files
Routines for parsing Affymetrix data files based upon file format
information. Primary focus is on accessing the CEL and CDF file
@ -16,6 +16,7 @@ class RAffyio(RPackage):
homepage = "https://bioconductor.org/packages/affyio"
git = "https://git.bioconductor.org/packages/affyio.git"
version('1.60.0', commit='ee20528b32700e99768da48143d6d45c9a7bbe91')
version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f')
version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963')
version('1.50.0', commit='911ea4f8e4cdf7b649b87ef7ed1a5f5b111ef38a')

3
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.
@ -18,6 +18,7 @@ class RAffyplm(RPackage):
homepage = "https://bioconductor.org/packages/affyPLM"
git = "https://git.bioconductor.org/packages/affyPLM.git"
version('1.66.0', commit='f0780c3d0e9dccaff83861b98beb5c1d324c4399')
version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d')
version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8')
version('1.56.0', commit='13dfc558281af9a177d4d592c34cf7ace629af0e')

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var/spack/repos/builtin/packages/r-affyqcreport/package.py
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@ -7,7 +7,7 @@
class RAffyqcreport(RPackage):
"""QC Report Generation for affyBatch objects.
"""QC Report Generation for affyBatch objects
This package creates a QC report for an AffyBatch object. The report is
intended to allow the user to quickly assess the quality of a set of
@ -16,6 +16,7 @@ class RAffyqcreport(RPackage):
homepage = "https://bioconductor.org/packages/affyQCReport"
git = "https://git.bioconductor.org/packages/affyQCReport.git"
version('1.68.0', commit='34b42a16f87a90a595146f4a1802ed04f6bfccca')
version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4')
version('1.60.0', commit='d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa')
version('1.58.0', commit='14be93a1e7a6d1a64c38ed2f53e0c52a389b2a1b')
@ -26,6 +27,7 @@ class RAffyqcreport(RPackage):
depends_on('r-affy', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-affyplm', type=('build', 'run'))
depends_on('r-biobase', when='@1.68.0:', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-simpleaffy', type=('build', 'run'))

3
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
@ -19,6 +19,7 @@ class RAffyrnadegradation(RPackage):
homepage = "https://bioconductor.org/packages/AffyRNADegradation"
git = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
version('1.36.0', commit='89662b93076659db2967a526899184c12c156bc5')
version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1')
version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24')
version('1.26.0', commit='6ab03ad624701464280bf7dfe345d200e846298a')

3
var/spack/repos/builtin/packages/r-agdex/package.py
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@ -7,7 +7,7 @@
class RAgdex(RPackage):
"""Agreement of Differential Expression Analysis.
"""Agreement of Differential Expression Analysis
A tool to evaluate agreement of differential expression for cross-
species genomics"""
@ -15,6 +15,7 @@ class RAgdex(RPackage):
homepage = "https://bioconductor.org/packages/AGDEX"
git = "https://git.bioconductor.org/packages/AGDEX.git"
version('1.38.0', commit='7e2c1f5f27ccbea6a7157f5122212e40408b74da')
version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf')
version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b')
version('1.28.0', commit='7d78ee424485018b73cd019ceaed7a2ed53adf3f')

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var/spack/repos/builtin/packages/r-agilp/package.py
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@ -7,13 +7,14 @@
class RAgilp(RPackage):
"""Agilent expression array processing package.
"""Agilent expression array processing package
More about what it does (maybe more than one line)"""
More about what it does (maybe more than one line)."""
homepage = "https://bioconductor.org/packages/agilp"
git = "https://git.bioconductor.org/packages/agilp.git"
version('3.22.0', commit='7d089d576752e0526f15a1007e94436089954313')
version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47')
version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61')
version('3.12.0', commit='a86dea1b03b2b56c2c8317d4b10903fb8948ffcb')

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var/spack/repos/builtin/packages/r-agimicrorna/package.py
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@ -8,17 +8,21 @@
class RAgimicrorna(RPackage):
"""Processing and Differential Expression Analysis of Agilent microRNA
chips."""
chips
Processing and Analysis of Agilent microRNA data."""
homepage = "https://bioconductor.org/packages/AgiMicroRna"
git = "https://git.bioconductor.org/packages/AgiMicroRna.git"
version('2.40.0', commit='cfa4acb2215da44767ab3a45845bcd587c309e74')
version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a')
version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8')
version('2.30.0', commit='99b5a8284cfe3e93c3ae85a2436e87101b9599dd')
version('2.28.0', commit='62c4a12f1168c7aa1ab46d2c97090ef71478328e')
version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
depends_on('r+X', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))

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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.
"""AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
This package contains the AIMS implementation. It contains necessary
functions to assign the five intrinsic molecular subtypes (Luminal A,
@ -18,6 +18,7 @@ class RAims(RPackage):
homepage = "https://bioconductor.org/packages/AIMS"
git = "https://git.bioconductor.org/packages/AIMS.git"
version('1.22.0', commit='34a38978b24377abb864eff7683bb36344ff171d')
version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84')
version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f')
version('1.12.0', commit='d7eaa723d19a6aca37df244fd0b3d5426ed0a626')

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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-
@ -24,16 +24,17 @@ class RAldex2(RPackage):
homepage = "https://bioconductor.org/packages/ALDEx2"
git = "https://git.bioconductor.org/packages/ALDEx2.git"
version('1.22.0', commit='ac7f0ab3f094ec52713da7620a27058b14c7181d')
version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f')
version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8')
version('1.12.0', commit='9efde428d22a0be1fe7b6655d45ddce8fcded180')
version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a')
version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-zcompositions', when='@1.22.0:', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-multtest', when='@1.10.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-allelicimbalance/package.py
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@ -7,7 +7,7 @@
class RAllelicimbalance(RPackage):
"""Investigates Allele Specific Expression.
"""Investigates Allele Specific Expression
Provides a framework for allelic specific expression investigation using
RNA-seq data."""
@ -15,6 +15,7 @@ class RAllelicimbalance(RPackage):
homepage = "https://bioconductor.org/packages/AllelicImbalance"
git = "https://git.bioconductor.org/packages/AllelicImbalance.git"
version('1.28.0', commit='ac5d13c9ee0935bf9500ee542792644e752a1fde')
version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3')
version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea')
@ -22,18 +23,29 @@ class RAllelicimbalance(RPackage):
version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r@4.0.0:', when='@1.28.0:', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-bsgenome', type=('build', 'run'))
depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-gviz', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-latticeextra', type=('build', 'run'))
@ -41,15 +53,3 @@ class RAllelicimbalance(RPackage):
depends_on('r-seqinr', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-alpine/package.py
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@ -7,7 +7,7 @@
class RAlpine(RPackage):
"""alpine.
"""alpine
Fragment sequence bias modeling and correction for RNA-seq transcript
abundance estimation."""
@ -15,6 +15,7 @@ class RAlpine(RPackage):
homepage = "https://bioconductor.org/packages/alpine"
git = "https://git.bioconductor.org/packages/alpine.git"
version('1.16.0', commit='aee397774ac6cd17ad45dc05be14c526647f3c13')
version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c')
version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4')
version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274')

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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
@ -19,6 +19,7 @@ class RAlsace(RPackage):
homepage = "https://bioconductor.org/packages/alsace"
git = "https://git.bioconductor.org/packages/alsace.git"
version('1.26.0', commit='40a76404acb1466723a78a55d87c67eec3e6f306')
version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389')
version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191')
version('1.16.0', commit='5a51a19aeccbba0123222201cb7a228559f29653')

5
var/spack/repos/builtin/packages/r-altcdfenvs/package.py
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@ -7,13 +7,14 @@
class RAltcdfenvs(RPackage):
"""alternative CDF environments (aka probeset mappings).
"""alternative CDF environments (aka probeset mappings)
Convenience data structures and functions to handle cdfenvs"""
Convenience data structures and functions to handle cdfenvs."""
homepage = "https://bioconductor.org/packages/altcdfenvs"
git = "https://git.bioconductor.org/packages/altcdfenvs.git"
version('2.52.0', commit='21329abf82eae26f84b7c0270e81c8e089c548ce')
version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b')
version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133')
version('2.42.0', commit='00ec6461877a063d938494b8ed0cd273a3b20b85')

