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Replace git-based Bioconductor R packages (#12005)

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* Replace git-based Bioconductor R packages

The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.

* Fix some broken package names, add periods to title docstrings

* r-clue: new package at 0.3-57

* r-genomeinfodbdata: add 1.2.1

* r-gofuncr: new package at 1.4.0

* r-pfam-db: add 3.8.2

* Add missed package r-genelendatabase

* update r-goseq package

* update r-glimma package

* update r-rots package

* r-org-hs-eg-db: add 3.8.2

* r-vgam: fix incorrect R version

* r-rnaseqmap: new package at 2.42.0

* r-rhdf5lib: new package at 1.6.0

* r-scrime: new package at 1.3.5

* r-delayedmatrixstats: new package at 1.6.0

* r-hdf5array: new package at 1.12.1

* r-biocfilecache: new package at 1.8.0

* r-ctc: add new versions, dependencies

* r-genemeta: new package at 1.56.0

* r-scrime: fix flake8

* r-ensembldb: add missing dependencies

* Added missing dependencies to packages with certain DESCRIPTIONS

* r-mapplots: new package at 1.5.1

* r-beachmat: new package at 2.0.0

* r-beeswarm: new package at 0.2.3

* r-biocneighbors: new package at 1.2.0

* r-biocsingular: new package at 1.0.0

* r-ecp: new package at 3.1.1

* r-enrichplot: new package at 1.4.0

* r-europepmc: new package at 0.3

* r-ggbeeswarm: new package at 0.6.0

* r-ggplotify: new package at 0.0.3

* r-ggraph: new package at 1.0.2

* r-gridgraphics: new package at 0.4-1

* r-rcppannoy: new package at 0.0.12

* r-rcpphnsw: new package at 0.1.0

* r-rsvd: new package at 1.0.1

* r-scater: new package at 1.12.2

* r-singlecellexperiment: new package at 1.6.0

* r-tximport: new package at 1.12.3

* r-upsetr: new package at 1.4.0

* r-vioplot: new package at 0.3.2

* r-readr: add 1.3.1

* r-matrixstats: add 0.54.0

* r-ecp: flake8 fix

* r-biocmanager: new package at 1.30.4

* update bioconductor packages requiring BiocManager, new versions

* r-lambda-r: add 1.2.3

* r-vegan: add 2.5-5

* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF

* r-chemometrics: flake8 fixes

* r-vgam: flake8 fixes

* CRAN packages: use cloud.r-project.org

* Use DESCRIPTION for R version constraints over bioconductor releases

* Update missed packages ABAData, acde, affydata

* Update remaining missed packages

* bio: Drop 'when' clause from first checksummed versions

* bio: improve package description generation logic

* r-genomeinfodbdata: use explicit sha256 sums

* r-pfam-db: update dependencies, add 3.10.0

* update r-org-hs-eg-db

* r-dirichletmultinomial: re-add gsl

* r-polyclip: new package at 1.10-0

* r-farver: new package at 1.1.0

* r-tweenr: new package at 1.0.1

* r-ggforce: new package at 0.3.1

* r-ggforce: remove redundant dep

* r-ggraph: add missing deps

* r-rcpphnsw: remove redundant depends_on

* r-reportingtools: re-add r-r-utils dep

* r-rhdf5: add gmake dep

* r-rhtslib: add system dependencies

* r-rsamtools: add gmake dep

* r-farver: remove redundant dep

* r-tweenr: remove redundant dep

* r-variantannotation: add gmake dep

* r-rgraphviz: add graphviz dep

* r-vsn: correct r-hexbin constraint

* r-scater: fix obsolete deps

* r-variantannotation: fix gmake dep type

* r-scater: tighten R version constraints

* r-rsamtools: fix gmake dep type

* r-rhtslib: fix gmake dep type

* r-rhtslib: use xz over lzma

* r-rhdf5: fix gmake dep type

* r-farver: replace with newer recipe for 2.0.1

* r-mzr: remove old dependency

* r-reportingtools: remove builtin dependency

* r-mzr: add gmake dep

* r-rhtslib: make system libraries link deps

* r-genomeinfodbdata: fix R version constraints

* r-geoquery: remove old deps from new versions

* r-genomicfeatures: tighten r-rmysql dep

* r-ensembldb: tighten r-annotationhub dep

* r-complexheatmap: fix r-dendextend dep

* r-cner: fix utils dep name

* r-clusterprofiler: fix r-gosemsim version req

* r-biostrings: fix r-iranges version reqs

* r-rhdf5lib: add gmake dep

* r-oligoclasses: fix r-biocinstaller dep range

* r-organismdbi: fix r-biocinstaller dep range

* r-hdf5array: add gmake dep

* r-gtrellis: tighten r-circlize version req

* r-gostats: fix r-graph version req

* r-glimma: fix old dependency ranges

* r-biostrings: syntax fix

* r-organismdbi: syntax fix

* r-dose: fix r-igraph dep

* r-dose: fix r-scales, r-rvcheck deps

* r-affy: fix r-biocinstaller dep

* r-ampliqueso: fix homepage

* r-aneufinder: fix r-biocgenerics dep

* r-beachmat: fix changed deps

* r-biocneighbors: fix old R constraint

* r-biocmanager: rewrite recipe for 1.30.10

* Update var/spack/repos/builtin/packages/r-biocinstaller/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/r-oligoclasses/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Justin S
2019-11-27 20:57:15 -06:00
committed by Adam J. Stewart
parent 0f46c3452f
commit 1b24dfb8ba
186 changed files with 3311 additions and 1317 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
var/spack/repos/builtin/packages/r-a4/package.py
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@@ -9,12 +9,15 @@
class RA4(RPackage):
"""Automated Affymetrix Array Analysis Umbrella Package."""
homepage = "https://www.bioconductor.org/packages/a4/"
homepage = "https://bioconductor.org/packages/a4"
git = "https://git.bioconductor.org/packages/a4.git"
version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712')
version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d')
version('1.28.0', commit='e81a8c15e1062ed9433e2d4d333f0484bc0e8bfb')
version('1.26.0', commit='e6af2cba5b684f81cc6e44dbc432916f75a2f774')
version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-a4base', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-a4classif', type=('build', 'run'))

9
var/spack/repos/builtin/packages/r-a4base/package.py
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@@ -7,14 +7,17 @@
class RA4base(RPackage):
"""Automated Affymetrix Array Analysis."""
"""Automated Affymetrix Array Analysis Base Package."""
homepage = "https://www.bioconductor.org/packages/a4Base/"
homepage = "https://bioconductor.org/packages/a4Base"
git = "https://git.bioconductor.org/packages/a4Base.git"
version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7')
version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229')
version('1.28.0', commit='3918a9ebafa065027c29620ee4d83789cb02f932')
version('1.26.0', commit='9b8ee4a8be90f5035a4b105ecebb8bb5b50cd0d9')
version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annaffy', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-a4classif/package.py
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@@ -9,12 +9,15 @@
class RA4classif(RPackage):
"""Automated Affymetrix Array Analysis Classification Package."""
homepage = "https://www.bioconductor.org/packages/a4Classif/"
homepage = "https://bioconductor.org/packages/a4Classif"
git = "https://git.bioconductor.org/packages/a4Classif.git"
version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88')
version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3')
version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7')
version('1.26.0', commit='bc4018c3c441e1840bb3e2959c07611489439a50')
version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-mlinterfaces', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-a4core/package.py
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@@ -9,11 +9,14 @@
class RA4core(RPackage):
"""Automated Affymetrix Array Analysis Core Package."""
homepage = "https://www.bioconductor.org/packages/a4Core/"
homepage = "https://bioconductor.org/packages/a4Core"
git = "https://git.bioconductor.org/packages/a4Core.git"
version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce')
version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141')
version('1.28.0', commit='39b6ee29bc2f2fdc5733438c14dc02f8abc6460b')
version('1.26.0', commit='e7be935f20b486165a2b27dbbf9e99ba07151bcd')
version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-glmnet', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-a4preproc/package.py
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@@ -9,10 +9,13 @@
class RA4preproc(RPackage):
"""Automated Affymetrix Array Analysis Preprocessing Package."""
homepage = "https://www.bioconductor.org/packages/a4Preproc/"
homepage = "https://bioconductor.org/packages/a4Preproc"
git = "https://git.bioconductor.org/packages/a4Preproc.git"
version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558')
version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978')
version('1.28.0', commit='435d66727f1187020d034a1beaf4cd8bd4f76981')
version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea')
version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-annotationdbi', type=('build', 'run'))

7
var/spack/repos/builtin/packages/r-a4reporting/package.py
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@@ -9,11 +9,14 @@
class RA4reporting(RPackage):
"""Automated Affymetrix Array Analysis Reporting Package."""
homepage = "https://www.bioconductor.org/packages/a4Reporting"
homepage = "https://bioconductor.org/packages/a4Reporting"
git = "https://git.bioconductor.org/packages/a4Reporting.git"
version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792')
version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390')
version('1.28.0', commit='0fe72f48374353c39479a45e5516d0709f8c9ef7')
version('1.26.0', commit='cce201502e2d3b28fd2823b66d9f81b034dc7eaa')
version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r-annaffy', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))

30
var/spack/repos/builtin/packages/r-abadata/package.py
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@@ -7,16 +7,24 @@
class RAbadata(RPackage):
"""Provides the data for the gene expression enrichment analysis
conducted in the package 'ABAEnrichment'. The package includes three
datasets which are derived from the Allen Brain Atlas: (1) Gene
expression data from Human Brain (adults) averaged across donors,
(2) Gene expression data from the Developing Human Brain pooled into
five age categories and averaged across donors and (3) a developmental
effect score based on the Developing Human Brain expression data.
All datasets are restricted to protein coding genes."""
"""Averaged gene expression in human brain regions from Allen Brain Atlas.
homepage = "https://bioconductor.org/packages/ABAData/"
url = "https://bioconductor.org/packages/release/data/experiment/src/contrib/ABAData_1.14.0.tar.gz"
Provides the data for the gene expression enrichment analysis conducted
in the package 'ABAEnrichment'. The package includes three datasets
which are derived from the Allen Brain Atlas: (1) Gene expression data
from Human Brain (adults) averaged across donors, (2) Gene expression
data from the Developing Human Brain pooled into five age categories and
averaged across donors and (3) a developmental effect score based on the
Developing Human Brain expression data. All datasets are restricted to
protein coding genes."""
version('1.14.0', sha256='d203d968044c292cdfab57a4d6bf52dfb60470bd78b4c9bd88892577ac42b2b7')
homepage = "https://bioconductor.org/packages/ABAData"
git = "https://git.bioconductor.org/packages/ABAData.git"
version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd')
version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d')
version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a')
version('1.8.0', commit='181a4af1af349064eb432255970e925ae2564e1a')
version('1.6.0', commit='517c18a3d1809dde0291eeb47dd2545c7cfcdabe')
depends_on('r@3.2:', type=('build', 'run'))

49
var/spack/repos/builtin/packages/r-abaenrichment/package.py
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@@ -7,28 +7,37 @@
class RAbaenrichment(RPackage):
"""The package ABAEnrichment is designed to test for enrichment
of user defined candidate genes in the set of expressed genes in
different human brain regions. The core function 'aba_enrich'
integrates the expression of the candidate gene set (averaged
across donors) and the structural information of the brain using
an ontology, both provided by the Allen Brain Atlas project.
'aba_enrich' interfaces the ontology enrichment software FUNC to
perform the statistical analyses. Additional functions provided
in this package like 'get_expression' and 'plot_expression'
facilitate exploring the expression data. From version 1.3.5
onwards genomic regions can be provided as input, too; and from
version 1.5.9 onwards the function 'get_annotated_genes' offers
an easy way to obtain annotations of genes to enriched or
user-defined brain regions."""
"""Gene expression enrichment in human brain regions.
homepage = "https://bioconductor.org/packages/ABAEnrichment/"
The package ABAEnrichment is designed to test for enrichment of user
defined candidate genes in the set of expressed genes in different human
brain regions. The core function 'aba_enrich' integrates the expression
of the candidate gene set (averaged across donors) and the structural
information of the brain using an ontology, both provided by the Allen
Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment
software FUNC to perform the statistical analyses. Additional functions
provided in this package like 'get_expression' and 'plot_expression'
facilitate exploring the expression data, and besides the standard
candidate vs. background gene set enrichment, also three additional
tests are implemented, e.g. for cases when genes are ranked instead of
divided into candidate and background."""
homepage = "https://bioconductor.org/packages/ABAEnrichment"
git = "https://git.bioconductor.org/packages/ABAEnrichment.git"
version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23')
version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7')
version('1.10.0', commit='15f33ccb694a91d2d2067c937682c4bc952def6c')
version('1.8.0', commit='cb8155ee9a04fb55b2a2e8c23df7c0be15bb2624')
version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
depends_on('r@3.4.0:3.4.9', when='@1.6.0')
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-gplots', type=('build', 'run'))
depends_on('r-gtools', type=('build', 'run'))
depends_on('r-abadata', type=('build', 'run'))
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r-rcpp@0.11.5:', type=('build', 'run'))
depends_on('r-gplots@2.14.2:', type=('build', 'run'))
depends_on('r-gtools@3.5.0:', type=('build', 'run'))
depends_on('r-abadata@0.99.2:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run'))
depends_on('r-data-table@1.10.4:', when='@1.8.0:', type=('build', 'run'))
depends_on('r-gofuncr@1.1.2:', when='@1.12.0:', type=('build', 'run'))

19
var/spack/repos/builtin/packages/r-absseq/package.py
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@@ -7,16 +7,23 @@
class RAbsseq(RPackage):
"""Inferring differential expression genes by absolute counts
difference between two groups, utilizing Negative binomial
distribution and moderating fold-change according to heterogeneity
of dispersion across expression level."""
"""ABSSeq: a new RNA-Seq analysis method based on modelling absolute
expression differences.
homepage = "https://www.bioconductor.org/packages/ABSSeq/"
Inferring differential expression genes by absolute counts difference
between two groups, utilizing Negative binomial distribution and
moderating fold-change according to heterogeneity of dispersion across
expression level."""
homepage = "https://bioconductor.org/packages/ABSSeq"
git = "https://git.bioconductor.org/packages/ABSSeq.git"
version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce')
version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a')
version('1.34.1', commit='0c3a2514ef644c6e0de3714bc91959a302c9e006')
version('1.32.3', commit='189d81c3d70f957bf50780f76a6ddcee499b4784')
version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
depends_on('r@3.4.0:3.4.9', when='@1.22.8')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))

