From d7e21f8ae13a54eb8dfc873dcf8d89bbf4e74ac1 Mon Sep 17 00:00:00 2001
From: Andrei Kramer <andreikr@kth.se>
Date: Fri, 24 Feb 2023 00:21:02 +0100
Subject: [PATCH] added a new dependency for uqsa for of a new
uqsa-functionality
---
packages/r-dynutils/package.py | 31 +++++++++++++++++++++++++++++
packages/r-gillespiessa2/package.py | 28 ++++++++++++++++++++++++++
packages/r-proxyc/package.py | 20 +++++++++++++++++++
packages/r-rcppxptrutils/package.py | 17 ++++++++++++++++
packages/r-uqsa/package.py | 2 +-
5 files changed, 97 insertions(+), 1 deletion(-)
create mode 100644 packages/r-dynutils/package.py
create mode 100644 packages/r-gillespiessa2/package.py
create mode 100644 packages/r-proxyc/package.py
create mode 100644 packages/r-rcppxptrutils/package.py
diff --git a/packages/r-dynutils/package.py b/packages/r-dynutils/package.py
new file mode 100644
index 00000000..fa917b9b
--- /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 00000000..92b94184
--- /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 00000000..a0eb6ed1
--- /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 00000000..0c74a9f8
--- /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 5fd65068..4b4b34fd 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")
--
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