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authorGlenn Johnson <glenn-johnson@uiowa.edu>2020-02-10 03:41:56 -0600
committerGitHub <noreply@github.com>2020-02-10 10:41:56 +0100
commit22df37c328855bbf5a06c03f9a034ec22f243c98 (patch)
tree4ed39c7d9798b94348bd01225b931859f3d9522e /var
parent716978e00c3989760adf3e9b3c15ab30c5750705 (diff)
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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
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/r-aroma-light/package.py23
-rw-r--r--var/spack/repos/builtin/packages/r-pscbs/package.py29
-rw-r--r--var/spack/repos/builtin/packages/r-r-cache/package.py29
-rw-r--r--var/spack/repos/builtin/packages/r-r-oo/package.py1
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')