36
var/spack/repos/builtin/packages/r-acde/package.py
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@@ -7,21 +7,27 @@
class RAcde(RPackage):
"""This package provides a multivariate inferential analysis method
for detecting differentially expressed genes in gene expression data.
It uses artificial components, close to the data's principal
components but with an exact interpretation in terms of differential
genetic expression, to identify differentially expressed genes while
controlling the false discovery rate (FDR). The methods on this
package are described in the vignette or in the article
'Multivariate Method for Inferential Identification of
Differentially Expressed Genes in Gene Expression Experiments' by
J. P. Acosta, L. Lopez-Kleine and S. Restrepo
(2015, pending publication)."""
"""Artificial Components Detection of Differentially Expressed Genes.
homepage = "https://www.bioconductor.org/packages/acde/"
url = "https://bioconductor.org/packages/release/bioc/src/contrib/acde_1.14.0.tar.gz"
This package provides a multivariate inferential analysis method for
detecting differentially expressed genes in gene expression data. It
uses artificial components, close to the data's principal components but
with an exact interpretation in terms of differential genetic
expression, to identify differentially expressed genes while controlling
the false discovery rate (FDR). The methods on this package are
described in the vignette or in the article 'Multivariate Method for
Inferential Identification of Differentially Expressed Genes in Gene
Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo
(2015, pending publication)."""
version('1.14.0', sha256='e8d9ad688610d4b72cab729141dc46fce580c97128d929885336bb138345b788')
homepage = "https://bioconductor.org/packages/acde"
git = "https://git.bioconductor.org/packages/acde.git"
depends_on('r-boot', type=('build', 'run'))
version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417')
version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4')
version('1.10.0', commit='2c303dec45f3c70bf333a6eacae568a08d5ca010')
version('1.8.0', commit='f7fc3e1dce958445f920d3b28b56abde70bfb9de')
version('1.6.0', commit='244c81f435a077bf7895ea565fa6695e8b079f67')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-boot@1.3:', type=('build', 'run'))

18
var/spack/repos/builtin/packages/r-acgh/package.py
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@@ -7,17 +7,23 @@
class RAcgh(RPackage):
"""Functions for reading aCGH data from image analysis output files
and clone information files, creation of aCGH S3 objects for storing
these data. Basic methods for accessing/replacing, subsetting,
printing and plotting aCGH objects."""
"""Classes and functions for Array Comparative Genomic Hybridization data..
homepage = "https://www.bioconductor.org/packages/aCGH/"
Functions for reading aCGH data from image analysis output files and
clone information files, creation of aCGH S3 objects for storing these
data. Basic methods for accessing/replacing, subsetting, printing and
plotting aCGH objects."""
homepage = "https://bioconductor.org/packages/aCGH"
git = "https://git.bioconductor.org/packages/aCGH.git"
version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f')
version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21')
version('1.58.0', commit='2decc79a21bff5a14d708cdc654e351515b20d3e')
version('1.56.0', commit='f3531ec99fc181044bdcb6a01c9976029efb6235')
version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693')
depends_on('r@3.4.0:3.4.9', when='@1.54.0')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-cluster', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))
depends_on('r-multtest', type=('build', 'run'))

30
var/spack/repos/builtin/packages/r-acme/package.py
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@@ -7,21 +7,27 @@
class RAcme(RPackage):
"""ACME (Algorithms for Calculating Microarray Enrichment) is a set
of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity,
or other experiments that result in regions of the genome showing
"enrichment". It does not rely on a specific array technology
(although the array should be a "tiling" array), is very general
(can be applied in experiments resulting in regions of enrichment),
and is very insensitive to array noise or normalization methods.
It is also very fast and can be applied on whole-genome tiling array
experiments quite easily with enough memory."""
"""Algorithms for Calculating Microarray Enrichment (ACME).
homepage = "https://www.bioconductor.org/packages/ACME/"
ACME (Algorithms for Calculating Microarray Enrichment) is a set of
tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or
other experiments that result in regions of the genome showing
"enrichment". It does not rely on a specific array technology (although
the array should be a "tiling" array), is very general (can be applied
in experiments resulting in regions of enrichment), and is very
insensitive to array noise or normalization methods. It is also very
fast and can be applied on whole-genome tiling array experiments quite
easily with enough memory."""
homepage = "https://bioconductor.org/packages/ACME"
git = "https://git.bioconductor.org/packages/ACME.git"
version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a')
version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b')
version('2.36.0', commit='39e056435b9775d35e7f7fc5446c2c3cafe15670')
version('2.34.0', commit='1f53d43e420e245423fdf2711d0dcb345f829469')
version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407')
depends_on('r@3.4.0:3.4.9', when='@2.32.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase@2.5.5:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))

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@@ -7,20 +7,26 @@
class RAdsplit(RPackage):
"""This package implements clustering of microarray gene expression
profiles according to functional annotations. For each term genes
are annotated to, splits into two subclasses are computed and a
significance of the supporting gene set is determined."""
"""Annotation-Driven Clustering.
homepage = "https://www.bioconductor.org/packages/adSplit/"
This package implements clustering of microarray gene expression
profiles according to functional annotations. For each term genes are
annotated to, splits into two subclasses are computed and a significance
of the supporting gene set is determined."""
homepage = "https://bioconductor.org/packages/adSplit"
git = "https://git.bioconductor.org/packages/adSplit.git"
version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652')
version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19')
version('1.50.0', commit='a02e2c994e78ececd5a248575109c5ed36c969db')
version('1.48.0', commit='57dfcd93b9232cf53f05c34179ecb759bb7aff46')
version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
depends_on('r@3.4.0:3.4.9', when='@1.46.0')
depends_on('r@2.1.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-cluster', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-kegg-db', type=('build', 'run'))
depends_on('r-multtest', type=('build', 'run'))
depends_on('r-biobase@1.5.12:', type=('build', 'run'))
depends_on('r-cluster@1.9.1:', type=('build', 'run'))
depends_on('r-go-db@1.8.1:', type=('build', 'run'))
depends_on('r-kegg-db@1.8.1:', type=('build', 'run'))
depends_on('r-multtest@1.6.0:', type=('build', 'run'))

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@@ -7,18 +7,24 @@
class RAffxparser(RPackage):
"""Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR).
It provides methods for fast and memory efficient parsing of
Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII-
and binary-based files are supported. Currently, there are methods
for reading chip definition file (CDF) and a cell intensity file (CEL).
These files can be read either in full or in part. For example,
probe signals from a few probesets can be extracted very quickly
from a set of CEL files into a convenient list structure."""
"""Affymetrix File Parsing SDK.
homepage = "https://www.bioconductor.org/packages/affxparser/"
Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It
provides methods for fast and memory efficient parsing of Affymetrix
files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based
files are supported. Currently, there are methods for reading chip
definition file (CDF) and a cell intensity file (CEL). These files can
be read either in full or in part. For example, probe signals from a few
probesets can be extracted very quickly from a set of CEL files into a
convenient list structure."""
homepage = "https://bioconductor.org/packages/affxparser"
git = "https://git.bioconductor.org/packages/affxparser.git"
version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056')
version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f')
version('1.52.0', commit='8e0c4b89ee1cb4ff95f58a5dd947249dc718bc58')
version('1.50.0', commit='01ef641727eadc2cc17b5dbb0b1432364436e3d5')
version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
depends_on('r@3.4.0:3.4.9', when='@1.48.0')
depends_on('r@2.14.0:', type=('build', 'run'))

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@@ -7,19 +7,27 @@
class RAffy(RPackage):
"""The package contains functions for exploratory oligonucleotide array
"""Methods for Affymetrix Oligonucleotide Arrays.
The package contains functions for exploratory oligonucleotide array
analysis. The dependence on tkWidgets only concerns few convenience
functions. 'affy' is fully functional without it."""
homepage = "https://bioconductor.org/packages/affy/"
homepage = "https://bioconductor.org/packages/affy"
git = "https://git.bioconductor.org/packages/affy.git"
version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605')
version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206')
version('1.58.0', commit='4698231f45f225228f56c0708cd477ad450b4ee6')
version('1.56.0', commit='d36a7b8f05b1ef60162d94e75037d45c48f88871')
version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affyio', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'))
depends_on('r@2.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.1.12:', type=('build', 'run'))
depends_on('r-biobase@2.5.5:', type=('build', 'run'))
depends_on('r-affyio@1.13.3:', type=('build', 'run'))
depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.54.0')
depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-affycomp/package.py
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@@ -7,13 +7,19 @@
class RAffycomp(RPackage):
"""The package contains functions that can be used to compare
expression measures for Affymetrix Oligonucleotide Arrays."""
"""Graphics Toolbox for Assessment of Affymetrix Expression Measures.
homepage = "https://www.bioconductor.org/packages/affycomp/"
The package contains functions that can be used to compare expression
measures for Affymetrix Oligonucleotide Arrays."""
homepage = "https://bioconductor.org/packages/affycomp"
git = "https://git.bioconductor.org/packages/affycomp.git"
version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c')
version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef')
version('1.56.0', commit='b0994da338be19396e647c680059fd35341b50a2')
version('1.54.0', commit='65281c1ca37147c2a54ad3722a8d5ff0ffa5acc5')
version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
depends_on('r@3.4.0:3.4.9', when='@1.52.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@2.13.0:', type=('build', 'run'))
depends_on('r-biobase@2.3.3:', type=('build', 'run'))

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@@ -7,19 +7,25 @@
class RAffycompatible(RPackage):
"""This package provides an interface to Affymetrix chip annotation
and sample attribute files. The package allows an easy way for users
to download and manage local data bases of Affynmetrix NetAffx
annotation files. The package also provides access to GeneChip
Operating System (GCOS) and GeneChip Command Console
(AGCC)-compatible sample annotation files."""
"""Affymetrix GeneChip software compatibility.
homepage = "https://www.bioconductor.org/packages/AffyCompatible/"
This package provides an interface to Affymetrix chip annotation and
sample attribute files. The package allows an easy way for users to
download and manage local data bases of Affynmetrix NetAffx annotation
files. The package also provides access to GeneChip Operating System
(GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation
files."""
homepage = "https://bioconductor.org/packages/AffyCompatible"
git = "https://git.bioconductor.org/packages/AffyCompatible.git"
version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476')
version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8')
version('1.40.0', commit='44838bdb5e8c26afbd898c49ed327ddd1a1d0301')
version('1.38.0', commit='d47ee3a3a3d3bce11121e80fe02ee216b9199b12')
version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
depends_on('r@3.4.0:3.4.9', when=('@1.36.0'))
depends_on('r-xml', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-xml@2.8-1:', type=('build', 'run'))
depends_on('r-rcurl@0.8-1:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))

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@@ -7,15 +7,21 @@
class RAffycontam(RPackage):
"""structured corruption of cel file data to demonstrate QA
effectiveness."""
"""structured corruption of affymetrix cel file data.
homepage = "https://www.bioconductor.org/packages/affyContam/"
structured corruption of cel file data to demonstrate QA
effectiveness"""
homepage = "https://bioconductor.org/packages/affyContam"
git = "https://git.bioconductor.org/packages/affyContam.git"
version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe')
version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614')
version('1.38.0', commit='84651e8eade61619afefc83bb290047da101a5bc')
version('1.36.0', commit='aeb684a7d3f6fa9243f3946d214de53649fa4fd6')
version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
depends_on('r@3.4.0:3.4.9', when=('@1.34.0'))
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-affydata', type=('build', 'run'))

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@@ -7,15 +7,21 @@
class RAffycoretools(RPackage):
"""Various wrapper functions that have been written to streamline
the more common analyses that a core Biostatistician might see."""
"""Functions useful for those doing repetitive analyses with Affymetrix
GeneChips.
homepage = "https://www.bioconductor.org/packages/affycoretools/"
Various wrapper functions that have been written to streamline the more
common analyses that a core Biostatistician might see."""
homepage = "https://bioconductor.org/packages/affycoretools"
git = "https://git.bioconductor.org/packages/affycoretools.git"
version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898')
version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845')
version('1.52.2', commit='2f98c74fad238b94c1e453b972524ab7b573b0de')
version('1.50.6', commit='4be92bcb55d7bace2a110865b7530dcfac14e76e')
version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
depends_on('r@3.4.0:3.4.9', when='@1.48.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
@@ -33,3 +39,5 @@ class RAffycoretools(RPackage):
depends_on('r-edger', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-dbi', when='@1.50.6:', type=('build', 'run'))

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@@ -7,14 +7,20 @@
class RAffydata(RPackage):
"""Example datasets of a slightly large size. They represent 'real
world examples', unlike the artificial examples included in the
package affy."""
"""Affymetrix Data for Demonstration Purpose.
homepage = "https://www.bioconductor.org/packages/affydata/"
url = "https://www.bioconductor.org/packages/release/data/experiment/src/contrib/affydata_1.32.0.tar.gz"
Example datasets of a slightly large size. They represent 'real world
examples', unlike the artificial examples included in the package
affy."""
version('1.32.0', sha256='059e05a2b8908720801d684d5617d5d5e45db7a5999c5659a22daf87658538d1')
homepage = "https://bioconductor.org/packages/affydata"
git = "https://git.bioconductor.org/packages/affydata.git"
depends_on('r@3.4.0:3.4.9', when=('@1.24.0'))
depends_on('r-affy', type=('build', 'run'))
version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd')
version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea')
version('1.28.0', commit='a106a5514c352bf0bbc624ded58a93886d4ce96f')
version('1.26.0', commit='eb0a44a39990b361f9fb1094837ffafb320f39a9')
version('1.24.0', commit='663991606507572f083232e2b393d901270291d4')
depends_on('r@2.4.0:', type=('build', 'run'))
depends_on('r-affy@1.23.4:', type=('build', 'run'))