1
var/spack/repos/builtin/packages/r-ampliqueso/package.py
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@ -21,6 +21,7 @@ class RAmpliqueso(RPackage):
version('1.16.0', commit='25d2543ff9dedef4f966f999c95cdf87185d3bb3')
version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
depends_on('r+X', type=('build', 'run'))
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-rnaseqmap@2.17.1:', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))

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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
@ -18,6 +18,7 @@ class RAnaquin(RPackage):
homepage = "https://bioconductor.org/packages/Anaquin"
git = "https://git.bioconductor.org/packages/Anaquin.git"
version('2.14.0', commit='d0a34c931a0e72080bff91dacb37dbbe26b45386')
version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601')
version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6')
version('2.4.0', commit='0d6ae80ff622151a782e4774ca274f06024a71d2')

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var/spack/repos/builtin/packages/r-aneufinder/package.py
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@ -7,7 +7,7 @@
class RAneufinder(RPackage):
"""Analysis of Copy Number Variation in Single-Cell-Sequencing Data.
"""Analysis of Copy Number Variation in Single-Cell-Sequencing Data
AneuFinder implements functions for copy-number detection, breakpoint
detection, and karyotype and heterogeneity analysis in single-cell whole
@ -16,6 +16,7 @@ class RAneufinder(RPackage):
homepage = "https://bioconductor.org/packages/AneuFinder"
git = "https://git.bioconductor.org/packages/AneuFinder.git"
version('1.18.0', commit='76ec9af947f97212084ca478e8e82f9e0eb79de9')
version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e')
version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd')
version('1.8.0', commit='36a729d244add5aafbe21c37a1baaea6a50354d3')
@ -23,27 +24,26 @@ class RAneufinder(RPackage):
version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-cowplot', type=('build', 'run'))
depends_on('r-aneufinderdata', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.4.0:1.6.0', type=('build', 'run'))
depends_on('r-biocgenerics@0.31.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-bamsignals', type=('build', 'run'))
depends_on('r-dnacopy', type=('build', 'run'))
depends_on('r-ecp', when='@1.8.0:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-ggdendro', type=('build', 'run'))
depends_on('r-ggrepel', type=('build', 'run'))
depends_on('r-reordercluster', type=('build', 'run'))
depends_on('r-mclust', type=('build', 'run'))
depends_on('r-ecp', when='@1.8.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-aneufinderdata/package.py
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@ -7,7 +7,7 @@
class RAneufinderdata(RPackage):
"""WGSCS Data for Demonstration Purposes.
"""WGSCS Data for Demonstration Purposes
Whole-genome single cell sequencing data for demonstration purposes in
the AneuFinder package."""
@ -15,6 +15,7 @@ class RAneufinderdata(RPackage):
homepage = "https://bioconductor.org/packages/AneuFinderData"
git = "https://git.bioconductor.org/packages/AneuFinderData.git"
version('1.18.0', commit='1bf1657b28fc8c1425e611980a692da952ce3d1e')
version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1')
version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035')
version('1.8.0', commit='4f00f8d5f2e968fea667a7feafc0a4607d6e0c6e')

3
var/spack/repos/builtin/packages/r-annaffy/package.py
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@ -7,7 +7,7 @@
class RAnnaffy(RPackage):
"""Annotation tools for Affymetrix biological metadata.
"""Annotation tools for Affymetrix biological metadata
Functions for handling data from Bioconductor Affymetrix annotation data
packages. Produces compact HTML and text reports including experimental
@ -17,6 +17,7 @@ class RAnnaffy(RPackage):
homepage = "https://bioconductor.org/packages/annaffy"
git = "https://git.bioconductor.org/packages/annaffy.git"
version('1.62.0', commit='ad9c37e0e7e45e0f35c208ce528ba48000b37432')
version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233')
version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484')
version('1.52.0', commit='ef84030163045f702941c8d5a59fbd4a09f30e2c')

6
var/spack/repos/builtin/packages/r-annotate/package.py
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@ -7,13 +7,14 @@
class RAnnotate(RPackage):
"""Annotation for microarrays.
"""Annotation for microarrays
Using R enviroments for annotation."""
homepage = "https://bioconductor.org/packages/annotate"
git = "https://git.bioconductor.org/packages/annotate.git"
version('1.68.0', commit='98cdb12c612b3f3fc06329a89a1ffb0a92b555c0')
version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd')
version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16')
version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc')
@ -27,4 +28,5 @@ class RAnnotate(RPackage):
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-httr', when='@1.68.0:', type=('build', 'run'))
depends_on('r-rcurl', when='@:1.62.0', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-annotationdbi/package.py
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@ -7,7 +7,7 @@
class RAnnotationdbi(RPackage):
"""Manipulation of SQLite-based annotations in Bioconductor.
"""Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based
annotation data packages."""
@ -15,6 +15,7 @@ class RAnnotationdbi(RPackage):
homepage = "https://bioconductor.org/packages/AnnotationDbi"
git = "https://git.bioconductor.org/packages/AnnotationDbi.git"
version('1.52.0', commit='c4e0ca9bd65362ae9cad6a98d90f54267b0ae838')
version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9')
version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac')
version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3')
@ -23,12 +24,10 @@ class RAnnotationdbi(RPackage):
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run'))
depends_on('r-biobase@1.17.0:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-annotationfilter/package.py
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@ -7,7 +7,7 @@
class RAnnotationfilter(RPackage):
"""Facilities for Filtering Bioconductor Annotation Resources.
"""Facilities for Filtering Bioconductor Annotation Resources
This package provides class and other infrastructure to implement
filters for manipulating Bioconductor annotation resources. The filters
@ -16,6 +16,7 @@ class RAnnotationfilter(RPackage):
homepage = "https://bioconductor.org/packages/AnnotationFilter"
git = "https://git.bioconductor.org/packages/AnnotationFilter.git"
version('1.14.0', commit='6ee3a13ed93a535ed452cbc8c118151a2cbb732c')
version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed')
version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3')
version('1.4.0', commit='acbd3309f478843a7899bd9773af5f19f986b829')

3
var/spack/repos/builtin/packages/r-annotationforge/package.py
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@ -7,7 +7,7 @@
class RAnnotationforge(RPackage):
"""Tools for building SQLite-based annotation data packages.
"""Tools for building SQLite-based annotation data packages
Provides code for generating Annotation packages and their databases.
Packages produced are intended to be used with AnnotationDbi."""
@ -15,6 +15,7 @@ class RAnnotationforge(RPackage):
homepage = "https://bioconductor.org/packages/AnnotationForge"
git = "https://git.bioconductor.org/packages/AnnotationForge.git"
version('1.32.0', commit='3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7')
version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e')
version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d')
version('1.22.2', commit='8eafb1690c1c02f6291ccbb38ac633d54b8217f8')

