r-dss: added new package at v2.36.0 with dependencies (#17661)

This PR adds the r-dss package and the r-bsseq package, also new, as a
dependency. This includes the latest versions, which required updates to
the following dependencies:

- r-biocgenerics
- r-iranges
- r-s4vectors
- r-summarizedexperiment

Older versions of r-dss and r-bsseq are included as well to ensure
compatibility with older versions of the above dependencies.

1 files changed, 55 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py
new file mode 100644
index 0000000000..c753c549a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bsseq/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2020 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 RBsseq(RPackage):
+    """A collection of tools for analyzing and visualizing bisulfite sequencing
+    data."""
+
+    homepage = "https://github.com/kasperdanielhansen/bsseq"
+    git      = "https://git.bioconductor.org/packages/bsseq"
+
+    version('1.24.4', commit='8fe7a03')
+    version('1.22.0', commit='d4f7301')
+    version('1.20.0', commit='07e398b')
+
+    depends_on('r@3.5:', type=('build', 'run'))
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.33.6:', when='@1.24.4:', type=('build', 'run'))
+
+    depends_on('r-summarizedexperiment@1.9.18:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.17.4:', when='@1.24.4:', type=('build', 'run'))
+
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'))
+    depends_on('r-iranges@2.22.2:', when='@1.24.4:', type=('build', 'run'))
+
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-locfit', type=('build', 'run'))
+    depends_on('r-gtools', type=('build', 'run'))
+    depends_on('r-data-table@1.11.8:', type=('build', 'run'))
+
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.23.11:', when='@1.22.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.25.14:', when='@1.24.4', type=('build', 'run'))
+
+    depends_on('r-r-utils@2.0.0:', type=('build', 'run'))
+    depends_on('r-delayedmatrixstats@1.5.2:', type=('build', 'run'))
+    depends_on('r-permute', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-delayedarray@0.9.8:', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-bsgenome', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-hdf5array@1.11.9:', type=('build', 'run'))
+    depends_on('r-rhdf5', type=('build', 'run'))
+    depends_on('r-beachmat', type=('build', 'run'))