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@@ -7,15 +7,21 @@
class RAffyexpress(RPackage):
"""The purpose of this package is to provide a comprehensive and
easy-to-use tool for quality assessment and to identify differentially
expressed genes in the Affymetrix gene expression data."""
"""Affymetrix Quality Assessment and Analysis Tool.
homepage = "https://www.bioconductor.org/packages/AffyExpress/"
The purpose of this package is to provide a comprehensive and easy-to-
use tool for quality assessment and to identify differentially expressed
genes in the Affymetrix gene expression data."""
homepage = "https://bioconductor.org/packages/AffyExpress"
git = "https://git.bioconductor.org/packages/AffyExpress.git"
version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96')
version('1.48.0', commit='dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92')
version('1.46.0', commit='2add4a4436e21aa20f1ededbfd5f1365a3d28c85')
version('1.44.0', commit='7517bc8b363ceb107d5dca66dd74f94edefde52a')
version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
depends_on('r@3.4.0:3.4.9', when='@1.42.0')
depends_on('r-affy', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-affy@1.23.4:', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))

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class RAffyilm(RPackage):
"""affyILM is a preprocessing tool which estimates gene
expression levels for Affymetrix Gene Chips. Input from
physical chemistry is employed to first background subtract
intensities before calculating concentrations on behalf
of the Langmuir model."""
"""Linear Model of background subtraction and the Langmuir isotherm.
homepage = "https://www.bioconductor.org/packages/affyILM/"
affyILM is a preprocessing tool which estimates gene expression levels
for Affymetrix Gene Chips. Input from physical chemistry is employed to
first background subtract intensities before calculating concentrations
on behalf of the Langmuir model."""
homepage = "https://bioconductor.org/packages/affyILM"
git = "https://git.bioconductor.org/packages/affyILM.git"
version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132')
version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564')
version('1.32.0', commit='860f2ddada80435d309ba334eff3fab503817755')
version('1.30.0', commit='c07d91ae52a2a48f0a5f212c3ecf3243741bee13')
version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
depends_on('r@3.4.0:3.4.9', when='@1.28.0')
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r-gcrma', type=('build', 'run'))
depends_on('r-affxparser', type=('build', 'run'))
depends_on('r-affxparser@1.16.0:', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))

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@@ -7,14 +7,20 @@
class RAffyio(RPackage):
"""Routines for parsing Affymetrix data files based upon file format
"""Tools for parsing Affymetrix data files.
Routines for parsing Affymetrix data files based upon file format
information. Primary focus is on accessing the CEL and CDF file
formats."""
homepage = "https://bioconductor.org/packages/affyio/"
homepage = "https://bioconductor.org/packages/affyio"
git = "https://git.bioconductor.org/packages/affyio.git"
version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f')
version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963')
version('1.50.0', commit='911ea4f8e4cdf7b649b87ef7ed1a5f5b111ef38a')
version('1.48.0', commit='01727a4492c3a0d50453fc91892e04bf5f7fcadb')
version('1.46.0', commit='977597f2772e08273d86579486f452170566c880')
depends_on('r@2.6.0:', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.46.0')

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@@ -7,13 +7,19 @@
class RAffypdnn(RPackage):
"""The package contains functions to perform the PDNN method
described by Li Zhang et al."""
"""Probe Dependent Nearest Neighbours (PDNN) for the affy package.
homepage = "https://www.bioconductor.org/packages/affypdnn/"
The package contains functions to perform the PDNN method described by
Li Zhang et al."""
homepage = "https://bioconductor.org/packages/affypdnn"
git = "https://git.bioconductor.org/packages/affypdnn.git"
version('1.58.0', commit='83d8b6b0d9606845bd77dbf7164dd5b160f32ccf')
version('1.56.0', commit='5fd9c5265fb895a1f646cf72e8d5169669d979f2')
version('1.54.0', commit='ea971b1b9cc443695a6614bef92e8e116ee87d55')
version('1.52.0', commit='17d74c593ce4f0dfd43f13a5016e482c1399d21e')
version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
depends_on('r@3.4.0:3.4.9', when='@1.50.0')
depends_on('r-affy', type=('build', 'run'))
depends_on('r@2.13.0:', type=('build', 'run'))
depends_on('r-affy@1.5:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-affyplm/package.py
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@@ -7,21 +7,27 @@
class RAffyplm(RPackage):
"""A package that extends and improves the functionality of
the base affy package. Routines that make heavy use of compiled
code for speed. Central focus is on implementation of methods
for fitting probe-level models and tools using these models.
PLM based quality assessment tools."""
"""Methods for fitting probe-level models.
homepage = "https://www.bioconductor.org/packages/affyPLM/"
A package that extends and improves the functionality of the base affy
package. Routines that make heavy use of compiled code for speed.
Central focus is on implementation of methods for fitting probe-level
models and tools using these models. PLM based quality assessment
tools."""
homepage = "https://bioconductor.org/packages/affyPLM"
git = "https://git.bioconductor.org/packages/affyPLM.git"
version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d')
version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8')
version('1.56.0', commit='13dfc558281af9a177d4d592c34cf7ace629af0e')
version('1.54.0', commit='09cf5f6e01dd2d0aae3e9ddab27301f04bfd645c')
version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
depends_on('r@3.4.0:3.4.9', when='@1.52.1')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@2.6.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.3.2:', type=('build', 'run'))
depends_on('r-affy@1.11.0:', type=('build', 'run'))
depends_on('r-biobase@2.17.8:', type=('build', 'run'))
depends_on('r-gcrma', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-preprocesscore@1.5.1:', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))

17
var/spack/repos/builtin/packages/r-affyqcreport/package.py
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@@ -7,17 +7,22 @@
class RAffyqcreport(RPackage):
"""This package creates a QC report for an AffyBatch object.
The report is intended to allow the user to quickly assess the
quality of a set of arrays in an AffyBatch object."""
"""QC Report Generation for affyBatch objects.
homepage = "https://www.bioconductor.org/packages/affyQCReport/"
This package creates a QC report for an AffyBatch object. The report is
intended to allow the user to quickly assess the quality of a set of
arrays in an AffyBatch object."""
homepage = "https://bioconductor.org/packages/affyQCReport"
git = "https://git.bioconductor.org/packages/affyQCReport.git"
version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4')
version('1.60.0', commit='d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa')
version('1.58.0', commit='14be93a1e7a6d1a64c38ed2f53e0c52a389b2a1b')
version('1.56.0', commit='5c824045c7364155eafc2dd5bb342374aa1ca072')
version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
depends_on('r@3.4.0:3.4.9', when='@1.54.0')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biobase@1.13.16:', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-affyplm', type=('build', 'run'))

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@@ -7,17 +7,23 @@
class RAffyrnadegradation(RPackage):
"""The package helps with the assessment and correction of
RNA degradation effects in Affymetrix 3' expression arrays.
The parameter d gives a robust and accurate measure of RNA
integrity. The correction removes the probe positional bias,
and thus improves comparability of samples that are affected
by RNA degradation."""
"""Analyze and correct probe positional bias in microarray data due to RNA
degradation.
homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/"
The package helps with the assessment and correction of RNA degradation
effects in Affymetrix 3' expression arrays. The parameter d gives a
robust and accurate measure of RNA integrity. The correction removes the
probe positional bias, and thus improves comparability of samples that
are affected by RNA degradation."""
homepage = "https://bioconductor.org/packages/AffyRNADegradation"
git = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1')
version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24')
version('1.26.0', commit='6ab03ad624701464280bf7dfe345d200e846298a')
version('1.24.0', commit='1f85f3da4720cef94623828713eb84d8accbcf8a')
version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
depends_on('r@3.4.0:3.4.9', when='@1.22.0')
depends_on('r@2.9.0:', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-agdex/package.py
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@@ -7,14 +7,20 @@
class RAgdex(RPackage):
"""A tool to evaluate agreement of differential expression
for cross-species genomics."""
"""Agreement of Differential Expression Analysis.
homepage = "http://bioconductor.org/packages/AGDEX/"
A tool to evaluate agreement of differential expression for cross-
species genomics"""
homepage = "https://bioconductor.org/packages/AGDEX"
git = "https://git.bioconductor.org/packages/AGDEX.git"
version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf')
version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b')
version('1.28.0', commit='7d78ee424485018b73cd019ceaed7a2ed53adf3f')
version('1.26.0', commit='260bc641111770176707d4d43e67b5877bf5eb82')
version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-gseabase', type=('build', 'run'))

12
var/spack/repos/builtin/packages/r-agilp/package.py
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@@ -7,11 +7,17 @@
class RAgilp(RPackage):
"""Agilent expression array processing package."""
"""Agilent expression array processing package.
homepage = "http://bioconductor.org/packages/agilp/"
More about what it does (maybe more than one line)"""
homepage = "https://bioconductor.org/packages/agilp"
git = "https://git.bioconductor.org/packages/agilp.git"
version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47')
version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61')
version('3.12.0', commit='a86dea1b03b2b56c2c8317d4b10903fb8948ffcb')
version('3.10.0', commit='cffec1004704a0c5119a50e3ad474897978981be')
version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
depends_on('r@3.4.0:3.4.9', when='@3.8.0')
depends_on('r@2.14.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-agimicrorna/package.py
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@@ -7,16 +7,21 @@
class RAgimicrorna(RPackage):
"""Processing and Analysis of Agilent microRNA data."""
"""Processing and Differential Expression Analysis of Agilent microRNA
chips."""
homepage = "https://www.bioconductor.org/packages/AgiMicroRna/"
homepage = "https://bioconductor.org/packages/AgiMicroRna"
git = "https://git.bioconductor.org/packages/AgiMicroRna.git"
version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a')
version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8')
version('2.30.0', commit='99b5a8284cfe3e93c3ae85a2436e87101b9599dd')
version('2.28.0', commit='62c4a12f1168c7aa1ab46d2c97090ef71478328e')
version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
depends_on('r@3.4.0:3.4.9', when='@2.26.0')
depends_on('r-affycoretools', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-affy@1.22:', type=('build', 'run'))
depends_on('r-preprocesscore', type=('build', 'run'))
depends_on('r-affycoretools', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-aims/package.py
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@@ -7,17 +7,23 @@
class RAims(RPackage):
"""This package contains the AIMS implementation. It contains
necessary functions to assign the five intrinsic molecular
subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like,
Normal-like). Assignments could be done on individual samples
as well as on dataset of gene expression data."""
"""AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype.
homepage = "http://bioconductor.org/packages/AIMS/"
This package contains the AIMS implementation. It contains necessary
functions to assign the five intrinsic molecular subtypes (Luminal A,
Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be
done on individual samples as well as on dataset of gene expression
data."""
homepage = "https://bioconductor.org/packages/AIMS"
git = "https://git.bioconductor.org/packages/AIMS.git"
version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84')
version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f')
version('1.12.0', commit='d7eaa723d19a6aca37df244fd0b3d5426ed0a626')
version('1.10.0', commit='972945980b39168502a02ac3aa396f9b99fb3d71')
version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357')
depends_on('r@3.4.0:3.4.9', when='@1.8.0')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-e1071', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))

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@@ -7,26 +7,33 @@
class RAldex2(RPackage):
"""A differential abundance analysis for the comparison of
two or more conditions. For example, single-organism and
meta-RNA-seq high-throughput sequencing assays, or of
selected and unselected values from in-vitro sequence selections.
Uses a Dirichlet-multinomial model to infer abundance from counts,
that has been optimized for three or more experimental replicates.
Infers sampling variation and calculates the expected false
discovery rate given the biological and sampling variation
using the Wilcox rank test or Welches t-test (aldex.ttest) or
the glm and Kruskal Wallis tests (aldex.glm). Reports both P
and fdr values calculated by the Benjamini Hochberg correction."""
"""Analysis Of Differential Abundance Taking Sample Variation Into Account.
homepage = "http://bioconductor.org/packages/ALDEx2/"
A differential abundance analysis for the comparison of two or more
conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-
seq assays as well as selected and unselected values from in-vitro
sequence selections. Uses a Dirichlet-multinomial model to infer
abundance from counts, optimized for three or more experimental
replicates. The method infers biological and sampling variation to
calculate the expected false discovery rate, given the variation, based
on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a
Kruskal-Wallis test (via aldex.kw), a generalized linear model (via
aldex.glm), or a correlation test (via aldex.corr). All tests report
p-values and Benjamini-Hochberg corrected p-values."""
homepage = "https://bioconductor.org/packages/ALDEx2"
git = "https://git.bioconductor.org/packages/ALDEx2.git"
version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f')
version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8')
version('1.12.0', commit='9efde428d22a0be1fe7b6655d45ddce8fcded180')
version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a')
version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
depends_on('r@3.4.0:3.4.9', when='@1.8.0')
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-multtest', when='@1.10.0:', type=('build', 'run'))