17
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
@ -21,6 +21,7 @@ class RAnnotationhub(RPackage):
homepage = "https://bioconductor.org/packages/AnnotationHub"
git = "https://git.bioconductor.org/packages/AnnotationHub.git"
version('2.22.0', commit='3ab7dceebbc31ac14ca931f66c662cf9538b7d0a')
version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed')
version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12')
version('2.12.1', commit='471407bd9cdc612e01deb071c91bd9e5f1ea5e55')
@ -28,18 +29,16 @@ class RAnnotationhub(RPackage):
version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'))
depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run'))
depends_on('r-biocversion', when='@2.22.0:', type=('build', 'run'))
depends_on('r-curl', when='@2.10.1:', type=('build', 'run'))
depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run'))
depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-interactivedisplaybase', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-yaml', type=('build', 'run'))
depends_on('r-curl', when='@2.10.1:', type=('build', 'run'))
depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run'))
depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run'))
depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run'))
depends_on('r-dplyr', when='@2.16.1:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@:2.16.1', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-aroma-light/package.py
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@ -7,17 +7,23 @@
class RAromaLight(RPackage):
"""Methods for microarray analysis that take basic data types such as
"""Light-Weight Methods for Normalization and Visualization of Microarray
Data using Only Basic R Data Types
Methods for microarray analysis that take basic data types such as
matrices and lists of vectors. These methods can be used standalone, be
utilized in other packages, or be wrapped up in higher-level classes."""
homepage = "https://www.aroma-project.org/"
git = "https://git.bioconductor.org/packages/aroma.light"
version('3.20.0', commit='02cde7fa166259bce73c396a87dca2ecc8249c39')
version('3.16.0', commit='fc16179fc4bee8954c5415d7cd13e3112b75b4fd')
depends_on('r@2.15.2:', type=('build', 'run'))
depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
depends_on('r-r-oo@1.22.0:', type=('build', 'run'))
depends_on('r-r-oo@1.23.0:', when='@3.20.0:', type=('build', 'run'))
depends_on('r-r-utils@2.9.0:', type=('build', 'run'))
depends_on('r-matrixstats@0.54.0:', type=('build', 'run'))
depends_on('r-matrixstats@0.55.0:', when='@3.20.0:', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-bamsignals/package.py
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@ -7,7 +7,7 @@
class RBamsignals(RPackage):
"""Extract read count signals from bam files.
"""Extract read count signals from bam files
This package allows to efficiently obtain count vectors from indexed bam
files. It counts the number of reads in given genomic ranges and it
@ -17,6 +17,7 @@ class RBamsignals(RPackage):
homepage = "https://bioconductor.org/packages/bamsignals"
git = "https://git.bioconductor.org/packages/bamsignals.git"
version('1.22.0', commit='5f533969c84212406bcb3ebf725ebb6d77e9947a')
version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657')
version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d')
version('1.12.1', commit='06b6282df377cf9db58e8016be4ac8ddcc960939')
@ -30,7 +31,9 @@ class RBamsignals(RPackage):
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-rhtslib', type=('build', 'run'))
depends_on('r-rhtslib@1.12.1:', when='@1.12.1:', type=('build', 'run'))
depends_on('r-rhtslib@1.13.1:', when='@1.14.0:', type=('build', 'run'))
depends_on('gmake', type='build')
# this is no listed but is needed
depends_on('curl')

25
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
@ -18,23 +18,24 @@ class RBeachmat(RPackage):
homepage = "https://bioconductor.org/packages/beachmat"
git = "https://git.bioconductor.org/packages/beachmat.git"
version('2.6.4', commit='7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb')
version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab')
version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a')
version('1.2.1', commit='ebae81772045a314e568c2f7d73ea3b27e7bf7d8')
version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run'))
depends_on('r-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@3.5:', when='@1.2.1:1.4.0', type=('build', 'run'))
depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run'))
depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run'))
depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run'))
depends_on('r-hdf5array@1.9.5:', when='@1.4.0', type=('build', 'run'))
depends_on('r-delayedarray@0.7.38:', when='@1.4.0', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run'))

4
var/spack/repos/builtin/packages/r-biobase/package.py
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@ -7,7 +7,7 @@
class RBiobase(RPackage):
"""Biobase: Base functions for Bioconductor.
"""Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R
functions."""
@ -15,6 +15,7 @@ class RBiobase(RPackage):
homepage = "https://bioconductor.org/packages/Biobase"
git = "https://git.bioconductor.org/packages/Biobase.git"
version('2.50.0', commit='9927f90d0676382f2f99e099d8d2c8e2e6f1b4de')
version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3')
version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d')
version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5')
@ -23,5 +24,4 @@ class RBiobase(RPackage):
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.3.2:', type=('build', 'run'))
depends_on('r-biocgenerics@0.27.1:', when='@2.42.0:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-biocfilecache/package.py
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@ -7,7 +7,7 @@
class RBiocfilecache(RPackage):
"""Manage Files Across Sessions.
"""Manage Files Across Sessions
This package creates a persistent on-disk cache of files that the user
can add, update, and retrieve. It is useful for managing resources (such
@ -17,6 +17,7 @@ class RBiocfilecache(RPackage):
homepage = "https://bioconductor.org/packages/BiocFileCache"
git = "https://git.bioconductor.org/packages/BiocFileCache.git"
version('1.14.0', commit='cdcde4b59ae73dda12aa225948dbd0a058d9be6d')
version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0')
version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba')
version('1.4.0', commit='a2c473d17f78899c7899b9638faea8c30735eb80')
@ -24,11 +25,10 @@ class RBiocfilecache(RPackage):
version('1.0.1', commit='dbf4e8dd4d8d9f475066cd033481efe95c56df75')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-dbplyr@1.0.0:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-dbplyr@1.0.0:', when='@1.2.3:', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rappdirs', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-curl', when='@1.6.0:', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))

4
var/spack/repos/builtin/packages/r-biocgenerics/package.py
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@ -7,13 +7,14 @@
class RBiocgenerics(RPackage):
"""S4 generic functions used in Bioconductor.
"""S4 generic functions used in Bioconductor
The package defines S4 generic functions used in Bioconductor."""
homepage = "https://bioconductor.org/packages/BiocGenerics"
git = "https://git.bioconductor.org/packages/BiocGenerics.git"
version('0.36.0', commit='0d5d169d7d64d648a22f9043837c93bc784e71ed')
version('0.34.0', commit='f7c2020')
version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8')
version('0.28.0', commit='041fc496504f2ab1d4d863fffb23372db214394b')
@ -22,3 +23,4 @@ class RBiocgenerics(RPackage):
version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run'))
depends_on('r@4.0.0:', when='@0.36.0:', type=('build', 'run'))

11
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
@ -22,14 +22,15 @@ class RBiocneighbors(RPackage):
homepage = "https://bioconductor.org/packages/BiocNeighbors"
git = "https://git.bioconductor.org/packages/BiocNeighbors.git"
version('1.8.2', commit='889bc91f8cb45d210b47ae5c0b9cfb86fb071ca2')
version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273')
version('1.0.0', commit='e252fc04b6d22097f2c5f74406e77d85e7060770')
depends_on('r@3.5:', when='@1.0.0', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-rcppannoy', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.2.0:', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-matrix', when='@1.8.2:', type=('build', 'run'))
depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run'))
depends_on('r-rcppannoy', when='@:1.2.0', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.2.0', type=('build', 'run'))

4
var/spack/repos/builtin/packages/r-biocparallel/package.py
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@ -7,7 +7,7 @@
class RBiocparallel(RPackage):
"""Bioconductor facilities for parallel evaluation.
"""Bioconductor facilities for parallel evaluation
This package provides modified versions and novel implementation of
functions for parallel evaluation, tailored to use with Bioconductor
@ -16,6 +16,7 @@ class RBiocparallel(RPackage):
homepage = "https://bioconductor.org/packages/BiocParallel"
git = "https://git.bioconductor.org/packages/BiocParallel.git"
version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f')
version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e')
version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4')
version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299')
@ -24,5 +25,4 @@ class RBiocparallel(RPackage):
depends_on('r-futile-logger', type=('build', 'run'))
depends_on('r-snow', type=('build', 'run'))
depends_on('r-bh', when='@1.12.0:', type=('build', 'run'))

3
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
@ -18,6 +18,7 @@ class RBiocsingular(RPackage):
homepage = "https://bioconductor.org/packages/BiocSingular"
git = "https://git.bioconductor.org/packages/BiocSingular.git"
version('1.6.0', commit='11baf1080d6f791439cd5d97357589d6451643d9')
version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833')
depends_on('r-biocgenerics', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-biocstyle/package.py
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@ -7,7 +7,7 @@
class RBiocstyle(RPackage):
"""Standard styles for vignettes and other Bioconductor documents.
"""Standard styles for vignettes and other Bioconductor documents
Provides standard formatting styles for Bioconductor PDF and HTML
documents. Package vignettes illustrate use and functionality."""
@ -15,15 +15,17 @@ class RBiocstyle(RPackage):
homepage = "https://bioconductor.org/packages/BiocStyle"
git = "https://git.bioconductor.org/packages/BiocStyle.git"
version('2.18.1', commit='956f0654e8e18882ba09305742401128c9c7d47d')
version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498')
version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70')
version('2.8.2', commit='3210c19ec1e5e0ed8d5a2d31da990aa47b42dbd8')
version('2.6.1', commit='5ff52cbb439a45575d0f58c4f7a83195a8b7337b')
version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
depends_on('r+X', type=('build', 'run'))
depends_on('r-bookdown', type=('build', 'run'))
depends_on('r-knitr@1.12:', type=('build', 'run'))
depends_on('r-knitr@1.30:', when='@2.18.1:', type=('build', 'run'))
depends_on('r-rmarkdown@1.2:', type=('build', 'run'))
depends_on('r-yaml', type=('build', 'run'))
depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run'))

