diff --git a/packages/r-dynutils/package.py b/packages/r-dynutils/package.py new file mode 100644 index 0000000000000000000000000000000000000000..fa917b9b410636a5933ecafe02753928c5db88a1 --- /dev/null +++ b/packages/r-dynutils/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2023 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.package import * + + +class RDynutils(RPackage): + """Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.""" + + homepage = "https://cran.r-project.org/package=dynutils" + cran = "dynutils" + + version("1.0.11", sha256="09ce9efda019e5c345ad6a7131f41f7fe9c8458c1b105191d8618416ea125619") + + depends_on("r-assertthat") + depends_on("r-crayon") + depends_on("r-desc") + depends_on("r-dplyr") + depends_on("r-magrittr") + depends_on("r-matrix") + depends_on("r-proxyc") + depends_on("r-purrr") + depends_on("r-rcpp") + depends_on("r-remotes") + depends_on("r-stringr") + depends_on("r-tibble") + + + diff --git a/packages/r-gillespiessa2/package.py b/packages/r-gillespiessa2/package.py new file mode 100644 index 0000000000000000000000000000000000000000..92b94184289ec4f55d9d88e1f927a65435c7e130 --- /dev/null +++ b/packages/r-gillespiessa2/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2023 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.package import * + + +class RGillespiessa2(RPackage): + """A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) <doi:10.1038/s41467-021-24152-2>.""" + + homepage = "https://cran.r-project.org/package=GillespieSSA2" + cran = "GillespieSSA2" + + version("0.3.0", sha256="206497ae7be8ff88a5edafe81b0295eb4b14109c546878ace16a7396a0035f72") + + depends_on("r-assertthat") + depends_on("r-dplyr") + depends_on("r-dynutils") + depends_on("r-matrix") + depends_on("r-purrr") + depends_on("r-rcpp") + depends_on("r-rcppxptrutils") + depends_on("r-readr") + depends_on("r-rlang") + depends_on("r-stringr") + depends_on("r-tidyr") + diff --git a/packages/r-proxyc/package.py b/packages/r-proxyc/package.py new file mode 100644 index 0000000000000000000000000000000000000000..a0eb6ed1793d9ac149d2a64446fab74e2f337ab2 --- /dev/null +++ b/packages/r-proxyc/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2023 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.package import * + + +class RProxyc(RPackage): + """Computes proximity between rows or columns of large matrices efficiently in C++. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast.""" + + homepage = "https://cran.r-project.org/package=proxyC" + cran = "proxyC" + + version("0.3.3", sha256="3e25da94633da0b5c6cdac03f5b6d8205d078f60c5a09073e90a1b6f0930e302") + + depends_on("r-rcpp") + depends_on("r-rcppparallel") + depends_on("r-rcpparmadillo") + depends_on("r-matrix") diff --git a/packages/r-rcppxptrutils/package.py b/packages/r-rcppxptrutils/package.py new file mode 100644 index 0000000000000000000000000000000000000000..0c74a9f8bcb94bc49efa73674c5a1ec859b8a827 --- /dev/null +++ b/packages/r-rcppxptrutils/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2023 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.package import * + + +class RRcppxptrutils(RPackage): + """Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.""" + + homepage = "https://cran.r-project.org/package=RcppXPtrUtils" + cran = "RcppXPtrUtils" + + version("0.1.2", sha256="34d0cab1891c95453c357cf93ab97b6ea42ef98cdc4809c9abfafd469c3da542") + + depends_on("r-rcpp") diff --git a/packages/r-uqsa/package.py b/packages/r-uqsa/package.py index 5fd65068efbaeb4f950020f23ef58c7a1c1c92e0..4b4b34fd06176066292109b75de90b6e61b3912d 100644 --- a/packages/r-uqsa/package.py +++ b/packages/r-uqsa/package.py @@ -27,4 +27,4 @@ class RUqsa(RPackage): depends_on("r-mass") depends_on("r-r-utils") depends_on("r-ks") - + depends_on("r-gillespiessa2")