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@@ -7,24 +7,30 @@
class RAllelicimbalance(RPackage):
"""Provides a framework for allelic specific expression
investigation using RNA-seq data."""
"""Investigates Allele Specific Expression.
homepage = "http://bioconductor.org/packages/AllelicImbalance/"
Provides a framework for allelic specific expression investigation using
RNA-seq data."""
homepage = "https://bioconductor.org/packages/AllelicImbalance"
git = "https://git.bioconductor.org/packages/AllelicImbalance.git"
version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3')
version('1.18.0', commit='6d6eed7487e9207dba556bc76283bcc7745808ea')
version('1.16.0', commit='85f652ae8a0dd15535819b6e934065182df5544a')
version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
depends_on('r@3.4.0:3.4.9', when='@1.14.0')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-bsgenome', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
@@ -35,3 +41,15 @@ class RAllelicimbalance(RPackage):
depends_on('r-seqinr', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-alpine/package.py
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@@ -7,15 +7,21 @@
class RAlpine(RPackage):
"""Fragment sequence bias modeling and correction for RNA-seq
transcript abundance estimation."""
"""alpine.
homepage = "http://bioconductor.org/packages/alpine/"
Fragment sequence bias modeling and correction for RNA-seq transcript
abundance estimation."""
homepage = "https://bioconductor.org/packages/alpine"
git = "https://git.bioconductor.org/packages/alpine.git"
version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c')
version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4')
version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274')
version('1.4.0', commit='c85beb208fd6bfc0a61a483a98498b589640f946')
version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
depends_on('r@3.4.0:3.4.9', when='@1.2.0')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-alsace/package.py
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@@ -7,18 +7,24 @@
class RAlsace(RPackage):
"""Alternating Least Squares (or Multivariate Curve Resolution)
for analytical chemical data, in particular hyphenated data where
the first direction is a retention time axis, and the second a
spectral axis. Package builds on the basic als function from the
ALS package and adds functionality for high-throughput analysis,
including definition of time windows, clustering of profiles,
retention time correction, etcetera."""
"""ALS for the Automatic Chemical Exploration of mixtures.
homepage = "https://www.bioconductor.org/packages/alsace/"
Alternating Least Squares (or Multivariate Curve Resolution) for
analytical chemical data, in particular hyphenated data where the first
direction is a retention time axis, and the second a spectral axis.
Package builds on the basic als function from the ALS package and adds
functionality for high-throughput analysis, including definition of time
windows, clustering of profiles, retention time correction, etcetera."""
homepage = "https://bioconductor.org/packages/alsace"
git = "https://git.bioconductor.org/packages/alsace.git"
version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389')
version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191')
version('1.16.0', commit='5a51a19aeccbba0123222201cb7a228559f29653')
version('1.14.0', commit='aebb13b00eb850f9569391c4c92183b55b70ae89')
version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-als', type=('build', 'run'))
depends_on('r-ptw', type=('build', 'run'))
depends_on('r-ptw@1.0.6:', type=('build', 'run'))

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@@ -7,17 +7,23 @@
class RAltcdfenvs(RPackage):
"""Convenience data structures and functions to handle cdfenvs."""
"""alternative CDF environments (aka probeset mappings).
homepage = "https://www.bioconductor.org/packages/altcdfenvs/"
Convenience data structures and functions to handle cdfenvs"""
homepage = "https://bioconductor.org/packages/altcdfenvs"
git = "https://git.bioconductor.org/packages/altcdfenvs.git"
version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b')
version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133')
version('2.42.0', commit='00ec6461877a063d938494b8ed0cd273a3b20b85')
version('2.40.0', commit='517a208f49f168bdd3cde40ed216282c417237d7')
version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
depends_on('r@3.4.0:3.4.9', when='@2.38.0')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@2.7:', type=('build', 'run'))
depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-biobase@2.15.1:', type=('build', 'run'))
depends_on('r-affy', type=('build', 'run'))
depends_on('r-makecdfenv', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))

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@@ -7,26 +7,32 @@
class RAmpliqueso(RPackage):
"""The package provides tools and reports for the analysis of
amplicon sequencing panels, such as AmpliSeq."""
"""Analysis of amplicon enrichment panels.
homepage = "https://www.bioconductor.org/packages/ampliQueso/"
The package provides tools and reports for the analysis of amplicon
sequencing panels, such as AmpliSeq"""
homepage = "https://bioconductor.org/packages/3.8/bioc/html/ampliQueso.html"
git = "https://git.bioconductor.org/packages/ampliQueso.git"
version('1.21.0', commit='ed99c5194a452ee299a93e981da2224e4dab5bdd')
version('1.20.0', commit='ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8')
version('1.18.0', commit='c27fa51094135ef8da52cd2b34a27ec6454abd8e')
version('1.16.0', commit='25d2543ff9dedef4f966f999c95cdf87185d3bb3')
version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
depends_on('r@3.4.0:3.4.9', when='@1.14.0')
depends_on('r-samr', type=('build', 'run'))
depends_on('r-deseq', type=('build', 'run'))
depends_on('r-edger', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-statmod', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-gplots', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-rgl', type=('build', 'run'))
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-rnaseqmap@2.17.1:', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))
depends_on('r-rnaseqmap', type=('build', 'run'))
depends_on('r-rgl', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-gplots', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
depends_on('r-statmod', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r-edger', type=('build', 'run'))
depends_on('r-deseq', type=('build', 'run'))
depends_on('r-samr', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-analysispageserver/package.py
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@@ -7,15 +7,21 @@
class RAnalysispageserver(RPackage):
"""AnalysisPageServer is a modular system that enables sharing
of customizable R analyses via the web."""
"""A framework for sharing interactive data and plots from R through the
web.
homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/"
AnalysisPageServer is a modular system that enables sharing of
customizable R analyses via the web."""
homepage = "https://bioconductor.org/packages/AnalysisPageServer"
git = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
version('1.18.1', commit='08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630')
version('1.16.0', commit='67b063523f80e2af1d26262367ff50f34e195174')
version('1.14.0', commit='620c0ea1e129ddd1a0866e2c9d7c3fcf06a8baf4')
version('1.12.0', commit='146501974ef1938ee1ec4eb293ea7eeca331a0dc')
version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50')
depends_on('r@3.4.0:3.4.9', when='@1.10.0')
depends_on('r-log4r', type=('build', 'run'))
depends_on('r-rjson', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-anaquin/package.py
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@@ -7,22 +7,28 @@
class RAnaquin(RPackage):
"""The project is intended to support the use of sequins
(synthetic sequencing spike-in controls) owned and made available
by the Garvan Institute of Medical Research. The goal is to
provide a standard open source library for quantitative analysis,
modelling and visualization of spike-in controls."""
"""Statistical analysis of sequins.
homepage = "https://www.bioconductor.org/packages/Anaquin/"
The project is intended to support the use of sequins (synthetic
sequencing spike-in controls) owned and made available by the Garvan
Institute of Medical Research. The goal is to provide a standard open
source library for quantitative analysis, modelling and visualization of
spike-in controls."""
homepage = "https://bioconductor.org/packages/Anaquin"
git = "https://git.bioconductor.org/packages/Anaquin.git"
version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601')
version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6')
version('2.4.0', commit='0d6ae80ff622151a782e4774ca274f06024a71d2')
version('2.2.0', commit='739f4ed2b73c43f934fd65a993ecb48242a5d5da')
version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
depends_on('r@3.4.0:3.4.9', when='@1.2.0')
depends_on('r-deseq2', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
depends_on('r-rocr', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-deseq2', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-aneufinder/package.py
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@@ -7,21 +7,28 @@
class RAneufinder(RPackage):
"""This package implements functions for CNV calling, plotting,
export and analysis from whole-genome single cell sequencing data."""
"""Analysis of Copy Number Variation in Single-Cell-Sequencing Data.
homepage = "https://www.bioconductor.org/packages/AneuFinder/"
AneuFinder implements functions for copy-number detection, breakpoint
detection, and karyotype and heterogeneity analysis in single-cell whole
genome sequencing and strand-seq data."""
homepage = "https://bioconductor.org/packages/AneuFinder"
git = "https://git.bioconductor.org/packages/AneuFinder.git"
version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e')
version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd')
version('1.8.0', commit='36a729d244add5aafbe21c37a1baaea6a50354d3')
version('1.6.0', commit='0cfbdd1951fb4df5622e002260cfa86294d65d1d')
version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
depends_on('r@3.4.0:3.4.9', when='@1.4.0')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-cowplot', type=('build', 'run'))
depends_on('r-aneufinderdata', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-doparallel', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.4.0:1.6.0', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
@@ -33,6 +40,10 @@ class RAneufinder(RPackage):
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-ggdendro', type=('build', 'run'))
depends_on('r-ggrepel', type=('build', 'run'))
depends_on('r-reordercluster', type=('build', 'run'))
depends_on('r-mclust', type=('build', 'run'))
depends_on('r-ggrepel', type=('build', 'run'))
depends_on('r-ecp', when='@1.8.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run'))

14
var/spack/repos/builtin/packages/r-aneufinderdata/package.py
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@@ -7,12 +7,18 @@
class RAneufinderdata(RPackage):
"""Whole-genome single cell sequencing data for demonstration
purposes in the AneuFinder package."""
"""WGSCS Data for Demonstration Purposes.
homepage = "https://www.bioconductor.org/packages/AneuFinderData/"
Whole-genome single cell sequencing data for demonstration purposes in
the AneuFinder package."""
homepage = "https://bioconductor.org/packages/AneuFinderData"
git = "https://git.bioconductor.org/packages/AneuFinderData.git"
version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1')
version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035')
version('1.8.0', commit='4f00f8d5f2e968fea667a7feafc0a4607d6e0c6e')
version('1.6.0', commit='8fe5b221619aab75fe84c9094708d240dd1e6730')
version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
depends_on('r@3.4.0:3.4.9', when='@1.4.0')
depends_on('r@3.3:', type=('build', 'run'))

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@@ -3,24 +3,29 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
#
#
from spack import *
class RAnnaffy(RPackage):
"""Functions for handling data from Bioconductor Affymetrix
annotation data packages. Produces compact HTML and text
reports including experimental data and URL links to many
online databases. Allows searching biological metadata
using various criteria."""
"""Annotation tools for Affymetrix biological metadata.
homepage = "https://www.bioconductor.org/packages/annaffy/"
Functions for handling data from Bioconductor Affymetrix annotation data
packages. Produces compact HTML and text reports including experimental
data and URL links to many online databases. Allows searching biological
metadata using various criteria."""
homepage = "https://bioconductor.org/packages/annaffy"
git = "https://git.bioconductor.org/packages/annaffy.git"
version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233')
version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484')
version('1.52.0', commit='ef84030163045f702941c8d5a59fbd4a09f30e2c')
version('1.50.0', commit='a822e20f3e961a8afa5eb23536343115a33fb259')
version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
depends_on('r@3.4.0:3.4.9', when='@1.48.0')
depends_on('r@2.5.0:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-kegg-db', type=('build', 'run'))
depends_on('r-annotationdbi@0.1.15:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-annotate/package.py
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@@ -7,17 +7,24 @@
class RAnnotate(RPackage):
"""Using R enviroments for annotation."""
"""Annotation for microarrays.
homepage = "https://www.bioconductor.org/packages/annotate/"
Using R enviroments for annotation."""
homepage = "https://bioconductor.org/packages/annotate"
git = "https://git.bioconductor.org/packages/annotate.git"
version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd')
version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16')
version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc')
version('1.56.2', commit='95ec3b004f5356bd78b2a60cbf7f93e0d48cf346')
version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-annotationdbi@1.27.5:', type=('build', 'run'))
depends_on('r-xml', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-xtable', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-annotationdbi/package.py
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@@ -7,19 +7,28 @@
class RAnnotationdbi(RPackage):
"""Provides user interface and database connection code for
annotation data packages using SQLite data storage."""
"""Manipulation of SQLite-based annotations in Bioconductor.
homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
Implements a user-friendly interface for querying SQLite-based
annotation data packages."""
homepage = "https://bioconductor.org/packages/AnnotationDbi"
git = "https://git.bioconductor.org/packages/AnnotationDbi.git"
version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9')
version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac')
version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3')
version('1.40.0', commit='e34dff07e10402eecbf95604a512bc1fc4edb127')
version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
depends_on('r@3.4.0:3.4.9', when='@1.38.2', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.42.1', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-biobase@1.17.0:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-annotationfilter/package.py
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@@ -7,16 +7,21 @@
class RAnnotationfilter(RPackage):
"""This package provides class and other infrastructure to implement
filters for manipulating Bioconductor annotation resources. The
filters will be used by ensembldb, Organism.dplyr, and other
packages."""
"""Facilities for Filtering Bioconductor Annotation Resources.
homepage = "https://bioconductor.org/packages/AnnotationFilter/"
This package provides class and other infrastructure to implement
filters for manipulating Bioconductor annotation resources. The filters
will be used by ensembldb, Organism.dplyr, and other packages."""
homepage = "https://bioconductor.org/packages/AnnotationFilter"
git = "https://git.bioconductor.org/packages/AnnotationFilter.git"
version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed')
version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3')
version('1.4.0', commit='acbd3309f478843a7899bd9773af5f19f986b829')
version('1.2.0', commit='744b82915d7b85031de462d9d0a2bf9fdfd0e29d')
version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-lazyeval', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.0.0')

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var/spack/repos/builtin/packages/r-annotationforge/package.py
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@@ -7,19 +7,24 @@
class RAnnotationforge(RPackage):
"""Provides code for generating Annotation packages and
their databases. Packages produced are intended to be used
with AnnotationDbi."""
"""Tools for building SQLite-based annotation data packages.
homepage = "https://www.bioconductor.org/packages/AnnotationForge/"
Provides code for generating Annotation packages and their databases.
Packages produced are intended to be used with AnnotationDbi."""
homepage = "https://bioconductor.org/packages/AnnotationForge"
git = "https://git.bioconductor.org/packages/AnnotationForge.git"
version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e')
version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d')
version('1.22.2', commit='8eafb1690c1c02f6291ccbb38ac633d54b8217f8')
version('1.20.0', commit='7b440f1570cb90acce8fe2fa8d3b5ac34f638882')
version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
depends_on('r@3.4.0:3.4.9', when='@1.18.2')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r@2.7.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-biobase@1.17.0:', type=('build', 'run'))
depends_on('r-annotationdbi@1.33.14:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-xml', type=('build', 'run'))

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@@ -7,25 +7,39 @@
class RAnnotationhub(RPackage):
"""This package provides a client for the Bioconductor AnnotationHub web
"""Client to access AnnotationHub resources.
This package provides a client for the Bioconductor AnnotationHub web
resource. The AnnotationHub web resource provides a central location
where genomic files (e.g., VCF, bed, wig) and other resources from
standard locations (e.g., UCSC, Ensembl) can be discovered. The
resource includes metadata about each resource, e.g., a textual
description, tags, and date of modification. The client creates and
manages a local cache of files retrieved by the user, helping with
quick and reproducible access."""
standard locations (e.g., UCSC, Ensembl) can be discovered. The resource
includes metadata about each resource, e.g., a textual description,
tags, and date of modification. The client creates and manages a local
cache of files retrieved by the user, helping with quick and
reproducible access."""
homepage = "https://bioconductor.org/packages/AnnotationHub/"
homepage = "https://bioconductor.org/packages/AnnotationHub"
git = "https://git.bioconductor.org/packages/AnnotationHub.git"
version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed')
version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12')
version('2.12.1', commit='471407bd9cdc612e01deb071c91bd9e5f1ea5e55')
version('2.10.1', commit='b7cb668de9b9625ac2beb3dcde1fa39e289eec29')
version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-interactivedisplaybase', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-yaml', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.8.3')
depends_on('r-curl', when='@2.10.1:', type=('build', 'run'))
depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run'))
depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run'))
depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run'))
depends_on('r-dplyr', when='@2.16.1:', type=('build', 'run'))