20
var/spack/repos/builtin/packages/r-biocversion/package.py Normal file
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@ -0,0 +1,20 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocversion(RPackage):
"""Set the appropriate version of Bioconductor packages
This package provides repository information for the appropriate
version of Bioconductor."""
homepage = "https://bioconductor.org/packages/BiocVersion/"
git = "https://git.bioconductor.org/packages/BiocVersion"
version('3.12.0', commit='23b971963c6b73550a7e330dab5a046d58ce0223')
depends_on('r@4.0.0:', type=('build', 'run'))

10
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
@ -25,6 +25,7 @@ class RBiomart(RPackage):
homepage = "https://bioconductor.org/packages/biomaRt"
git = "https://git.bioconductor.org/packages/biomaRt.git"
version('2.46.2', commit='90d6abfdfa04259006f7b47efb10271ada76aec1')
version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68')
version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658')
version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f')
@ -32,9 +33,12 @@ class RBiomart(RPackage):
version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
depends_on('r-xml', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-progress', when='@2.34.2:', type=('build', 'run'))
depends_on('r-stringr', when='@2.34.2:', type=('build', 'run'))
depends_on('r-httr', when='@2.34.2:', type=('build', 'run'))
depends_on('r-openssl', when='@2.46.2:', type=('build', 'run'))
depends_on('r-biocfilecache', when='@2.46.2:', type=('build', 'run'))
depends_on('r-rappdirs', when='@2.46.2:', type=('build', 'run'))
depends_on('r-xml2', when='@2.46.2:', type=('build', 'run'))
depends_on('r-rcurl', when='@:2.40.5', type=('build', 'run'))

3
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
@ -22,6 +22,7 @@ class RBiomformat(RPackage):
homepage = "https://bioconductor.org/packages/biomformat"
git = "https://git.bioconductor.org/packages/biomformat.git"
version('1.18.0', commit='dc18859c139f4d76805adb6f01e199573cdd5a8b')
version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a')
version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09')
version('1.8.0', commit='acd207377b24e4d8310eaff06c16dcfe6c04509a')

28
var/spack/repos/builtin/packages/r-biostrings/package.py
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@ -7,7 +7,7 @@
class RBiostrings(RPackage):
"""Efficient manipulation of biological strings.
"""Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and
other utilities, for fast manipulation of large biological sequences or
@ -16,6 +16,7 @@ class RBiostrings(RPackage):
homepage = "https://bioconductor.org/packages/Biostrings"
git = "https://git.bioconductor.org/packages/Biostrings.git"
version('2.58.0', commit='0ec1a5455d5e9eebd14b26228906bb04e2abb197')
version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5')
version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2')
version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b')
@ -23,18 +24,19 @@ class RBiostrings(RPackage):
version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
depends_on('r@2.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges@2.9.18:', when='@2.44.2:2.46.0', type=('build', 'run'))
depends_on('r-xvector@0.11.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@2.48.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@2.48.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run'))
depends_on('r-xvector@0.21.4:', when='@2.50.2:', type=('build', 'run'))
depends_on('r-iranges', when='@2.50.2:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.6:', type=('build', 'run'))
depends_on('r-biocgenerics@0.31.5:', when='@2.58.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-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-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'))

6
var/spack/repos/builtin/packages/r-biovizbase/package.py
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@ -7,7 +7,7 @@
class RBiovizbase(RPackage):
"""Basic graphic utilities for visualization of genomic data..
"""Basic graphic utilities for visualization of genomic data.
The biovizBase package is designed to provide a set of utilities, color
schemes and conventions for genomic data. It serves as the base for
@ -17,6 +17,7 @@ class RBiovizbase(RPackage):
homepage = "https://bioconductor.org/packages/biovizBase"
git = "https://git.bioconductor.org/packages/biovizBase.git"
version('1.38.0', commit='d0f3362e0ad0e90b4b1d3e47b13ed57907d03403')
version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82')
version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063')
@ -24,12 +25,14 @@ class RBiovizbase(RPackage):
version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.38.0:', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-dichromat', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-s4vectors@0.23.19:', when='@1.38.0:', type=('build', 'run'))
depends_on('r-iranges@1.99.28:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.5.14:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
@ -42,5 +45,4 @@ class RBiovizbase(RPackage):
depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
depends_on('r-annotationfilter@0.99.8:', type=('build', 'run'))
depends_on('r-rlang', when='@1.28.2:', type=('build', 'run'))

15
var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
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@ -7,13 +7,22 @@
class RBsgenomeHsapiensUcscHg19(RPackage):
"""Full genome sequences for Homo sapiens (Human) as provided by UCSC
"""Full genome sequences for Homo sapiens (UCSC version hg19, based on
GRCh37.p13)
Full genome sequences for Homo sapiens (Human) as provided by UCSC
(hg19, Feb. 2009) and stored in Biostrings objects."""
# This is a bioconductor package but there is no available git repo.
homepage = "http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html"
homepage = "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/"
url = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz"
version('1.4.0', sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8')
version('1.4.3',
sha256='5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a',
url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz')
version('1.4.0',
sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8',
url='https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz')
depends_on('r-bsgenome@1.33.5:', type=('build', 'run'))
depends_on('r-bsgenome@1.54.0:', when='@1.4.3:', type=('build', 'run'))

30
var/spack/repos/builtin/packages/r-bsgenome/package.py
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@ -8,11 +8,14 @@
class RBsgenome(RPackage):
"""Software infrastructure for efficient representation of full genomes and
their SNPs."""
their SNPs
Infrastructure shared by all the Biostrings-based genome data packages."""
homepage = "https://bioconductor.org/packages/BSgenome"
git = "https://git.bioconductor.org/packages/BSgenome.git"
version('1.58.0', commit='3a4926e03a7a1d7140a10c1b2bf6090808470145')
version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b')
version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9')
version('1.48.0', commit='092a1b90482ace329cbd8ca2a338e91449acb93e')
@ -22,21 +25,22 @@ class RBsgenome(RPackage):
depends_on('r@2.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))
depends_on('r-iranges@2.1.33:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-iranges@2.1.33:', 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-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.25.6:', when='@1.58.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-matrixstats', when='@1.58.0:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.29.3:', when='@1.58.0:', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-bsseq/package.py
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@ -7,49 +7,52 @@
class RBsseq(RPackage):
"""A collection of tools for analyzing and visualizing bisulfite sequencing
"""Analyze, manage and store bisulfite sequencing data
A collection of tools for analyzing and visualizing bisulfite sequencing
data."""
homepage = "https://github.com/kasperdanielhansen/bsseq"
git = "https://git.bioconductor.org/packages/bsseq"
version('1.26.0', commit='fae32292687625012a2938a48c93df55ad4257b5')
version('1.24.4', commit='8fe7a03')
version('1.22.0', commit='d4f7301')
version('1.20.0', commit='07e398b')
depends_on('r@3.5:', type=('build', 'run'))
depends_on('r@4.0:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', type=('build', 'run'))
depends_on('r-genomicranges@1.33.6:', when='@1.24.4:', type=('build', 'run'))
depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.18:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.17.4:', when='@1.24.4:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.19.5:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'))
depends_on('r-iranges@2.22.2:', when='@1.24.4:', type=('build', 'run'))
depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-gtools', type=('build', 'run'))
depends_on('r-data-table@1.11.8:', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.23.11:', when='@1.22.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.25.14:', when='@1.24.4', type=('build', 'run'))
depends_on('r-s4vectors@0.25.14:', when='@1.24.4:', type=('build', 'run'))
depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-r-utils@2.0.0:', type=('build', 'run'))
depends_on('r-delayedmatrixstats@1.5.2:', type=('build', 'run'))
depends_on('r-permute', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-delayedarray@0.9.8:', type=('build', 'run'))
depends_on('r-delayedarray@0.15.16:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-bsgenome', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-hdf5array@1.11.9:', type=('build', 'run'))
depends_on('r-hdf5array@1.15.19:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-rhdf5', type=('build', 'run'))
depends_on('r-beachmat', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-bumphunter/package.py
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@ -7,13 +7,14 @@
class RBumphunter(RPackage):
"""Bump Hunter.
"""Bump Hunter
Tools for finding bumps in genomic data"""
homepage = "https://bioconductor.org/packages/bumphunter"
git = "https://git.bioconductor.org/packages/bumphunter.git"
version('1.32.0', commit='b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0')
version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa')
version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b')
version('1.22.0', commit='fb71b193f4ef7fa12d100441e6eb498765f7afde')
@ -21,6 +22,8 @@ class RBumphunter(RPackage):
version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges@2.3.23:', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
@ -34,7 +37,3 @@ class RBumphunter(RPackage):
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-category/package.py
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@ -7,7 +7,7 @@
class RCategory(RPackage):
"""Category Analysis.
"""Category Analysis
A collection of tools for performing category (gene set enrichment)
analysis."""
@ -15,6 +15,7 @@ class RCategory(RPackage):
homepage = "https://bioconductor.org/packages/Category"
git = "https://git.bioconductor.org/packages/Category.git"
version('2.56.0', commit='ad478caa9d693dbc2770608e79dd852375b9a223')
version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9')
version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5')
version('2.46.0', commit='c8aeee4dee3fb120f25e0647dd06e895a3ffbc2a')

