From 22df37c328855bbf5a06c03f9a034ec22f243c98 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 10 Feb 2020 03:41:56 -0600 Subject: [PATCH] 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 --- .../builtin/packages/r-aroma-light/package.py | 23 +++++++++++++++ .../repos/builtin/packages/r-pscbs/package.py | 29 +++++++++++++++++++ .../builtin/packages/r-r-cache/package.py | 29 +++++++++++++++++++ .../repos/builtin/packages/r-r-oo/package.py | 1 + 4 files changed, 82 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-aroma-light/package.py create mode 100644 var/spack/repos/builtin/packages/r-pscbs/package.py create mode 100644 var/spack/repos/builtin/packages/r-r-cache/package.py 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')