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@@ -7,20 +7,30 @@
class RBamsignals(RPackage):
"""This package allows to efficiently obtain count vectors
from indexed bam files. It counts the number of reads in given
genomic ranges and it computes reads profiles and coverage
profiles. It also handles paired-end data."""
"""Extract read count signals from bam files.
homepage = "https://www.bioconductor.org/packages/bamsignals/"
This package allows to efficiently obtain count vectors from indexed bam
files. It counts the number of reads in given genomic ranges and it
computes reads profiles and coverage profiles. It also handles paired-
end data."""
homepage = "https://bioconductor.org/packages/bamsignals"
git = "https://git.bioconductor.org/packages/bamsignals.git"
version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657')
version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d')
version('1.12.1', commit='06b6282df377cf9db58e8016be4ac8ddcc960939')
version('1.10.0', commit='7499312ce71e8680680eda10b49d7dff682fc776')
version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
depends_on('r@3.4.0:3.4.9', when='@1.8.0')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-rcpp@0.10.6:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-rhtslib', type=('build', 'run'))
depends_on('r-rhtslib@1.12.1:', when='@1.12.1:', type=('build', 'run'))
depends_on('r-rhtslib@1.13.1:', when='@1.14.0:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBeachmat(RPackage):
"""Compiling Bioconductor to Handle Each Matrix Type.
Provides a consistent C++ class interface for reading from and writing
data to a variety of commonly used matrix types. Ordinary matrices and
several sparse/dense Matrix classes are directly supported, third-party
S4 classes may be supported by external linkage, while all other
matrices are handled by DelayedArray block processing."""
homepage = "https://bioconductor.org/packages/beachmat"
git = "https://git.bioconductor.org/packages/beachmat.git"
version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab')
version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a')
version('1.2.1', commit='ebae81772045a314e568c2f7d73ea3b27e7bf7d8')
version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-rcpp@0.12.14:', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r-rhdf5', when='@1.0.2:1.4.0', type=('build', 'run'))
depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run'))
depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run'))
depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run'))
depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run'))
depends_on('r-hdf5array@1.9.5:', when='@1.4.0', type=('build', 'run'))
depends_on('r-delayedarray@0.7.38:', when='@1.4.0', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBeeswarm(RPackage):
"""beeswarm: The Bee Swarm Plot, an Alternative to Stripchart"""
homepage = "http://www.cbs.dtu.dk/~eklund/beeswarm/"
url = "https://cloud.r-project.org/src/contrib/beeswarm_0.2.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/beeswarm"
version('0.2.3', sha256='0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843')

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var/spack/repos/builtin/packages/r-biobase/package.py
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@@ -3,21 +3,25 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
#
from spack import *
class RBiobase(RPackage):
"""Functions that are needed by many other packages
or which replace R functions."""
"""Biobase: Base functions for Bioconductor.
homepage = "https://www.bioconductor.org/packages/Biobase/"
Functions that are needed by many other packages or which replace R
functions."""
homepage = "https://bioconductor.org/packages/Biobase"
git = "https://git.bioconductor.org/packages/Biobase.git"
version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3')
version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d')
version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5')
version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
depends_on('r-biocgenerics@0.16.1:', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.36.2', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@2.40.0', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.3.2:', type=('build', 'run'))
depends_on('r-biocgenerics@0.27.1:', when='@2.42.0:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocfilecache(RPackage):
"""Manage Files Across Sessions.
This package creates a persistent on-disk cache of files that the user
can add, update, and retrieve. It is useful for managing resources (such
as custom Txdb objects) that are costly or difficult to create, web
resources, and data files used across sessions."""
homepage = "https://bioconductor.org/packages/BiocFileCache"
git = "https://git.bioconductor.org/packages/BiocFileCache.git"
version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0')
version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba')
version('1.4.0', commit='a2c473d17f78899c7899b9638faea8c30735eb80')
version('1.2.3', commit='d78bf5b46c8a329f5ddef879fe51230444bc42f8')
version('1.0.1', commit='dbf4e8dd4d8d9f475066cd033481efe95c56df75')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-dbplyr@1.0.0:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rappdirs', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-curl', when='@1.6.0:', type=('build', 'run'))

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class RBiocgenerics(RPackage):
"""S4 generic functions needed by many Bioconductor packages."""
"""S4 generic functions used in Bioconductor.
homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
The package defines S4 generic functions used in Bioconductor."""
homepage = "https://bioconductor.org/packages/BiocGenerics"
git = "https://git.bioconductor.org/packages/BiocGenerics.git"
version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8')
version('0.28.0', commit='041fc496504f2ab1d4d863fffb23372db214394b')
version('0.26.0', commit='5b2a6df639e48c3cd53789e0b174aec9dda6b67d')
version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
depends_on('r@3.4.0:3.4.9', when='@0.22.1', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@0.26.0', type=('build', 'run'))
depends_on('r@3.6.0:', when='@0.30.0', type=('build', 'run'))
depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run'))

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class RBiocinstaller(RPackage):
"""This package is used to install and update Bioconductor, CRAN,
and (some) github packages."""
"""Install/Update Bioconductor, CRAN, and github Packages.
homepage = "https://bioconductor.org/packages/BiocInstaller/"
This package is used to install and update Bioconductor, CRAN, and
(some) github packages."""
homepage = "https://bioconductor.org/packages/3.8/bioc/html/BiocInstaller.html"
git = "https://git.bioconductor.org/packages/BiocInstaller.git"
version('1.33.1', commit='6193f31c18e7e64d91e0e15ed0ba6924eda1416f')
version('1.32.1', commit='4c2a39e1cae470af3a5cf1491715f272b70f4bb4')
version('1.30.0', commit='27bcb7a378cb5d8b5d23b7b840340463f7e090bc')
version('1.28.0', commit='7261763529a0a1f730cde8a1bbdbf454c3e25603')
version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
depends_on('r@3.4.0:3.4.9', when='@1.26.1')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.30.0:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocmanager(RPackage):
"""BiocManager: Access the Bioconductor Project Package Repository"""
homepage = "https://cloud.r-project.org/package=BiocManager"
url = "https://cloud.r-project.org/src/contrib/BiocManager_1.30.10.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/BiocManager"
version('1.30.10', sha256='f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e')

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocneighbors(RPackage):
"""Nearest Neighbor Detection for Bioconductor Packages.
Implements exact and approximate methods for nearest neighbor detection,
in a framework that allows them to be easily switched within
Bioconductor packages or workflows. Exact searches can be performed
using the k-means for k-nearest neighbors algorithm or with vantage
point trees. Approximate searches can be performed using the Annoy or
HNSW libraries. Searching on either Euclidean or Manhattan distances is
supported. Parallelization is achieved for all methods by using
BiocParallel. Functions are also provided to search for all neighbors
within a given distance."""
homepage = "https://bioconductor.org/packages/BiocNeighbors"
git = "https://git.bioconductor.org/packages/BiocNeighbors.git"
version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273')
version('1.0.0', commit='e252fc04b6d22097f2c5f74406e77d85e7060770')
depends_on('r@3.5:', when='@1.0.0', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-rcppannoy', type=('build', 'run'))
depends_on('r-biocgenerics', when='@1.2.0:', type=('build', 'run'))
depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run'))

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class RBiocparallel(RPackage):
"""This package provides modified versions and novel implementation of
"""Bioconductor facilities for parallel evaluation.
This package provides modified versions and novel implementation of
functions for parallel evaluation, tailored to use with Bioconductor
objects."""
homepage = "https://bioconductor.org/packages/BiocParallel/"
homepage = "https://bioconductor.org/packages/BiocParallel"
git = "https://git.bioconductor.org/packages/BiocParallel.git"
version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e')
version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4')
version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299')
version('1.12.0', commit='2143a9addceed0151a27b95c70aadd2add5cbace')
version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
depends_on('r-futile-logger', type=('build', 'run'))
depends_on('r-snow', type=('build', 'run'))
depends_on('r-bh', type=('build', 'link', 'run'), when='@1.14.2:')
depends_on('r@3.4.0:3.4.9', when='@1.10.1', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.14.2', type=('build', 'run'))
depends_on('r-bh', when='@1.12.0:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocsingular(RPackage):
"""Singular Value Decomposition for Bioconductor Packages.
Implements exact and approximate methods for singular value
decomposition and principal components analysis, in a framework that
allows them to be easily switched within Bioconductor packages or
workflows. Where possible, parallelization is achieved using the
BiocParallel framework."""
homepage = "https://bioconductor.org/packages/BiocSingular"
git = "https://git.bioconductor.org/packages/BiocSingular.git"
version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-irlba', type=('build', 'run'))
depends_on('r-rsvd', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-beachmat', type=('build', 'run'))

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class RBiocstyle(RPackage):
"""Provides standard formatting styles for Bioconductor PDF and HTML
documents. Package vignettes illustrate use and functionality."""
"""Standard styles for vignettes and other Bioconductor documents.
homepage = "https://www.bioconductor.org/packages/BiocStyle/"
Provides standard formatting styles for Bioconductor PDF and HTML
documents. Package vignettes illustrate use and functionality."""
homepage = "https://bioconductor.org/packages/BiocStyle"
git = "https://git.bioconductor.org/packages/BiocStyle.git"
version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498')
version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70')
version('2.8.2', commit='3210c19ec1e5e0ed8d5a2d31da990aa47b42dbd8')
version('2.6.1', commit='5ff52cbb439a45575d0f58c4f7a83195a8b7337b')
version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
depends_on('r-bookdown', type=('build', 'run'))
depends_on('r-knitr@1.12:', type=('build', 'run'))
depends_on('r-rmarkdown@1.2:', type=('build', 'run'))
depends_on('r-yaml', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.4.1')
depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run'))

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class RBiomart(RPackage):
"""In recent years a wealth of biological data has become available in
"""Interface to BioMart databases (i.e. Ensembl).
In recent years a wealth of biological data has become available in
public data repositories. Easy access to these valuable data resources
and firm integration with data analysis is needed for comprehensive
bioinformatics data analysis. biomaRt provides an interface to a growing
collection of databases implementing the BioMart software suite
(http://www.biomart.org). The package enables retrieval of large amounts
of data in a uniform way without the need to know the underlying
database schemas or write complex SQL queries. Examples of BioMart
databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and
dbSNP mapped to Ensembl. These major databases give biomaRt users direct
access to a diverse set of data and enable a wide range of powerful
online queries from gene annotation to database mining."""
(<http://www.biomart.org>). The package enables retrieval of large
amounts of data in a uniform way without the need to know the underlying
database schemas or write complex SQL queries. The most prominent
examples of BioMart databases are maintain by Ensembl, which provides
biomaRt users direct access to a diverse set of data and enables a wide
range of powerful online queries from gene annotation to database
mining."""
homepage = "https://bioconductor.org/packages/biomaRt/"
homepage = "https://bioconductor.org/packages/biomaRt"
git = "https://git.bioconductor.org/packages/biomaRt.git"
version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68')
version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658')
version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f')
version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b')
version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
@@ -30,8 +34,7 @@ class RBiomart(RPackage):
depends_on('r-xml', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-progress', type=('build', 'run'), when='@2.34.2:')
depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:')
depends_on('r-httr', type=('build', 'run'), when='@2.34.2:')
depends_on('r@3.4.0:3.4.9', when='@2.32.1:2.35.9', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@2.36.1', type=('build', 'run'))
depends_on('r-progress', when='@2.34.2:', type=('build', 'run'))
depends_on('r-stringr', when='@2.34.2:', type=('build', 'run'))
depends_on('r-httr', when='@2.34.2:', type=('build', 'run'))

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class RBiomformat(RPackage):
"""This is an R package for interfacing with the BIOM format. This
package includes basic tools for reading biom-format files, accessing
and subsetting data tables from a biom object (which is more complex
than a single table), as well as limited support for writing a
biom-object back to a biom-format file. The design of this API is
intended to match the python API and other tools included with the
biom-format project, but with a decidedly "R flavor" that should be
familiar to R users. This includes S4 classes and methods, as well
as extensions of common core functions/methods."""
"""An interface package for the BIOM file format.
homepage = "https://www.bioconductor.org/packages/biomformat/"
This is an R package for interfacing with the BIOM format. This package
includes basic tools for reading biom-format files, accessing and
subsetting data tables from a biom object (which is more complex than a
single table), as well as limited support for writing a biom-object back
to a biom-format file. The design of this API is intended to match the
python API and other tools included with the biom-format project, but
with a decidedly "R flavor" that should be familiar to R users. This
includes S4 classes and methods, as well as extensions of common core
functions/methods."""
homepage = "https://bioconductor.org/packages/biomformat"
git = "https://git.bioconductor.org/packages/biomformat.git"
version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a')
version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09')
version('1.8.0', commit='acd207377b24e4d8310eaff06c16dcfe6c04509a')
version('1.6.0', commit='61fb8c7b34ad561c3c46cacc0dd1957be56da85e')
version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r-plyr@1.8:', type=('build', 'run'))
depends_on('r-jsonlite@0.9.16:', type=('build', 'run'))
depends_on('r-matrix@1.2:', type=('build', 'run'))
depends_on('r-rhdf5', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.4.0')