24
var/spack/repos/builtin/packages/r-clusterprofiler/package.py
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@ -8,7 +8,7 @@
class RClusterprofiler(RPackage):
"""statistical analysis and visualization of functional profiles for genes
and gene clusters.
and gene clusters
This package implements methods to analyze and visualize functional
profiles (GO and KEGG) of gene and gene clusters."""
@ -16,6 +16,7 @@ class RClusterprofiler(RPackage):
homepage = "https://bioconductor.org/packages/clusterProfiler"
git = "https://git.bioconductor.org/packages/clusterProfiler.git"
version('3.18.0', commit='064a6e612ce27e260e33af78b907bee4065ff821')
version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c')
version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36')
@ -23,20 +24,23 @@ class RClusterprofiler(RPackage):
version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
depends_on('r@3.3.1:', type=('build', 'run'))
depends_on('r-dose@3.1.3:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-downloader', when='@3.18.0:', type=('build', 'run'))
depends_on('r-dose@3.1.3:', type=('build', 'run'))
depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run'))
depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-dose@3.13.1:', when='@3.18.0:', type=('build', 'run'))
depends_on('r-dplyr', when='@3.18.0:', type=('build', 'run'))
depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-enrichplot@1.9.3:', when='@3.18.0:', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-rlang', when='@3.18.0:', type=('build', 'run'))
depends_on('r-rvcheck', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-ggplot2', when='@:3.12.0', type=('build', 'run'))

10
var/spack/repos/builtin/packages/r-cner/package.py
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@ -7,7 +7,7 @@
class RCner(RPackage):
"""CNE Detection and Visualization.
"""CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of
conserved noncoding elements."""
@ -15,6 +15,7 @@ class RCner(RPackage):
homepage = "https://bioconductor.org/packages/CNEr"
git = "https://git.bioconductor.org/packages/CNEr.git"
version('1.26.0', commit='e5e582da6feeae0618c4460f16ece724215e3b20')
version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5')
version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606')
version('1.16.1', commit='a2bec4b98d5938709f959a69c151f553ef357941')
@ -22,14 +23,16 @@ class RCner(RPackage):
version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017')
depends_on('r@3.2.2:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run'))
depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
depends_on('r-dbi@0.6:', type=('build', 'run'))
depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run'))
depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.5:', type=('build', 'run'))
depends_on('r-xvector@0.5.4:', type=('build', 'run'))
depends_on('r-genomicalignments@1.1.9:', type=('build', 'run'))
depends_on('r-dbi@0.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges@2.5.27:', type=('build', 'run'))
depends_on('r-readr@0.2.2:', type=('build', 'run'))
@ -41,6 +44,3 @@ class RCner(RPackage):
depends_on('r-go-db@3.3.0:', type=('build', 'run'))
depends_on('r-r-utils@2.3.0:', type=('build', 'run'))
depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run'))
depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run'))

6
var/spack/repos/builtin/packages/r-codex/package.py
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@ -7,7 +7,10 @@
class RCodex(RPackage):
"""A normalization and copy number variation calling procedure for whole
"""A Normalization and Copy Number Variation Detection Method for Whole
Exome Sequencing
A normalization and copy number variation calling procedure for whole
exome DNA sequencing data. CODEX relies on the availability of multiple
samples processed using the same sequencing pipeline for normalization, and
does not require matched controls. The normalization model in CODEX
@ -20,6 +23,7 @@ class RCodex(RPackage):
homepage = "http://www.bioconductor.org/packages/release/bioc/html/CODEX.html"
git = "https://git.bioconductor.org/packages/CODEX"
version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb')
version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
depends_on('r@3.2.3:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-complexheatmap/package.py
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@ -7,7 +7,7 @@
class RComplexheatmap(RPackage):
"""Make Complex Heatmaps.
"""Make Complex Heatmaps
Complex heatmaps are efficient to visualize associations between
different sources of data sets and reveal potential patterns. Here the
@ -17,6 +17,7 @@ class RComplexheatmap(RPackage):
homepage = "https://bioconductor.org/packages/ComplexHeatmap"
git = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
version('2.6.2', commit='0383bada2c76dc3dde71cf6a625016b619aec4d3')
version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4')
version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f')
version('1.18.1', commit='be0dd9d666a219c61335efe0dac50b2eed2a8825')
@ -25,16 +26,18 @@ class RComplexheatmap(RPackage):
depends_on('r@3.1.2:', type=('build', 'run'))
depends_on('r-circlize@0.3.4:', type=('build', 'run'))
depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run'))
depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-getoptlong', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', type=('build', 'run'))
depends_on('r-globaloptions@0.0.10:', type=('build', 'run'))
depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', type=('build', 'run'))
depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-clue', when='@2.0.0:', type=('build', 'run'))
depends_on('r-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'))

3
var/spack/repos/builtin/packages/r-ctc/package.py
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@ -7,7 +7,7 @@
class RCtc(RPackage):
"""Cluster and Tree Conversion..
"""Cluster and Tree Conversion.
Tools for export and import classification trees and clusters to other
programs"""
@ -15,6 +15,7 @@ class RCtc(RPackage):
homepage = "https://bioconductor.org/packages/ctc"
git = "https://git.bioconductor.org/packages/ctc.git"
version('1.64.0', commit='35dbe620a21056b8f69890e6f9a7c320528d8621')
version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb')
version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f')
version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e')

6
var/spack/repos/builtin/packages/r-decipher/package.py
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@ -7,11 +7,14 @@
class RDecipher(RPackage):
"""Tools for curating, analyzing, and manipulating biological sequences."""
"""Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences."""
homepage = "https://bioconductor.org/packages/DECIPHER"
git = "https://git.bioconductor.org/packages/DECIPHER.git"
version('2.18.1', commit='6a708421550e6705d05e2fb50a0f5ab4f9041cb0')
version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f')
version('2.10.2', commit='db7b017c9050a7ec1d4daa15352994890095e9c3')
version('2.8.1', commit='35aa66f48e06b93a98d1060c90c44d34ce05ccd9')
@ -19,6 +22,7 @@ class RDecipher(RPackage):
version('2.4.0', commit='1a57b8e4c7d7dec1c233f79c9a88d3705e0ad432')
depends_on('r@3.3.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@2.18.1:', type=('build', 'run'))
depends_on('r-biostrings@2.35.12:', type=('build', 'run'))
depends_on('r-rsqlite@1.1:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))

