bioconductor-*: rm in favor of r-* copies (#49089)

var/spack/repos/builtin/packages/bioconductor-dupradar/package.py

-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class BioconductorDupradar(RPackage):
-    """Assessment of duplication rates in RNA-Seq datasets"""
-
-    homepage = "https://bioconductor.org/packages/3.16/bioc/html/dupRadar.html"
-    url = "https://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.30.0.tar.gz"
-    maintainers("pabloaledo")
-
-    bioc = "dupradar"
-
-    version(
-        "1.30.0",
-        sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d",
-        deprecated=True,
-    )
-
-    depends_on("r-kernsmooth")
-    depends_on("subread")
-    depends_on("bioconductor-rsubread")

var/spack/repos/builtin/packages/bioconductor-ebseq/package.py

-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class BioconductorEbseq(RPackage):
-    """An R package for gene and isoform differential expression analysis of RNA-seq data.
-
-    R/EBSeq is an R package for identifying genes and isoforms differentially
-    expressed (DE) across two or more biological conditions in an RNA-seq
-    experiment. Details can be found in Leng et al., 2013. It provides the syntax
-    required for identifying DE genes and isoforms in a two-group RNA-seq
-    experiment as well for identifying DE genes across more than two conditions
-    (the commands for identifying DE isoforms across more than two conditions
-    are the same as those required for gene-level analysis)."""
-
-    homepage = "https://www.biostat.wisc.edu/~kendzior/EBSEQ/"
-    url = "https://bioconductor.org/packages/release/bioc/src/contrib/EBSeq_1.40.0.tar.gz"
-    maintainers("pabloaledo")
-
-    bioc = "ebseq"
-
-    version(
-        "1.40.0",
-        sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378",
-        deprecated=True,
-    )
-
-    depends_on("r-blockmodeling")
-    depends_on("r-gplots")
-    depends_on("r-testthat")

var/spack/repos/builtin/packages/bioconductor-rsubread/package.py

-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class BioconductorRsubread(RPackage):
-    """Mapping, quantification and variant analysis of sequencing data"""
-
-    homepage = "https://bioconductor.org/packages/3.16/bioc/html/Rsubread.html"
-    url = "https://bioconductor.org/packages/release/bioc/src/contrib/Rsubread_2.14.2.tar.gz"
-
-    bioc = "rsubread"
-
-    depends_on("r-matrix")
-    depends_on("zlib-api")
-
-    version(
-        "2.14.2",
-        sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5",
-        deprecated=True,
-    )

var/spack/repos/builtin/packages/bioconductor-tximeta/package.py

-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class BioconductorTximeta(RPackage):
-    """Transcript Quantification Import with Automatic Metadata
-
-    Transcript quantification import from Salmon and alevin with automatic
-    attachment of transcript ranges and release information, and other associated
-    metadata. De novo transcriptomes can be linked to the appropriate sources with
-    linkedTxomes and shared for computational reproducibility."""
-
-    homepage = "https://bioconductor.org/packages/release/bioc/html/tximeta.html"
-    url = "https://bioconductor.org/packages/release/bioc/src/contrib/tximeta_1.18.1.tar.gz"
-
-    bioc = "tximeta"
-
-    version(
-        "1.18.1",
-        sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408",
-        deprecated=True,
-    )
-
-    depends_on("r", type=("build", "run"))
-    depends_on("r-annotationdbi")
-    depends_on("r-annotationhub")
-    depends_on("r-biocfilecache")
-    depends_on("r-biostrings")
-    depends_on("r-ensembldb")
-    depends_on("r-genomeinfodb")
-    depends_on("r-genomicfeatures")
-    depends_on("r-genomicranges")
-    depends_on("r-iranges")
-    depends_on("r-s4vectors")
-    depends_on("r-summarizedexperiment")
-    depends_on("r-tximport")
-    depends_on("r-jsonlite")
-    depends_on("r-matrix")
-    depends_on("r-tibble")