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class RBiostrings(RPackage):
"""Memory efficient string containers, string matching algorithms, and
other utilities, for fast manipulation of large biological sequences
or sets of sequences."""
"""Efficient manipulation of biological strings.
homepage = "https://bioconductor.org/packages/Biostrings/"
Memory efficient string containers, string matching algorithms, and
other utilities, for fast manipulation of large biological sequences or
sets of sequences."""
homepage = "https://bioconductor.org/packages/Biostrings"
git = "https://git.bioconductor.org/packages/Biostrings.git"
version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5')
version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2')
version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b')
version('2.46.0', commit='3bf6978c155498b50607d1bb471d1687d185a0fa')
version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.6:', when='@2.48.0', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@2.48.0', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r@2.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges@2.9.18:', when='@2.44.2:2.46.0', type=('build', 'run'))
depends_on('r-xvector@0.11.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@2.48.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@2.48.0', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.44.2', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@2.48.0', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@2.48.0:', type=('build', 'run'))
depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run'))
depends_on('r-xvector@0.21.4:', when='@2.50.2:', type=('build', 'run'))
depends_on('r-iranges', when='@2.50.2:', type=('build', 'run'))
depends_on('r-s4vectors@0.21.13:', when='@2.52.0:', type=('build', 'run'))
depends_on('r-xvector@0.23.2:', when='@2.52.0:', type=('build', 'run'))

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@@ -7,33 +7,40 @@
class RBiovizbase(RPackage):
"""The biovizBase package is designed to provide a set of
utilities, color schemes and conventions for genomic data.
It serves as the base for various high-level packages for
biological data visualization. This saves development effort
and encourages consistency."""
"""Basic graphic utilities for visualization of genomic data..
homepage = "http://bioconductor.org/packages/biovizBase/"
The biovizBase package is designed to provide a set of utilities, color
schemes and conventions for genomic data. It serves as the base for
various high-level packages for biological data visualization. This
saves development effort and encourages consistency."""
homepage = "https://bioconductor.org/packages/biovizBase"
git = "https://git.bioconductor.org/packages/biovizBase.git"
version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82')
version('1.28.2', commit='43d09060028665a237b04bfeb9e2575782b08063')
version('1.26.0', commit='640742f48384f01d117b70dc5c64737e97ae9b4b')
version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
depends_on('r@3.4.0:3.4.9', when='@1.24.0')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-dichromat', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges@1.99.28:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.5.14:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-biostrings@2.33.11:', type=('build', 'run'))
depends_on('r-rsamtools@1.17.28:', type=('build', 'run'))
depends_on('r-genomicalignments@1.1.16:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.21.19:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-variantannotation', type=('build', 'run'))
depends_on('r-ensembldb', type=('build', 'run'))
depends_on('r-annotationfilter', type=('build', 'run'))
depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
depends_on('r-annotationfilter@0.99.8:', type=('build', 'run'))
depends_on('r-rlang', when='@1.28.2:', type=('build', 'run'))

33
var/spack/repos/builtin/packages/r-bsgenome/package.py
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@@ -7,25 +7,36 @@
class RBsgenome(RPackage):
"""Infrastructure shared by all the Biostrings-based genome data
packages."""
"""Software infrastructure for efficient representation of full genomes and
their SNPs."""
homepage = "https://www.bioconductor.org/packages/BSgenome/"
homepage = "https://bioconductor.org/packages/BSgenome"
git = "https://git.bioconductor.org/packages/BSgenome.git"
version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b')
version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9')
version('1.48.0', commit='092a1b90482ace329cbd8ca2a338e91449acb93e')
version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
depends_on('r@2.8.0:', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))
depends_on('r-iranges@2.1.33:', type=('build', 'run'), when='@1.44.2')
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0')
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'), when='@1.44.2')
depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0')
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'), when='@1.44.2')
depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0')
depends_on('r-iranges@2.1.33:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.44.2:')
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.16:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run'))

20
var/spack/repos/builtin/packages/r-bumphunter/package.py
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@@ -7,15 +7,22 @@
class RBumphunter(RPackage):
"""Tools for finding bumps in genomic data"""
"""Bump Hunter.
homepage = "http://bioconductor.org/packages/bumphunter/"
Tools for finding bumps in genomic data"""
homepage = "https://bioconductor.org/packages/bumphunter"
git = "https://git.bioconductor.org/packages/bumphunter.git"
version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa')
version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b')
version('1.22.0', commit='fb71b193f4ef7fa12d100441e6eb498765f7afde')
version('1.20.0', commit='c9d8e7ab0c19299988e5d7fa74970312e9a1eac0')
version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges@2.3.23:', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
@@ -27,4 +34,7 @@ class RBumphunter(RPackage):
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.16.0')
depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run'))
depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run'))

12
var/spack/repos/builtin/packages/r-category/package.py
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@@ -7,14 +7,20 @@
class RCategory(RPackage):
"""A collection of tools for performing category analysis."""
"""Category Analysis.
homepage = "https://www.bioconductor.org/packages/Category/"
A collection of tools for performing category (gene set enrichment)
analysis."""
homepage = "https://bioconductor.org/packages/Category"
git = "https://git.bioconductor.org/packages/Category.git"
version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9')
version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5')
version('2.46.0', commit='c8aeee4dee3fb120f25e0647dd06e895a3ffbc2a')
version('2.44.0', commit='eaba50c1a801ba7983e6ffdf41ab0fc9cfe5a626')
version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
depends_on('r@3.4.0:3.4.9', when='@2.42.1')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))

5
var/spack/repos/builtin/packages/r-chemometrics/package.py
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@@ -7,8 +7,9 @@
class RChemometrics(RPackage):
"""R companion to the book "Introduction to Multivariate Statistical Analysis
in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)."""
"""R companion to the book "Introduction to Multivariate Statistical
Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser
(2009)."""
homepage = "https://cloud.r-project.org/package=chemometrics"
url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"

19
var/spack/repos/builtin/packages/r-clue/package.py Normal file
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@@ -0,0 +1,19 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RClue(RPackage):
"""clue: Cluster Ensembles"""
homepage = "https://cloud.r-project.org/package=clue"
url = "https://cloud.r-project.org/src/contrib/clue_0.3-57.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/clue"
version('0.3-57', sha256='6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17')
depends_on('r@3.2.0:', type=('build', 'run'))
depends_on('r-cluster', type=('build', 'run'))

40
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@@ -7,22 +7,36 @@
class RClusterprofiler(RPackage):
"""This package implements methods to analyze and visualize functional
profiles (GO and KEGG) of gene and gene clusters."""
"""statistical analysis and visualization of functional profiles for genes
and gene clusters.
homepage = "https://www.bioconductor.org/packages/clusterProfiler/"
This package implements methods to analyze and visualize functional
profiles (GO and KEGG) of gene and gene clusters."""
homepage = "https://bioconductor.org/packages/clusterProfiler"
git = "https://git.bioconductor.org/packages/clusterProfiler.git"
version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c')
version('3.8.1', commit='81e1a7ac49e4713703c55f87f945b20de5e7ab36')
version('3.6.0', commit='ff15e3dba69b93bc872d5f5d07821cd9ae20d829')
version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
depends_on('r@3.4.0:3.4.9', when='@3.4.4')
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-rvcheck', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r@3.3.1:', type=('build', 'run'))
depends_on('r-dose@3.1.3:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-dose', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-rvcheck', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run'))
depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-cner/package.py
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@@ -7,22 +7,29 @@
class RCner(RPackage):
""""Large-scale identification and advanced visualization of sets of
conserved noncoding elements."""
"""CNE Detection and Visualization.
homepage = "https://bioconductor.org/packages/CNEr/"
Large-scale identification and advanced visualization of sets of
conserved noncoding elements."""
homepage = "https://bioconductor.org/packages/CNEr"
git = "https://git.bioconductor.org/packages/CNEr.git"
version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5')
version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606')
version('1.16.1', commit='a2bec4b98d5938709f959a69c151f553ef357941')
version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017')
depends_on('r@3.2.2:', type=('build', 'run'))
depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
depends_on('r-dbi@0.7:', type=('build', 'run'))
depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.5:', type=('build', 'run'))
depends_on('r-xvector@0.5.4:', type=('build', 'run'))
depends_on('r-genomicalignments@1.1.9:', type=('build', 'run'))
depends_on('r-dbi@0.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges@2.5.27:', type=('build', 'run'))
depends_on('r-readr@0.2.2:', type=('build', 'run'))
@@ -32,6 +39,8 @@ class RCner(RPackage):
depends_on('r-powerlaw@0.60.3:', type=('build', 'run'))
depends_on('r-annotate@1.50.0:', type=('build', 'run'))
depends_on('r-go-db@3.3.0:', type=('build', 'run'))
depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
depends_on('r-r-utils@2.3.0:', type=('build', 'run'))
depends_on('r@3.4.3:3.4.9', when='@1.14.0')
depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run'))
depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run'))

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@@ -7,20 +7,34 @@
class RComplexheatmap(RPackage):
"""Complex heatmaps are efficient to visualize associations between
different sources of data sets and reveal potential structures. Here
the ComplexHeatmap package provides a highly flexible way to arrange
multiple heatmaps and supports self-defined annotation graphics."""
"""Make Complex Heatmaps.
homepage = "https://bioconductor.org/packages/ComplexHeatmap/"
Complex heatmaps are efficient to visualize associations between
different sources of data sets and reveal potential patterns. Here the
ComplexHeatmap package provides a highly flexible way to arrange
multiple heatmaps and supports various annotation graphics."""
homepage = "https://bioconductor.org/packages/ComplexHeatmap"
git = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4')
version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f')
version('1.18.1', commit='be0dd9d666a219c61335efe0dac50b2eed2a8825')
version('1.17.1', commit='f647c97e556d9e918a17be15883a0b72a91d688f')
version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
depends_on('r-circlize', type=('build', 'run'))
depends_on('r@3.1.2:', type=('build', 'run'))
depends_on('r-circlize@0.3.4:', type=('build', 'run'))
depends_on('r-getoptlong', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-dendextend', type=('build', 'run'))
depends_on('r-globaloptions', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.14.0')
depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', type=('build', 'run'))
depends_on('r-globaloptions@0.0.10:', type=('build', 'run'))
depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', type=('build', 'run'))
depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run'))
depends_on('r-clue', when='@2.0.0:', type=('build', 'run'))
depends_on('r-png', when='@2.0.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-ctc/package.py
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@@ -7,13 +7,18 @@
class RCtc(RPackage):
"""Tools for export and import classification trees and clusters
to other programs"""
"""Cluster and Tree Conversion..
homepage = "https://www.bioconductor.org/packages/release/bioc/html/ctc.html"
Tools for export and import classification trees and clusters to other
programs"""
homepage = "https://bioconductor.org/packages/ctc"
git = "https://git.bioconductor.org/packages/ctc.git"
version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb')
version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f')
version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e')
version('1.52.0', commit='ffff8693cab5ebad610d139367f089418f1830a1')
version('1.50.0', commit='4ee7519c3e5172e140c2658b4cf5271d229acc7e')
depends_on('r-amap', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.54.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-delayedarray/package.py
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@@ -7,37 +7,42 @@
class RDelayedarray(RPackage):
"""Wrapping an array-like object (typically an on-disk object) in a
DelayedArray object allows one to perform common array operations on it
without loading the object in memory. In order to reduce memory usage
and optimize performance, operations on the object are either delayed
or executed using a block processing mechanism. Note that this also
works on in-memory array-like objects like DataFrame objects (typically
with Rle columns), Matrix objects, and ordinary arrays and data frames.
"""A unified framework for working transparently with on-disk and in-memory
array-like datasets.
Wrapping an array-like object (typically an on-disk object) in a
DelayedArray object allows one to perform common array operations on it
without loading the object in memory. In order to reduce memory usage
and optimize performance, operations on the object are either delayed
or executed using a block processing mechanism. Note that this also
works on in-memory array-like objects like DataFrame objects (typically
with Rle columns), Matrix objects, and ordinary arrays and data
frames."""
and optimize performance, operations on the object are either delayed or
executed using a block processing mechanism. Note that this also works
on in-memory array-like objects like DataFrame objects (typically with
Rle columns), Matrix objects, and ordinary arrays and data frames."""
homepage = "https://bioconductor.org/packages/DelayedArray/"
homepage = "https://bioconductor.org/packages/DelayedArray"
git = "https://git.bioconductor.org/packages/DelayedArray.git"
version('0.6.5', commit='7d1cb6477cb024c38bf1ee0c9155e010249ed94e')
version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a')
version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f')
version('0.6.6', commit='bdb0ac0eee71edd40ccca4808f618fa77f595a64')
version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
depends_on('r-biocparallel', when='@0.6.5:', type=('build', 'run'))
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.1:', when='@0.6.5', type=('build', 'run'))
depends_on('r-s4vectors@0.14.3:', when='@0.2.7', type=('build', 'run'))
depends_on('r-s4vectors@0.15.3:', when='@0.4.1', type=('build', 'run'))
depends_on('r-s4vectors@0.17.43:', when='@0.6.5', type=('build', 'run'))
depends_on('r-s4vectors@0.14.3:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-matrixstats', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@0.2.7', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@0.6.5', type=('build', 'run'))
depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', type=('build', 'run'))
depends_on('r-biocparallel', when='@0.6.6:', type=('build', 'run'))
depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.15:', when='@0.8.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.21.7:', when='@0.10.0:', type=('build', 'run'))
depends_on('r-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run'))
depends_on('r-matrix', when='@0.10.0:', type=('build', 'run'))

41
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@@ -0,0 +1,41 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDelayedmatrixstats(RPackage):
"""Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects.
A port of the 'matrixStats' API for use with DelayedMatrix objects from
the 'DelayedArray' package. High-performing functions operating on rows
and columns of DelayedMatrix objects, e.g. col / rowMedians(), col /
rowRanks(), and col / rowSds(). Functions optimized per data type and
for subsetted calculations such that both memory usage and processing
time is minimized."""
homepage = "https://bioconductor.org/packages/DelayedMatrixStats"
git = "https://git.bioconductor.org/packages/DelayedMatrixStats.git"
version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d')
version('1.4.0', commit='eb5b390ef99651fe87a346848f807de95afe8971')
version('1.2.0', commit='de868e730be6280dfad41a280ab09f4d3083c9ac')
version('1.0.3', commit='e29a3444980ff727c5b12286884b06dfaebf5b5b')
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-matrixstats@0.53.1:', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run'))
depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run'))
depends_on('r-biocparallel', when='@1.4.0:', type=('build', 'run'))
depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run'))
depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run'))