36
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
@ -21,6 +21,7 @@ class RDelayedarray(RPackage):
homepage = "https://bioconductor.org/packages/DelayedArray"
git = "https://git.bioconductor.org/packages/DelayedArray.git"
version('0.16.1', commit='c95eba771ad3fee1b49ec38c51cd8fd1486feadc')
version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a')
version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f')
version('0.6.6', commit='bdb0ac0eee71edd40ccca4808f618fa77f595a64')
@ -28,21 +29,20 @@ class RDelayedarray(RPackage):
version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors@0.14.3:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-matrixstats', type=('build', 'run'))
depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', type=('build', 'run'))
depends_on('r-biocparallel', when='@0.6.6:', type=('build', 'run'))
depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.15:', when='@0.8.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.21.7:', when='@0.10.0:', type=('build', 'run'))
depends_on('r-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run'))
depends_on('r-matrix', when='@0.10.0:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run'))
depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.31.5:', when='@0.16.1:', type=('build', 'run'))
depends_on('r-matrixgenerics@1.1.3:', when='@0.16.1:', type=('build', 'run'))
depends_on('r-s4vectors@0.14.3:', type=('build', 'run'))
depends_on('r-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-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'))

23
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
@ -16,26 +16,29 @@ class RDelayedmatrixstats(RPackage):
for subsetted calculations such that both memory usage and processing
time is minimized."""
homepage = "https://bioconductor.org/packages/DelayedMatrixStats"
homepage = "https://github.com/PeteHaitch/DelayedMatrixStats"
git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git"
version('1.12.3', commit='2b3091dfa9b3bab914e3a4157182063714ba86ae')
version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d')
version('1.4.0', commit='eb5b390ef99651fe87a346848f807de95afe8971')
version('1.2.0', commit='de868e730be6280dfad41a280ab09f4d3083c9ac')
version('1.0.3', commit='e29a3444980ff727c5b12286884b06dfaebf5b5b')
depends_on('r-matrixgenerics', when='@1.12.2:', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run'))
depends_on('r-delayedarray@0.15.3:', when='@1.12.2:', type=('build', 'run'))
depends_on('r-matrixstats@0.53.1:', type=('build', 'run'))
depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run'))
depends_on('r-matrixstats@0.56.0:', when='@1.12.2:', type=('build', 'run'))
depends_on('r-sparsematrixstats', when='@1.12.2:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run'))
depends_on('r-hdf5array@1.17.2:', when='@1.12.2:', type=('build', 'run'))
depends_on('r-biocparallel', when='@1.4.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run'))
depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-deseq/package.py
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@ -8,7 +8,7 @@
class RDeseq(RPackage):
"""Differential gene expression analysis based on the negative binomial
distribution.
distribution
Estimate variance-mean dependence in count data from high-throughput
sequencing assays and test for differential expression based on a model
@ -17,6 +17,7 @@ class RDeseq(RPackage):
homepage = "https://bioconductor.org/packages/DESeq"
git = "https://git.bioconductor.org/packages/DESeq.git"
version('1.42.0', commit='da76bc64e8c4073b58eaf1c93aa4e89bec5c4e50')
version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e')
version('1.34.1', commit='e86f1b03a30bc02de4bfd4a0759af2f65cb48c62')
version('1.32.0', commit='e3d623b815b53d79eae7cdd09d097cc6098d28c9')

4
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('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77')
version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce')
version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
@ -24,6 +25,7 @@ class RDeseq2(RPackage):
version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb')
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-s4vectors@0.23.18:', when='@1.30.0:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run'))

3
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
@ -19,6 +19,7 @@ class RDirichletmultinomial(RPackage):
homepage = "https://bioconductor.org/packages/DirichletMultinomial"
git = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
version('1.32.0', commit='6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16')
version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f')
version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35')
version('1.22.0', commit='5864f4298105d12f345f27df77ad13bae4061ca5')

3
var/spack/repos/builtin/packages/r-dnacopy/package.py
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@ -7,7 +7,7 @@
class RDnacopy(RPackage):
"""DNA copy number data analysis.
"""DNA copy number data analysis
Implements the circular binary segmentation (CBS) algorithm to segment
DNA copy number data and identify genomic regions with abnormal copy
@ -16,6 +16,7 @@ class RDnacopy(RPackage):
homepage = "https://bioconductor.org/packages/DNAcopy"
git = "https://git.bioconductor.org/packages/DNAcopy.git"
version('1.64.0', commit='01650266ea7a4e5c600de545fe70a1103e79b2d8')
version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23')
version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a')
version('1.54.0', commit='fe2657936afbce8ee03221461dff4265e3ded4c4')

5
var/spack/repos/builtin/packages/r-do-db/package.py
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@ -7,7 +7,9 @@
class RDoDb(RPackage):
"""A set of annotation maps describing the entire Disease
"""A set of annotation maps describing the entire Disease Ontology
A set of annotation maps describing the entire Disease
Ontology assembled using data from DO."""
homepage = "https://bioconductor.org/packages/DO.db/"
@ -15,4 +17,5 @@ class RDoDb(RPackage):
version('2.9', sha256='762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881')
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))

12
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
@ -19,6 +19,7 @@ class RDose(RPackage):
homepage = "https://bioconductor.org/packages/DOSE"
git = "https://git.bioconductor.org/packages/DOSE.git"
version('3.16.0', commit='a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd')
version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3')
version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639')
version('3.6.1', commit='f2967f0482cea39222bfd15767d0f4a5994f241b')
@ -26,18 +27,17 @@ class RDose(RPackage):
version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
depends_on('r@3.3.1:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@3.16.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-do-db', type=('build', 'run'))
depends_on('r-fgsea', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-gosemsim@2.0.0:', type=('build', 'run'))
depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors', when='@:3.10.2', type=('build', 'run'))
depends_on('r-scales', when='@3.2.0:3.4.0', type=('build', 'run'))
depends_on('r-rvcheck', when='@3.4.0', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run'))
depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run'))

5
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
@ -19,12 +19,13 @@ class RDss(RPackage):
homepage = "http://bioconductor.org/packages/DSS/"
git = "https://git.bioconductor.org/packages/DSS"
version('2.38.0', commit='82e65b92e6e227f1f99620362db8b03059e07e98')
version('2.36.0', commit='841c7ed')
version('2.34.0', commit='f9819c7')
version('2.32.0', commit='ffb502d')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-bsseq', type=('build', 'run'))
depends_on('r-biocparallel', when='@2.36.0:', type=('build', 'run'))
depends_on('r-bsseq', type=('build', 'run'))
depends_on('r-delayedarray', when='@2.36.0:', type=('build', 'run'))

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
@ -20,6 +20,7 @@ class REdger(RPackage):
homepage = "https://bioconductor.org/packages/edgeR"
git = "https://git.bioconductor.org/packages/edgeR.git"
version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a')
version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d')
version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902')
@ -27,10 +28,9 @@ class REdger(RPackage):
version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run'))
depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run'))
depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run'))
depends_on('r-limma@3.41.5:', when='@3.32.1:', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run'))

28
var/spack/repos/builtin/packages/r-enrichplot/package.py
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@ -7,7 +7,7 @@
class REnrichplot(RPackage):
"""Visualization of Functional Enrichment Result.
"""Visualization of Functional Enrichment Result
The 'enrichplot' package implements several visualization methods for
interpreting functional enrichment results obtained from ORA or GSEA
@ -17,24 +17,30 @@ class REnrichplot(RPackage):
homepage = "https://bioconductor.org/packages/enrichplot"
git = "https://git.bioconductor.org/packages/enrichplot.git"
version('1.10.2', commit='77ee04f60a07cc31151f8f47f8ee64f3a43c9760')
version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e')
version('1.2.0', commit='2eeaafb571d35a106eba8ae7df014f3201066e8b')
version('1.0.2', commit='ba7726fa0d4b581b7514dcbb04889cdbdd75ff29')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.10.2:', type=('build', 'run'))
depends_on('r-cowplot', type=('build', 'run'))
depends_on('r-dose@3.5.1:', type=('build', 'run'))
depends_on('r-dose', type=('build', 'run'))
depends_on('r-dose@3.5.1:', when='@:1.4.0', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-ggraph', type=('build', 'run'))
depends_on('r-ggridges', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-upsetr', type=('build', 'run'))
depends_on('r-europepmc', when='@1.2.0:', type=('build', 'run'))
depends_on('r-ggplotify', when='@1.2.0:', type=('build', 'run'))
depends_on('r-gridextra', when='@1.2.0:', type=('build', 'run'))
depends_on('r-plyr', when='@1.10.2:', type=('build', 'run'))
depends_on('r-purrr', when='@1.2.0:', type=('build', 'run'))
depends_on('r-rcolorbrewer', when='@1.2.0:', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-scatterpie', when='@1.10.2:', type=('build', 'run'))
depends_on('r-shadowtext', when='@1.10.2:', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-magrittr', when='@1.10.2:', type=('build', 'run'))
depends_on('r-ggridges', when='@:1.4.0', type=('build', 'run'))
depends_on('r-upsetr', when='@:1.4.0', type=('build', 'run'))
depends_on('r-annotationdbi', when='@:1.4.0', type=('build', 'run'))
depends_on('r-europepmc', when='@1.2.0:1.4.0', type=('build', 'run'))
depends_on('r-ggplotify', when='@1.2.0:1.4.0', type=('build', 'run'))
depends_on('r-gridextra', when='@1.2.0:1.4.0', type=('build', 'run'))

