Replace git-based Bioconductor R packages (#12005)

* 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>

var/spack/repos/builtin/packages/r-biocsingular/package.py

@@ -0,0 +1,31 @@
+# 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'))