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@@ -7,18 +7,24 @@
class RDeseq(RPackage):
"""Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution."""
"""Differential gene expression analysis based on the negative binomial
distribution.
homepage = "https://www.bioconductor.org/packages/DESeq/"
Estimate variance-mean dependence in count data from high-throughput
sequencing assays and test for differential expression based on a model
using the negative binomial distribution"""
homepage = "https://bioconductor.org/packages/DESeq"
git = "https://git.bioconductor.org/packages/DESeq.git"
version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e')
version('1.34.1', commit='e86f1b03a30bc02de4bfd4a0759af2f65cb48c62')
version('1.32.0', commit='e3d623b815b53d79eae7cdd09d097cc6098d28c9')
version('1.30.0', commit='90c93d991dd980d538c13b0361d3345f9546794e')
version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocgenerics@0.7.5:', type=('build', 'run'))
depends_on('r-biobase@2.21.7:', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))

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@@ -7,24 +7,27 @@
class RDeseq2(RPackage):
"""Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution."""
"""Differential gene expression analysis based on the negative binomial
distribution.
homepage = "https://www.bioconductor.org/packages/DESeq2/"
Estimate variance-mean dependence in count data from high-throughput
sequencing assays and test for differential expression based on a model
using the negative binomial distribution."""
homepage = "https://bioconductor.org/packages/DESeq2"
git = "https://git.bioconductor.org/packages/DESeq2.git"
version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce')
version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5')
version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb')
depends_on("r-rcpparmadillo", type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run'))
depends_on('r-biocgenerics@0.7.5:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))
@@ -32,6 +35,5 @@ class RDeseq2(RPackage):
depends_on('r-geneplotter', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run'))
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
depends_on('r-rcpparmadillo', type=('build', 'run'))

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@@ -7,19 +7,25 @@
class RDirichletmultinomial(RPackage):
"""Dirichlet-multinomial mixture models can be used to describe
variability in microbial metagenomic data.
"""Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome
Data.
This package is an interface to code originally made available by
Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed
further in the man page for this package, ?DirichletMultinomial."""
Dirichlet-multinomial mixture models can be used to describe variability
in microbial metagenomic data. This package is an interface to code
originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE
7(2): 1-15, as discussed further in the man page for this package,
?DirichletMultinomial."""
homepage = "https://bioconductor.org/packages/DirichletMultinomial/"
homepage = "https://bioconductor.org/packages/DirichletMultinomial"
git = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f')
version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35')
version('1.22.0', commit='5864f4298105d12f345f27df77ad13bae4061ca5')
version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272')
version('1.18.0', commit='81ccc8d83b8ef84f5d3e877bc0a04233a0f63c51')
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('gsl')
depends_on('r@3.4.0:')

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class RDnacopy(RPackage):
"""Implements the circular binary segmentation (CBS) algorithm
to segment DNA copy number data and identify genomic regions
with abnormal copy number."""
"""DNA copy number data analysis.
homepage = "https://www.bioconductor.org/packages/DNAcopy/"
Implements the circular binary segmentation (CBS) algorithm to segment
DNA copy number data and identify genomic regions with abnormal copy
number."""
homepage = "https://bioconductor.org/packages/DNAcopy"
git = "https://git.bioconductor.org/packages/DNAcopy.git"
version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23')
version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a')
version('1.54.0', commit='fe2657936afbce8ee03221461dff4265e3ded4c4')
version('1.52.0', commit='2632fbecec4cef3705b85676942a59188ae9bba4')
version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')

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@@ -7,27 +7,37 @@
class RDose(RPackage):
"""This package implements five methods proposed by Resnik, Schlicker,
Jiang, Lin and Wang respectively for measuring semantic similarities
among DO terms and gene products. Enrichment analyses including
hypergeometric model and gene set enrichment analysis are also
implemented for discovering disease associations of high-throughput
biological data."""
"""Disease Ontology Semantic and Enrichment analysis.
homepage = "https://www.bioconductor.org/packages/DOSE/"
This package implements five methods proposed by Resnik, Schlicker,
Jiang, Lin and Wang respectively for measuring semantic similarities
among DO terms and gene products. Enrichment analyses including
hypergeometric model and gene set enrichment analysis are also
implemented for discovering disease associations of high-throughput
biological data."""
homepage = "https://bioconductor.org/packages/DOSE"
git = "https://git.bioconductor.org/packages/DOSE.git"
version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3')
version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639')
version('3.6.1', commit='f2967f0482cea39222bfd15767d0f4a5994f241b')
version('3.4.0', commit='dabb70de1a0f91d1767601e871f2f1c16d29a612')
version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
depends_on('r@3.4.0:3.4.9', when='@3.2.0')
depends_on('r-scales', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-fgsea', type=('build', 'run'))
depends_on('r-do-db', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r@3.3.1:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-do-db', type=('build', 'run'))
depends_on('r-fgsea', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-gosemsim@2.0.0:', type=('build', 'run'))
depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run'))
depends_on('r-qvalue', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-scales', when='@3.2.0:3.4.0', type=('build', 'run'))
depends_on('r-rvcheck', when='@3.4.0', type=('build', 'run'))
depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class REcp(RPackage):
"""ecp: Non-Parametric Multiple Change-Point Analysis of
MultivariateData"""
homepage = "https://cloud.r-project.org/package=ecp"
url = "https://cloud.r-project.org/src/contrib/ecp_3.1.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ecp"
version('3.1.1', sha256='d2ab194e22e6ab0168222fbccfcf2e25c6cd51a73edc959086b0c6e0a7410268')
depends_on('r@3.00:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))

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@@ -7,22 +7,30 @@
class REdger(RPackage):
"""Differential expression analysis of RNA-seq expression profiles with
"""Empirical Analysis of Digital Gene Expression Data in R.
Differential expression analysis of RNA-seq expression profiles with
biological replication. Implements a range of statistical methodology
based on the negative binomial distributions, including empirical Bayes
estimation, exact tests, generalized linear models and quasi-likelihood
tests. As well as RNA-seq, it be applied to differential signal analysis
of other types of genomic data that produce counts, including ChIP-seq,
SAGE and CAGE."""
Bisulfite-seq, SAGE and CAGE."""
homepage = "https://bioconductor.org/packages/edgeR/"
homepage = "https://bioconductor.org/packages/edgeR"
git = "https://git.bioconductor.org/packages/edgeR.git"
version('3.22.3', commit='e82e54afc9398ac54dc4caba0f7ae5c43e572203')
version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d')
version('3.22.5', commit='44461aa0412ef4a0d955730f365e44fc64fe1902')
version('3.20.9', commit='acbcbbee939f399673678653678cd9cb4917c4dc')
version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
depends_on('r@2.15.0:', type=('build', 'run'))
depends_on('r-limma', type=('build', 'run'))
depends_on('r-locfit', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'link', 'run'))
depends_on('r@3.5.0:3.5.9', when='@3.22.3')
depends_on('r@3.4.0:3.4.9', when='@3.18.1')
depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run'))
depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run'))
depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class REnrichplot(RPackage):
"""Visualization of Functional Enrichment Result.
The 'enrichplot' package implements several visualization methods for
interpreting functional enrichment results obtained from ORA or GSEA
analysis. All the visualization methods are developed based on 'ggplot2'
graphics."""
homepage = "https://bioconductor.org/packages/enrichplot"
git = "https://git.bioconductor.org/packages/enrichplot.git"
version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e')
version('1.2.0', commit='2eeaafb571d35a106eba8ae7df014f3201066e8b')
version('1.0.2', commit='ba7726fa0d4b581b7514dcbb04889cdbdd75ff29')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-cowplot', type=('build', 'run'))
depends_on('r-dose@3.5.1:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-ggraph', type=('build', 'run'))
depends_on('r-ggridges', type=('build', 'run'))
depends_on('r-gosemsim', type=('build', 'run'))
depends_on('r-igraph', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-upsetr', type=('build', 'run'))
depends_on('r-europepmc', when='@1.2.0:', type=('build', 'run'))
depends_on('r-ggplotify', when='@1.2.0:', type=('build', 'run'))
depends_on('r-gridextra', when='@1.2.0:', type=('build', 'run'))
depends_on('r-purrr', when='@1.2.0:', type=('build', 'run'))
depends_on('r-rcolorbrewer', when='@1.2.0:', type=('build', 'run'))

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@@ -7,36 +7,54 @@
class REnsembldb(RPackage):
"""The package provides functions to create and use transcript centric
"""Utilities to create and use Ensembl-based annotation databases.
The package provides functions to create and use transcript centric
annotation databases/packages. The annotation for the databases are
directly fetched from Ensembl using their Perl API. The functionality
and data is similar to that of the TxDb packages from the
GenomicFeatures package, but, in addition to retrieve all
gene/transcript models and annotations from the database, the ensembldb
package provides also a filter framework allowing to retrieve
annotations for specific entries like genes encoded on a chromosome
region or transcript models of lincRNA genes."""
gene/transcript models and annotations from the database, ensembldb
provides a filter framework allowing to retrieve annotations for
specific entries like genes encoded on a chromosome region or transcript
models of lincRNA genes. EnsDb databases built with ensembldb contain
also protein annotations and mappings between proteins and their
encoding transcripts. Finally, ensembldb provides functions to map
between genomic, transcript and protein coordinates."""
homepage = "https://bioconductor.org/packages/ensembldb/"
homepage = "https://bioconductor.org/packages/ensembldb"
git = "https://git.bioconductor.org/packages/ensembldb.git"
version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c')
version('2.4.1', commit='b5b6b94826a2f46a4faecb9dde750ecd3bfaf327')
version('2.2.2', commit='d71610e58aed88dbbe6a74e7a8ddfb7451398060')
version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-annotationfilter', type=('build', 'run'))
depends_on('r-rsqlite', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run'))
depends_on('r-annotationfilter@0.99.7:', type=('build', 'run'))
depends_on('r-rsqlite@1.1:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
depends_on('r-rtracklayer', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-annotationhub', type=('build', 'run'))
depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-protgenerics', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run'))
depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class REuropepmc(RPackage):
"""europepmc: R Interface to the Europe PubMed Central RESTful Web
Service"""
homepage = "http://github.com/ropensci/europepmc/"
url = "https://cloud.r-project.org/src/contrib/europepmc_0.3.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/europepmc"
version('0.3', sha256='5044a253d223e2bb8502063cd03c0fe4db856467e497d650da7ccd8f75d0f8d9')
depends_on('r@3.00:', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-progress', type=('build', 'run'))
depends_on('r-purrr', type=('build', 'run'))
depends_on('r-urltools', type=('build', 'run'))
depends_on('r-xml2', type=('build', 'run'))

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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RFarver(RPackage):
"""farver: High Performance Colour Space Manipulation"""
homepage = "https://github.com/thomasp85/farver"
url = "https://cloud.r-project.org/src/contrib/farver_2.0.1.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/farver"
version('2.0.1', sha256='1642ca1519ef80616ab044ae7f6eaf464118356f2a7875e9d0e3df60ca84012b')

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@@ -7,20 +7,30 @@
class RFgsea(RPackage):
"""The package implements an algorithm for fast gene set enrichment
analysis. Using the fast algorithm allows to make more permutations
and get more fine grained p-values, which allows to use accurate
stantard approaches to multiple hypothesis correction."""
"""Fast Gene Set Enrichment Analysis.
homepage = "https://www.bioconductor.org/packages/fgsea/"
The package implements an algorithm for fast gene set enrichment
analysis. Using the fast algorithm allows to make more permutations and
get more fine grained p-values, which allows to use accurate stantard
approaches to multiple hypothesis correction."""
homepage = "https://bioconductor.org/packages/fgsea"
git = "https://git.bioconductor.org/packages/fgsea.git"
version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b')
version('1.6.0', commit='52b801b7c2dfd8238fa8f2b402fddb4fda60271d')
version('1.4.1', commit='73de5ff364e520ac99507a9ee5a61a0d23d3c44e')
version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')
depends_on('r@3.4.0:3.4.9', when='@1.2.1')
depends_on('r-fastmatch', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-fastmatch', type=('build', 'run'))
depends_on('r-matrix', when='@1.6.0:', type=('build', 'run'))
depends_on('r-bh', when='@1.10.1:', type=('build', 'run'))

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@@ -7,17 +7,23 @@
class RGcrma(RPackage):
"""Background adjustment using sequence information"""
"""Background Adjustment Using Sequence Information."""
homepage = "https://bioconductor.org/packages/gcrma/"
homepage = "https://bioconductor.org/packages/gcrma"
git = "https://git.bioconductor.org/packages/gcrma.git"
version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224')
version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc')
version('2.52.0', commit='d6e90b05432d2a8b0583d3fed001811ecdf49d7d')
version('2.50.0', commit='cbba460d131e1073059500b8d7b168a78f963992')
version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
depends_on('r-affy', type=('build', 'run'))
depends_on('r@2.6.0:', type=('build', 'run'))
depends_on('r-affy@1.23.2:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-affyio', type=('build', 'run'))
depends_on('r-affyio@1.13.3:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biostrings@2.11.32:', type=('build', 'run'))
depends_on('r-biocinstaller', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.48.0')
depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run'))

