New package: r-biomartr (#14812)

This PR creates the r-biomartr package as well as needed new packages
and updates.

- new dependency: r-philentropy
- update: r-curl

3 files changed, 77 insertions, 3 deletions

diff --git a/var/spack/repos/builtin/packages/r-biomartr/package.py b/var/spack/repos/builtin/packages/r-biomartr/package.py
new file mode 100644
index 0000000000..6cb63e979c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biomartr/package.py
@@ -0,0 +1,44 @@
+# 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 RBiomartr(RPackage):
+    """Perform large scale genomic data retrieval and functional annotation
+    retrieval. This package aims to provide users with a standardized way to
+    automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and
+    metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
+    'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the
+    'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>)
+    allows users to retrieve functional annotation for genomic loci. In
+    addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt
+    et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI
+    Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as
+    'ENSEMBL' and 'ENSEMBLGENOMES' with only one command."""
+
+    homepage = "https://docs.ropensci.org/biomartr"
+    url      = "https://cloud.r-project.org/src/contrib/biomartr_0.9.2.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/biomartr"
+
+    version('0.9.2', sha256='d88085696e9c5614828602254c33f2cdd3bbfeebc2f21a705eee3cb961097c89')
+
+    depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-curl', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-data-table@1.9.4:', type=('build', 'run'))
+    depends_on('r-dplyr@0.3.0:', type=('build', 'run'))
+    depends_on('r-readr@0.2.2:', type=('build', 'run'))
+    depends_on('r-downloader@0.3:', type=('build', 'run'))
+    depends_on('r-rcurl@1.95-4.5:', type=('build', 'run'))
+    depends_on('r-xml@3.98-1.1:', type=('build', 'run'))
+    depends_on('r-httr@0.6.1:', type=('build', 'run'))
+    depends_on('r-stringr@0.6.2:', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-r-utils', type=('build', 'run'))
+    depends_on('r-philentropy', type=('build', 'run'))
+    depends_on('r-fs@1.3.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
index 25081b86f7..f1a7a2de60 100644
--- a/var/spack/repos/builtin/packages/r-curl/package.py
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -21,12 +21,14 @@ class RCurl(RPackage):
     url      = "https://cloud.r-project.org/src/contrib/curl_2.3.tar.gz"
     list_url = "https://cloud.r-project.org/src/contrib/Archive/curl"
 
+    version('4.3', sha256='7406d485bb50a6190e3ed201e3489063fd249b8b3b1b4f049167ac405a352edb')
     version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171')
     version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd')
     version('3.0', sha256='7bf8e3ae7cc77802ae300277e85d925d4c0611a9b7dad5c5601e0d2cbe14a506')
-    version('2.3',   sha256='f901dad6bb70a6875a85da75bcbb42afffdcdf4ef221909733826bcb012d7c3d')
-    version('1.0',   sha256='f8927228754fdfb21dbf08b9e67c5f97e06764c4adf327a4126eed84b1508f3d')
+    version('2.3', sha256='f901dad6bb70a6875a85da75bcbb42afffdcdf4ef221909733826bcb012d7c3d')
+    version('1.0', sha256='f8927228754fdfb21dbf08b9e67c5f97e06764c4adf327a4126eed84b1508f3d')
     version('0.9.7', sha256='46e150998723fd1937da598f47f49fe47e40c1f57ec594436c6ef1e0145b44dc')
 
     depends_on('r@3.0.0:', type=('build', 'run'))
-    depends_on('curl')
+    depends_on('curl', when='@4.3:')
+    depends_on('curl@:7.63', when='@:4.0')
diff --git a/var/spack/repos/builtin/packages/r-philentropy/package.py b/var/spack/repos/builtin/packages/r-philentropy/package.py
new file mode 100644
index 0000000000..2814ebc676
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-philentropy/package.py
@@ -0,0 +1,28 @@
+# 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 RPhilentropy(RPackage):
+    """Computes 46 optimized distance and similarity measures for comparing
+    probability functions (Drost (2018) <doi:10.21105/joss.00765>). These
+    comparisons between probability functions have their foundations in a broad
+    range of scientific disciplines from mathematics to ecology. The aim of
+    this package is to provide a core framework for clustering, classification,
+    statistical inference, goodness-of-fit, non-parametric statistics,
+    information theory, and machine learning tasks that are based on comparing
+    univariate or multivariate probability functions."""
+
+    homepage = "https://github.com/HajkD/philentropy"
+    url      = "https://cloud.r-project.org/src/contrib/philentropy_0.4.0.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/philentropy"
+
+    version('0.4.0', sha256='bfd30bf5635aab6a82716299a87d44cf96c7ab7f4ee069843869bcc85c357127')
+
+    depends_on('r@3.1.2:', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-kernsmooth', type=('build', 'run'))