23
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
@ -25,6 +25,7 @@ class REnsembldb(RPackage):
homepage = "https://bioconductor.org/packages/ensembldb"
git = "https://git.bioconductor.org/packages/ensembldb.git"
version('2.14.0', commit='c7150519ed4ef38e5eac1043209863dbc7be43a1')
version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c')
version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327')
@ -33,8 +34,12 @@ class REnsembldb(RPackage):
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-annotationfilter@0.99.7:', type=('build', 'run'))
depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run'))
depends_on('r-rsqlite@1.1:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
@ -42,19 +47,13 @@ class REnsembldb(RPackage):
depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
depends_on('r-rtracklayer', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run'))
depends_on('r-s4vectors@0.23.10:', when='@2.14.0:', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-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-protgenerics', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))
depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run'))

5
var/spack/repos/builtin/packages/r-exomecopy/package.py
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@ -7,7 +7,9 @@
class RExomecopy(RPackage):
"""Detection of copy number variants (CNV) from exome sequencing samples,
"""Copy number variant detection from exome sequencing read depth
Detection of copy number variants (CNV) from exome sequencing samples,
including unpaired samples. The package implements a hidden Markov model
which uses positional covariates, such as background read depth and
GC-content, to simultaneously normalize and segment the samples into
@ -16,6 +18,7 @@ class RExomecopy(RPackage):
homepage = "http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
git = "https://git.bioconductor.org/packages/exomeCopy"
version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26')
version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')
depends_on('r-iranges@2.5.27:', type=('build', 'run'))

4
var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py
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@ -7,7 +7,9 @@
class RFdbInfiniummethylationHg18(RPackage):
"""Compiled HumanMethylation27 and HumanMethylation450 annotations"""
"""Annotation package for Illumina Infinium DNA methylation probes
Compiled HumanMethylation27 and HumanMethylation450 annotations"""
# This is a bioconductor package but there is no available git repository
homepage = "http://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg18.html"

4
var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py
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@ -7,7 +7,9 @@
class RFdbInfiniummethylationHg19(RPackage):
"""Compiled HumanMethylation27 and HumanMethylation450 annotations."""
"""Annotation package for Illumina Infinium DNA methylation probes
Compiled HumanMethylation27 and HumanMethylation450 annotations."""
# No available git repository
homepage = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg19.html"

5
var/spack/repos/builtin/packages/r-fgsea/package.py
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@ -7,7 +7,7 @@
class RFgsea(RPackage):
"""Fast Gene Set Enrichment Analysis.
"""Fast Gene Set Enrichment Analysis
The package implements an algorithm for fast gene set enrichment
analysis. Using the fast algorithm allows to make more permutations and
@ -17,6 +17,7 @@ class RFgsea(RPackage):
homepage = "https://bioconductor.org/packages/fgsea"
git = "https://git.bioconductor.org/packages/fgsea.git"
version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318')
version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b')
version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d')
@ -30,7 +31,5 @@ class RFgsea(RPackage):
depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-fastmatch', type=('build', 'run'))
depends_on('r-matrix', when='@1.6.0:', type=('build', 'run'))
depends_on('r-bh', when='@1.10.1:', type=('build', 'run'))

8
var/spack/repos/builtin/packages/r-gcrma/package.py
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@ -7,11 +7,14 @@
class RGcrma(RPackage):
"""Background Adjustment Using Sequence Information."""
"""Background Adjustment Using Sequence Information
Background adjustment using sequence information."""
homepage = "https://bioconductor.org/packages/gcrma"
git = "https://git.bioconductor.org/packages/gcrma.git"
version('2.62.0', commit='b91bdf5bf4e875defedb4d4e3e1e75867773287a')
version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224')
version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc')
version('2.52.0', commit='d6e90b05432d2a8b0583d3fed001811ecdf49d7d')
@ -24,6 +27,5 @@ class RGcrma(RPackage):
depends_on('r-affyio@1.13.3:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-biostrings@2.11.32:', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'))
depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@:2.52.0', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-gdsfmt/package.py
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@ -7,7 +7,7 @@
class RGdsfmt(RPackage):
"""R Interface to CoreArray Genomic Data Structure (GDS) Files.
"""R Interface to CoreArray Genomic Data Structure (GDS) Files
This package provides a high-level R interface to CoreArray Genomic Data
Structure (GDS) data files, which are portable across platforms with
@ -25,6 +25,7 @@ class RGdsfmt(RPackage):
homepage = "https://bioconductor.org/packages/gdsfmt"
git = "https://git.bioconductor.org/packages/gdsfmt.git"
version('1.26.1', commit='bd180b21b1ace120035f0da255cbf6f13088f069')
version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00')
version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9')
version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95')

10
var/spack/repos/builtin/packages/r-genefilter/package.py
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@ -7,12 +7,14 @@
class RGenefilter(RPackage):
"""genefilter: methods for filtering genes from high-throughput
experiments."""
"""genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes."""
homepage = "https://bioconductor.org/packages/genefilter"
git = "https://git.bioconductor.org/packages/genefilter.git"
version('1.72.1', commit='b01b00a766982ef7d80b90a252085c8c4f085e1b')
version('1.72.0', commit='8cb0b2e73531a417d53e5625bcf436265cdbe101')
version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf')
version('1.64.0', commit='82e91b7751bae997b9c898c219ea201fd02a8512')
@ -20,9 +22,9 @@ class RGenefilter(RPackage):
version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4')
version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
depends_on('r-biocgenerics@0.31.2:', type=('build', 'run'), when='@1.68.0:')
depends_on('r-s4vectors@0.9.42:', type=('build', 'run'), when='@:1.66.0')
depends_on('r-biocgenerics@0.31.2:', when='@1.68.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotate', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))
depends_on('r-s4vectors@0.9.42:', when='@:1.66.0', type=('build', 'run'))

3
var/spack/repos/builtin/packages/r-genelendatabase/package.py
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@ -7,7 +7,7 @@
class RGenelendatabase(RPackage):
"""Lengths of mRNA transcripts for a number of genomes.
"""Lengths of mRNA transcripts for a number of genomes
Length of mRNA transcripts for a number of genomes and gene ID formats,
largely based on UCSC table browser"""
@ -15,6 +15,7 @@ class RGenelendatabase(RPackage):
homepage = "https://bioconductor.org/packages/geneLenDataBase"
git = "https://git.bioconductor.org/packages/geneLenDataBase.git"
version('1.26.0', commit='2724715ae23a6647d1c0c6e934720aad9377d65e')
version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4')
version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07')
version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198')

3
var/spack/repos/builtin/packages/r-genemeta/package.py
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@ -7,7 +7,7 @@
class RGenemeta(RPackage):
"""MetaAnalysis for High Throughput Experiments.
"""MetaAnalysis for High Throughput Experiments
A collection of meta-analysis tools for analysing high throughput
experimental data"""
@ -15,6 +15,7 @@ class RGenemeta(RPackage):
homepage = "https://bioconductor.org/packages/GeneMeta"
git = "https://git.bioconductor.org/packages/GeneMeta.git"
version('1.62.0', commit='eb4273ff5867e39592f50b97b454fa5e32b4a9bf')
version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d')
version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7')
version('1.52.0', commit='1f21759984a5852c42a19e89ee53ffd72053d49c')

