spack/var/spack/repos/builtin/packages/r-dose/package.py
Glenn Johnson e4a9d9ae5b
Bioc updates (#37297)
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
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* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
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* add version 1.32.0 to bioconductor package r-aims
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* add version 1.62.0 to bioconductor package r-annotationdbi
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* add version 3.30.0 to bioconductor package r-aroma-light
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* add version 2.16.0 to bioconductor package r-beachmat
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* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
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* add version 2.28.0 to bioconductor package r-biocstyle
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* add version 1.36.0 to bioconductor package r-bsseq
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* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
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* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
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* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
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* add version 1.82.0 to bioconductor package r-genefilter
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* add version 1.78.0 to bioconductor package r-geneplotter
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* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
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* add version 1.52.0 to bioconductor package r-genomicranges
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* update r-go-db
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* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
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* add version 1.38.0 to bioconductor package r-interactivedisplaybase
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* add version 3.56.0 to bioconductor package r-limma
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* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
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* add version 1.34.0 to bioconductor package r-missmethyl
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* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
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* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
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* add version 1.76.0 to bioconductor package r-roc
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* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
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* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
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* add version 2.52.0 to bioconductor package r-topgo
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* add version 1.28.0 to bioconductor package r-tximport
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* add version 1.46.0 to bioconductor package r-variantannotation
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* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
  This reverts commit 1702071c6d.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
  This reverts commit 58a7df2387.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
  This reverts commit 0a1f59de6c.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
  This reverts commit cd49fb8e4c.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
  This reverts commit 6e9a951cbe.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23 11:40:00 -07:00

51 lines
2.5 KiB
Python

# Copyright 2013-2023 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.package import *
class RDose(RPackage):
"""Disease Ontology Semantic and Enrichment analysis.
This package implements five methods proposed by Resnik, Schlicker,
Jiang, Lin and Wang respectively for measuring semantic similarities
among DO terms and gene products. Enrichment analyses including
hypergeometric model and gene set enrichment analysis are also
implemented for discovering disease associations of high-throughput
biological data."""
bioc = "DOSE"
version("3.26.0", commit="9c91fb45a2ab9a875a6a7259610b7d5bc86933f6")
version("3.24.1", commit="a78995d3b12bd4baabb69c497102687814cd4c68")
version("3.22.1", commit="6b711a0f076a9fefcb00ddef66e8f198039e6dfa")
version("3.22.0", commit="242ac1b746c44fbbf281fbe6e5e4424a8dc74375")
version("3.20.1", commit="bf434f24d035217822cb1b0ab08a486b9a53edb4")
version("3.16.0", commit="a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd")
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@3.3.1:", type=("build", "run"))
depends_on("r@3.4.0:", type=("build", "run"), when="@3.6.1:")
depends_on("r@3.5.0:", type=("build", "run"), when="@3.16.0:")
depends_on("r-annotationdbi", type=("build", "run"))
depends_on("r-hdo-db", type=("build", "run"), when="@3.24.1:")
depends_on("r-biocparallel", 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-gosemsim@2.23.1:", type=("build", "run"), when="@3.24.1:")
depends_on("r-qvalue", type=("build", "run"))
depends_on("r-reshape2", type=("build", "run"))
depends_on("r-s4vectors", type=("build", "run"), when="@:3.10.2")
depends_on("r-scales", type=("build", "run"), when="@3.2.0:3.4.0")
depends_on("r-rvcheck", type=("build", "run"), when="@3.4.0")
depends_on("r-igraph", type=("build", "run"), when="@3.2.0:3.4.0")
depends_on("r-do-db", type=("build", "run"), when="@:3.22.1")