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@@ -7,22 +7,28 @@
class RGdsfmt(RPackage):
"""This package provides a high-level R interface to CoreArray Genomic
Data Structure (GDS) data files, which are portable across platforms
with hierarchical structure to store multiple scalable array-oriented
data sets with metadata information. It is suited for large-scale
datasets, especially for data which are much larger than the available
random-access memory. The gdsfmt package offers the efficient
operations specifically designed for integers of less than 8 bits,
since a diploid genotype, like single-nucleotide polymorphism (SNP),
usually occupies fewer bits than a byte. Data compression and
decompression are available with relatively efficient random access.
It is also allowed to read a GDS file in parallel with multiple R
processes supported by the package parallel."""
"""R Interface to CoreArray Genomic Data Structure (GDS) Files.
homepage = "http://bioconductor.org/packages/gdsfmt/"
This package provides a high-level R interface to CoreArray Genomic Data
Structure (GDS) data files, which are portable across platforms with
hierarchical structure to store multiple scalable array-oriented data
sets with metadata information. It is suited for large-scale datasets,
especially for data which are much larger than the available random-
access memory. The gdsfmt package offers the efficient operations
specifically designed for integers of less than 8 bits, since a diploid
genotype, like single-nucleotide polymorphism (SNP), usually occupies
fewer bits than a byte. Data compression and decompression are available
with relatively efficient random access. It is also allowed to read a
GDS file in parallel with multiple R processes supported by the package
parallel."""
homepage = "https://bioconductor.org/packages/gdsfmt"
git = "https://git.bioconductor.org/packages/gdsfmt.git"
version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00')
version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9')
version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95')
version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
version('1.12.0', commit='d705a95b0bea7be2a2b37e939f45017337ba0fb6')
depends_on('r@3.4.0:3.4.9', when='@1.14.1')
depends_on('r@2.15.0:', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-genefilter/package.py
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@@ -7,17 +7,20 @@
class RGenefilter(RPackage):
"""Some basic functions for filtering genes"""
"""genefilter: methods for filtering genes from high-throughput
experiments."""
homepage = "https://bioconductor.org/packages/genefilter/"
homepage = "https://bioconductor.org/packages/genefilter"
git = "https://git.bioconductor.org/packages/genefilter.git"
version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf')
version('1.64.0', commit='82e91b7751bae997b9c898c219ea201fd02a8512')
version('1.62.0', commit='eb119894f015c759f93f458af7733bdb770a22ad')
version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4')
version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.9.42:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotate', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.58.1', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.62.0', type=('build', 'run'))
depends_on('r-survival', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-genelendatabase/package.py
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@@ -7,14 +7,20 @@
class RGenelendatabase(RPackage):
"""Length of mRNA transcripts for a number of genomes and gene ID
formats, largely based on UCSC table browser"""
"""Lengths of mRNA transcripts for a number of genomes.
homepage = "https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html"
Length of mRNA transcripts for a number of genomes and gene ID formats,
largely based on UCSC table browser"""
homepage = "https://bioconductor.org/packages/geneLenDataBase"
git = "https://git.bioconductor.org/packages/geneLenDataBase.git"
version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4')
version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07')
version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198')
version('1.14.0', commit='b456b3ffb04eaf335893fdec2bb10f6795dd7e08')
version('1.12.0', commit='85d6536763c12850e6c01da9e2f9e0b9c07601fe')
depends_on('r@3.5.0:3.5.9', when='@1.16.0:', type=('build', 'run'))
depends_on('r@2.11.0:', type=('build', 'run'))
depends_on('r-rtracklayer', type=('build', 'run'))
depends_on('r-genomicfeatures@1.3.15:', type=('build', 'run'))

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@@ -0,0 +1,26 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGenemeta(RPackage):
"""MetaAnalysis for High Throughput Experiments.
A collection of meta-analysis tools for analysing high throughput
experimental data"""
homepage = "https://bioconductor.org/packages/GeneMeta"
git = "https://git.bioconductor.org/packages/GeneMeta.git"
version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d')
version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7')
version('1.52.0', commit='1f21759984a5852c42a19e89ee53ffd72053d49c')
version('1.50.0', commit='0f8603653285698ed451fcbf536a4b3f90015f92')
version('1.48.0', commit='68c65304d37f5a4722cf4c25afb23214c3a2f4c8')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase@2.5.5:', type=('build', 'run'))
depends_on('r-genefilter', type=('build', 'run'))

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@@ -7,19 +7,21 @@
class RGeneplotter(RPackage):
"""Functions for plotting genomic data."""
"""Graphics related functions for Bioconductor."""
homepage = "https://www.bioconductor.org/packages/geneplotter/"
homepage = "https://bioconductor.org/packages/geneplotter"
git = "https://git.bioconductor.org/packages/geneplotter.git"
version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48')
version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad')
version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde')
version('1.56.0', commit='881d25aece3dc00cc4280457ffecdc25e93bb1f1')
version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-annotate', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))

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@@ -7,13 +7,17 @@
class RGenie3(RPackage):
"""This package implements the GENIE3 algorithm for inferring gene
regulatory networks from expression data."""
"""GEne Network Inference with Ensemble of trees.
homepage = "https://bioconductor.org/packages/GENIE3/"
This package implements the GENIE3 algorithm for inferring gene
regulatory networks from expression data."""
homepage = "https://bioconductor.org/packages/GENIE3"
git = "https://git.bioconductor.org/packages/GENIE3.git"
version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502')
version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08')
version('1.2.1', commit='1b56fe8184d521d1bb247f000efe9e2b540604c9')
version('1.0.0', commit='eb7c95ed12ea50d61e8fa20bc2b25ae9d74c302f')
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r@3.5.0:', when='@1.2.0')

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@@ -7,25 +7,29 @@
class RGenomeinfodb(RPackage):
"""Contains data and functions that define and allow translation between
different chromosome sequence naming conventions (e.g., "chr1"
versus "1"), including a function that attempts to place sequence
names in their natural, rather than lexicographic, order."""
"""Utilities for manipulating chromosome names, including modifying them to
follow a particular naming style.
homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
Contains data and functions that define and allow translation between
different chromosome sequence naming conventions (e.g., "chr1" versus
"1"), including a function that attempts to place sequence names in
their natural, rather than lexicographic, order."""
homepage = "https://bioconductor.org/packages/GenomeInfoDb"
git = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265')
version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f')
version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa')
version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', when='@1.16.0', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.16.0', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.16.0', type=('build', 'run'))
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
depends_on('r-iranges@1.99.26:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-genomeinfodbdata', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.12.3', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run'))

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@@ -13,8 +13,11 @@ class RGenomeinfodbdata(RPackage):
homepage = "https://bioconductor.org/packages/GenomeInfoDbData/"
url = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
version('1.2.1', sha256='75e6d683a29b8baeec66ba5194aa59a6aa69b04fae5a9c718a105c155fb41711',
url='https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz')
version('1.1.0', sha256='6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c',
url='https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz')
version('0.99.0', sha256='457049804bbd70f218c1c84067a23e83bdecb7304a3e4d8b697fee0b16dc1888')
depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run'))
depends_on('r@3.3:', when='@0.99.0:1.1.0', type=('build', 'run'))
depends_on('r@3.5:', when='@1.2.1:', type=('build', 'run'))

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@@ -7,35 +7,44 @@
class RGenomicalignments(RPackage):
"""Provides efficient containers for storing and manipulating short genomic
alignments (typically obtained by aligning short reads to a reference
genome). This includes read counting, computing the coverage, junction
detection, and working with the nucleotide content of the alignments."""
"""Representation and manipulation of short genomic alignments.
homepage = "https://bioconductor.org/packages/GenomicAlignments/"
Provides efficient containers for storing and manipulating short genomic
alignments (typically obtained by aligning short reads to a reference
genome). This includes read counting, computing the coverage, junction
detection, and working with the nucleotide content of the alignments."""
homepage = "https://bioconductor.org/packages/GenomicAlignments"
git = "https://git.bioconductor.org/packages/GenomicAlignments.git"
version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab')
version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', when='@1.16.0', type=('build', 'run'))
depends_on('r-iranges@2.5.36:', when='@1.12.2', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.14.2', type=('build', 'run'))
depends_on('r-iranges@2.13.25:', when='@1.16.0', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', when='@1.12.2', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.19:', when='@1.12.2', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.14.2', type=('build', 'run'))
depends_on('r-genomicranges@1.31.19:', when='@1.16.0', type=('build', 'run'))
depends_on('r-iranges@2.5.36:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0', type=('build', 'run'))
depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.16.0', type=('build', 'run'))
depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.16.0', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.15.9', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run'))
depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run'))
depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run'))

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@@ -7,7 +7,9 @@
class RGenomicfeatures(RPackage):
"""A set of tools and methods for making and manipulating transcript
"""Conveniently import and query gene models.
A set of tools and methods for making and manipulating transcript
centric annotations. With these tools the user can easily download the
genomic locations of the transcripts, exons and cds of a given organism,
from either the UCSC Genome Browser or a BioMart database (more sources
@@ -16,35 +18,40 @@ class RGenomicfeatures(RPackage):
exons, cds and genes. Flexible methods are provided for extracting the
desired features in a convenient format."""
homepage = "http://bioconductor.org/packages/GenomicFeatures/"
homepage = "https://bioconductor.org/packages/GenomicFeatures"
git = "https://git.bioconductor.org/packages/GenomicFeatures.git"
version('1.32.2', commit='8487aedc8be85a99f0c3fc90cd62430b3fec3a03')
version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555')
version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387')
version('1.32.3', commit='80807d88048858846de3750cecb9431a0e5e69e1')
version('1.30.3', commit='496bbf81beebd7c934b8d3dcea001e3e4a7d7dee')
version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-s4vectors@0.17.29:', when='@1.32.2', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.13.23:', when='@1.32.2', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.4:', when='@1.32.2', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomicranges@1.31.17:', when='@1.32.2', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationdbi@1.41.4:', when='@1.32.2', type=('build', 'run'))
depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-iranges@2.9.19:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
depends_on('r-annotationdbi@1.33.15:', type=('build', 'run'))
depends_on('r-dbi', type=('build', 'run'))
depends_on('r-rsqlite@2.0:', when='@1.28.5:', type=('build', 'run'))
depends_on('r-rsqlite@2.0:', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run'))
depends_on('r-rtracklayer', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.32.2', type=('build', 'run'))
depends_on('r-biomart', type=('build', 'run'))
depends_on('r-biomart@2.17.1:', when='@1.32.2', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-biobase@2.15.1:', when='@1.32.2', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.28.5', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run'))
depends_on('r-biostrings@2.23.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.29.24:', type=('build', 'run'))
depends_on('r-biomart@2.17.1:', type=('build', 'run'))
depends_on('r-biobase@2.15.1:', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-rmysql', when='@1.30.3', type=('build', 'run'))
depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run'))

40
var/spack/repos/builtin/packages/r-genomicranges/package.py
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@@ -7,35 +7,45 @@
class RGenomicranges(RPackage):
"""The ability to efficiently represent and manipulate genomic annotations
"""Representation and manipulation of genomic intervals.
The ability to efficiently represent and manipulate genomic annotations
and alignments is playing a central role when it comes to analyzing
high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges
package defines general purpose containers for storing and manipulating
genomic intervals and variables defined along a genome. More specialized
containers for representing and manipulating short alignments against a
reference genome, or a matrix-like summarization of an experiment, are
defined in the GenomicAlignments and SummarizedExperiment packages
defined in the GenomicAlignments and SummarizedExperiment packages,
respectively. Both packages build on top of the GenomicRanges
infrastructure."""
homepage = "https://bioconductor.org/packages/GenomicRanges/"
homepage = "https://bioconductor.org/packages/GenomicRanges"
git = "https://git.bioconductor.org/packages/GenomicRanges.git"
version('1.32.6', commit='31426be0fd6b76f7858971dc45aaf6e6d1dbac4e')
version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a')
version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd')
version('1.32.7', commit='4c56dc836dbfd0d228dc810e8d401811cdbc267c')
version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997')
version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.3:', when='@1.32.6', type=('build', 'run'))
depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.32:', when='@1.32.6', type=('build', 'run'))
depends_on('r-iranges@2.9.11:', when='@1.28.6', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3', type=('build', 'run'))
depends_on('r-iranges@2.14.4:', when='@1.32.6', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', when='@1.28.6', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.32.6', type=('build', 'run'))
depends_on('r-iranges@2.9.11:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
depends_on('r-xvector', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@1.32.6', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@1.28.6', type=('build', 'run'))
depends_on('r@3.5.0:3.5.9', when='@1.32.6', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.3:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run'))
depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run'))
depends_on('r-iranges@2.15.12:', when='@1.34.0:', type=('build', 'run'))
depends_on('r-iranges@2.17.1:', when='@1.36.1:', type=('build', 'run'))

28
var/spack/repos/builtin/packages/r-geoquery/package.py
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@@ -7,18 +7,32 @@
class RGeoquery(RPackage):
"""The NCBI Gene Expression Omnibus (GEO) is a public repository of
microarray data. Given the rich and varied nature of this resource,
it is only natural to want to apply BioConductor tools to these data.
"""Get data from NCBI Gene Expression Omnibus (GEO).
The NCBI Gene Expression Omnibus (GEO) is a public repository of
microarray data. Given the rich and varied nature of this resource, it
is only natural to want to apply BioConductor tools to these data.
GEOquery is the bridge between GEO and BioConductor."""
homepage = "https://bioconductor.org/packages/GEOquery/"
homepage = "https://bioconductor.org/packages/GEOquery"
git = "https://git.bioconductor.org/packages/GEOquery.git"
version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643')
version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97')
version('2.48.0', commit='6a8d1ca195b5c26fb717ae93beb1a8d9b7031c5e')
version('2.46.15', commit='a52b195ac640caae9679610d5b486b7cb828c0fd')
version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-xml', type=('build', 'run'))
depends_on('r-rcurl', type=('build', 'run'))
depends_on('r-xml', when='@2.42.0', type=('build', 'run'))
depends_on('r-rcurl', when='@2.42.0', type=('build', 'run'))
depends_on('r-httr', type=('build', 'run'))
depends_on('r@3.4.0:3.4.9', when='@2.42.0')
depends_on('r-readr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-xml2', when='@2.46.15:', type=('build', 'run'))
depends_on('r-dplyr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-tidyr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-magrittr', when='@2.46.15:', type=('build', 'run'))
depends_on('r-limma', when='@2.46.15:', type=('build', 'run'))
depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run'))

21
var/spack/repos/builtin/packages/r-ggbeeswarm/package.py Normal file
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@@ -0,0 +1,21 @@
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGgbeeswarm(RPackage):
"""ggbeeswarm: Categorical Scatter (Violin Point) Plots"""
homepage = "https://github.com/eclarke/ggbeeswarm"
url = "https://cloud.r-project.org/src/contrib/ggbeeswarm_0.6.0.tar.gz"
list_url = "https://cloud.r-project.org/src/contrib/Archive/ggbeeswarm"
version('0.6.0', sha256='bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-beeswarm', type=('build', 'run'))
depends_on('r-ggplot2@2.0:', type=('build', 'run'))
depends_on('r-vipor', type=('build', 'run'))

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