5
var/spack/repos/builtin/packages/r-geneplotter/package.py
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@ -7,11 +7,14 @@
class RGeneplotter(RPackage):
"""Graphics related functions for Bioconductor."""
"""Graphics related functions for Bioconductor
Functions for plotting genomic data."""
homepage = "https://bioconductor.org/packages/geneplotter"
git = "https://git.bioconductor.org/packages/geneplotter.git"
version('1.68.0', commit='f1fea7e468fb24fdfa93ef4493600a4d8d183f69')
version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48')
version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad')
version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde')

3
var/spack/repos/builtin/packages/r-genie3/package.py
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@ -7,7 +7,7 @@
class RGenie3(RPackage):
"""GEne Network Inference with Ensemble of trees.
"""GEne Network Inference with Ensemble of trees
This package implements the GENIE3 algorithm for inferring gene
regulatory networks from expression data."""
@ -15,6 +15,7 @@ class RGenie3(RPackage):
homepage = "https://bioconductor.org/packages/GENIE3"
git = "https://git.bioconductor.org/packages/GENIE3.git"
version('1.12.0', commit='14289cee9bed113ab35ba03bcaac4a30e5784497')
version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502')
version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08')
version('1.2.1', commit='1b56fe8184d521d1bb247f000efe9e2b540604c9')

9
var/spack/repos/builtin/packages/r-genomeinfodb/package.py
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@ -8,7 +8,7 @@
class RGenomeinfodb(RPackage):
"""Utilities for manipulating chromosome names, including modifying them to
follow a particular naming style.
follow a particular naming style
Contains data and functions that define and allow translation between
different chromosome sequence naming conventions (e.g., "chr1" versus
@ -18,6 +18,7 @@ class RGenomeinfodb(RPackage):
homepage = "https://bioconductor.org/packages/GenomeInfoDb"
git = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
version('1.26.2', commit='96dd27a7e3ef476790b1475aab50dbbed7df67a2')
version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265')
version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f')
version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa')
@ -27,9 +28,9 @@ class RGenomeinfodb(RPackage):
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.25.12:', when='@1.26.2:', type=('build', 'run'))
depends_on('r-iranges@1.99.26:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-genomeinfodbdata', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run'))

40
var/spack/repos/builtin/packages/r-genomicalignments/package.py
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@ -7,7 +7,7 @@
class RGenomicalignments(RPackage):
"""Representation and manipulation of short genomic alignments.
"""Representation and manipulation of short genomic alignments
Provides efficient containers for storing and manipulating short genomic
alignments (typically obtained by aligning short reads to a reference
@ -17,6 +17,7 @@ class RGenomicalignments(RPackage):
homepage = "https://bioconductor.org/packages/GenomicAlignments"
git = "https://git.bioconductor.org/packages/GenomicAlignments.git"
version('1.26.0', commit='6c74c74ee53efcd880171126366fee4bd72357bc')
version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab')
version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
@ -26,25 +27,26 @@ class RGenomicalignments(RPackage):
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges@2.5.36:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run'))
depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-iranges@2.5.36:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run'))
depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run'))
depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-biostrings@2.55.7:', when='@1.26.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))

28
var/spack/repos/builtin/packages/r-genomicfeatures/package.py
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@ -7,7 +7,7 @@
class RGenomicfeatures(RPackage):
"""Conveniently import and query gene models.
"""Conveniently import and query gene models
A set of tools and methods for making and manipulating transcript
centric annotations. With these tools the user can easily download the
@ -21,6 +21,7 @@ class RGenomicfeatures(RPackage):
homepage = "https://bioconductor.org/packages/GenomicFeatures"
git = "https://git.bioconductor.org/packages/GenomicFeatures.git"
version('1.42.1', commit='2e82891974138b0e976799d64a8938f0be61284d')
version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555')
version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387')
version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1')
@ -29,29 +30,28 @@ class RGenomicfeatures(RPackage):
depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-iranges@2.9.19:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.25.7:', when='@1.42.1:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-annotationdbi@1.33.15:', type=('build', 'run'))
depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite@2.0:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-biostrings@2.23.3:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.29.24:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-biomart@2.17.1:', type=('build', 'run'))
depends_on('r-biobase@2.15.1:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-rmysql', when='@1.30.3', type=('build', 'run'))
depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run'))

28
var/spack/repos/builtin/packages/r-genomicranges/package.py
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@ -7,7 +7,7 @@
class RGenomicranges(RPackage):
"""Representation and manipulation of genomic intervals.
"""Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations
and alignments is playing a central role when it comes to analyzing
@ -23,6 +23,7 @@ class RGenomicranges(RPackage):
homepage = "https://bioconductor.org/packages/GenomicRanges"
git = "https://git.bioconductor.org/packages/GenomicRanges.git"
version('1.42.0', commit='32baca734b599d60fa13bdbe31c5712e648f538d')
version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a')
version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd')
version('1.32.7', commit='4c56dc836dbfd0d228dc810e8d401811cdbc267c')
@ -31,21 +32,20 @@ class RGenomicranges(RPackage):
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-iranges@2.9.11:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.3:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.27.12:', when='@1.42.0:', type=('build', 'run'))
depends_on('r-iranges@2.9.11:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-iranges@2.15.12:', when='@1.34.0:', type=('build', 'run'))
depends_on('r-iranges@2.17.1:', when='@1.36.1:', type=('build', 'run'))
depends_on('r-iranges@2.23.9:', when='@1.42.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-xvector@0.29.2:', when='@1.42.0:', type=('build', 'run'))

11
var/spack/repos/builtin/packages/r-geoquery/package.py
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@ -7,7 +7,7 @@
class RGeoquery(RPackage):
"""Get data from NCBI Gene Expression Omnibus (GEO).
"""Get data from NCBI Gene Expression Omnibus (GEO)
The NCBI Gene Expression Omnibus (GEO) is a public repository of
microarray data. Given the rich and varied nature of this resource, it
@ -17,6 +17,7 @@ class RGeoquery(RPackage):
homepage = "https://bioconductor.org/packages/GEOquery"
git = "https://git.bioconductor.org/packages/GEOquery.git"
version('2.58.0', commit='6332ca3791ddcfb233b9ad75b5904b3d60f49b93')
version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643')
version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97')
version('2.48.0', commit='6a8d1ca195b5c26fb717ae93beb1a8d9b7031c5e')
@ -24,15 +25,13 @@ class RGeoquery(RPackage):
version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-xml', when='@2.42.0', type=('build', 'run'))
depends_on('r-rcurl', when='@2.42.0', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-readr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run'))
depends_on('r-xml2', when='@2.46.15:', type=('build', 'run'))
depends_on('r-dplyr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-tidyr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-magrittr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-limma', when='@2.46.15:', type=('build', 'run'))
depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run'))
depends_on('r-xml', when='@2.42.0', type=('build', 'run'))
depends_on('r-rcurl', when='@2.42.0', type=('build', 'run'))

16
var/spack/repos/builtin/packages/r-ggbio/package.py
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@ -7,7 +7,7 @@
class RGgbio(RPackage):
"""Visualization tools for genomic data.
"""Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for
biological data. The graphics are designed to answer common scientific
@ -22,6 +22,7 @@ class RGgbio(RPackage):
homepage = "https://bioconductor.org/packages/ggbio"
git = "https://git.bioconductor.org/packages/ggbio.git"
version('1.38.0', commit='c39c51993f419cfc2f094e664477f25f5212a242')
version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88')
version('1.30.0', commit='8b05258b089b06a743352e92058edda06c24cfb7')
version('1.28.5', commit='594521ca556ef7d97cf4882ecfa54d22c2a2faba')
@ -36,11 +37,15 @@ class RGgbio(RPackage):
depends_on('r-gtable', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-biovizbase@1.23.3:', type=('build', 'run'))
depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run'))
depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.21.10:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-rsamtools@1.17.28:', type=('build', 'run'))
@ -49,17 +54,10 @@ class RGgbio(RPackage):
depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.16:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.17.13:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-organismdbi', type=('build', 'run'))
depends_on('r-ggally', type=('build', 'run'))
depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationfilter', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run'))
depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run'))
depends_on('r-rlang', when='@1.28.5:', type=('build', 'run'))
depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run'))

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