New package: r-pscbs (#14867)

This PR adds the r-pscbs package along with new dependencies and updates.

- new package: r-aroma-light
- new package: r-r-cache
- updated package: r-r-oo

4 files changed, 82 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-aroma-light/package.py b/var/spack/repos/builtin/packages/r-aroma-light/package.py
new file mode 100644
index 0000000000..a704ac72b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-aroma-light/package.py
@@ -0,0 +1,23 @@
+# 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 RAromaLight(RPackage):
+    """Methods for microarray analysis that take basic data types such as
+    matrices and lists of vectors. These methods can be used standalone, be
+    utilized in other packages, or be wrapped up in higher-level classes."""
+
+    homepage = "https://www.aroma-project.org/"
+    git      = "https://git.bioconductor.org/packages/aroma.light"
+
+    version('3.16.0', commit='fc16179fc4bee8954c5415d7cd13e3112b75b4fd')
+
+    depends_on('r@2.15.2:', type=('build', 'run'))
+    depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
+    depends_on('r-r-oo@1.22.0:', type=('build', 'run'))
+    depends_on('r-r-utils@2.9.0:', type=('build', 'run'))
+    depends_on('r-matrixstats@0.54.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pscbs/package.py b/var/spack/repos/builtin/packages/r-pscbs/package.py
new file mode 100644
index 0000000000..c3197b7795
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pscbs/package.py
@@ -0,0 +1,29 @@
+# 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 RPscbs(RPackage):
+    """Segmentation of allele-specific DNA copy number data and detection of
+    regions with abnormal copy number within each parental chromosome. Both
+    tumor-normal paired and tumor-only analyses are supported."""
+
+    homepage = "https://github.com/HenrikBengtsson/PSCBS"
+    url      = "https://cloud.r-project.org/src/contrib/PSCBS_0.65.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/PSCBS"
+
+    version('0.65.0', sha256='3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a')
+
+    depends_on('r@3.2.0:', type=('build', 'run'))
+    depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
+    depends_on('r-r-oo@1.22.1:', type=('build', 'run'))
+    depends_on('r-r-utils@2.8.0:', type=('build', 'run'))
+    depends_on('r-r-cache@0.13.0:', type=('build', 'run'))
+    depends_on('r-matrixstats@0.54.0:', type=('build', 'run'))
+    depends_on('r-aroma-light@2.4.0:', type=('build', 'run'))
+    depends_on('r-dnacopy@1.42.0:', type=('build', 'run'))
+    depends_on('r-listenv@0.7.0:', type=('build', 'run'))
+    depends_on('r-future@1.12.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-r-cache/package.py b/var/spack/repos/builtin/packages/r-r-cache/package.py
new file mode 100644
index 0000000000..a27cf38bba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-r-cache/package.py
@@ -0,0 +1,29 @@
+# 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 RRCache(RPackage):
+    """Memoization can be used to speed up repetitive and computational
+    expensive function calls. The first time a function that implements
+    memoization is called the results are stored in a cache memory. The next
+    time the function is called with the same set of parameters, the results
+    are momentarily retrieved from the cache avoiding repeating the
+    calculations. With this package, any R object can be cached in a key-value
+    storage where the key can be an arbitrary set of R objects. The cache
+    memory is persistent (on the file system)."""
+
+    homepage = "https://github.com/HenrikBengtsson/R.cache"
+    url      = "https://cloud.r-project.org/src/contrib/R.cache_0.14.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/R.cache"
+
+    version('0.14.0', sha256='18af4e372440b9f28b4b71346c8ed9de220232f9903730ccee2bfb3c612c16d9')
+
+    depends_on('r@2.14.0:', type=('build', 'run'))
+    depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
+    depends_on('r-r-oo@1.23.0:', type=('build', 'run'))
+    depends_on('r-r-utils@2.8.0:', type=('build', 'run'))
+    depends_on('r-digest@0.6.13:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py
index e25e515b7f..cedaafe72a 100644
--- a/var/spack/repos/builtin/packages/r-r-oo/package.py
+++ b/var/spack/repos/builtin/packages/r-r-oo/package.py
@@ -19,6 +19,7 @@ class RROo(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/R.oo_1.21.0.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/R.oo"
 
+    version('1.23.0', sha256='f5124ce3dbb0a62e8ef1bfce2de2d1dc2f776e8c48fd8cac358f7f5feb592ea1')
     version('1.22.0', sha256='c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c')
     version('1.21.0', sha256='645ceec2f815ed39650ca72db87fb4ece7357857875a4ec73e18bfaf647f431c')