old_contents: # Copyright 2013-2021 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 RApe(RPackage):
      """Functions for reading, writing, plotting, and manipulating phylogenetic
      trees, analyses of comparative data in a phylogenetic framework, ancestral
      character analyses, analyses of diversification and macroevolution,
      computing distances from DNA sequences, reading and writing nucleotide
      sequences as well as importing from BioConductor, and several tools such
      as Mantel's test, generalized skyline plots, graphical exploration of
      phylogenetic data (alex, trex, kronoviz), estimation of absolute
      evolutionary rates and clock-like trees using mean path lengths and
      penalized likelihood, dating trees with non-contemporaneous sequences,
      translating DNA into AA sequences, and assessing sequence alignments.
      Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
      triangle methods, and several methods handling incomplete distance
      matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
      functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
      whose results are returned into R."""
  
      homepage = "http://ape-package.ird.fr/"
      url      = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz"
      list_url = "https://cloud.r-project.org/src/contrib/Archive/ape"
  
      version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
      version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')
      version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e')
      version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960')
      version('4.1', sha256='935af5ddadcba832d3f9cc032a80fc1a2e627a7ed54ef5f3773f87e06374a924')
  
      depends_on('r@3.2:', type=('build', 'run'))
      depends_on('r-nlme', type=('build', 'run'))
      depends_on('r-lattice', type=('build', 'run'))
      depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
  
new_contents: # Copyright 2013-2021 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 RApe(RPackage):
      """Analyses of Phylogenetics and Evolution
  
      Functions for reading, writing, plotting, and manipulating phylogenetic
      trees, analyses of comparative data in a phylogenetic framework, ancestral
      character analyses, analyses of diversification and macroevolution,
      computing distances from DNA sequences, reading and writing nucleotide
      sequences as well as importing from BioConductor, and several tools such
      as Mantel's test, generalized skyline plots, graphical exploration of
      phylogenetic data (alex, trex, kronoviz), estimation of absolute
      evolutionary rates and clock-like trees using mean path lengths and
      penalized likelihood, dating trees with non-contemporaneous sequences,
      translating DNA into AA sequences, and assessing sequence alignments.
      Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
      triangle methods, and several methods handling incomplete distance
      matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some
      functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
      whose results are returned into R."""
  
      homepage = "http://ape-package.ird.fr/"
      url      = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz"
      list_url = "https://cloud.r-project.org/src/contrib/Archive/ape"
  
      version('5.4-1', sha256='f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4')
      version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
      version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')
      version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e')
      version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960')
      version('4.1', sha256='935af5ddadcba832d3f9cc032a80fc1a2e627a7ed54ef5f3773f87e06374a924')
  
      depends_on('r@3.2:', type=('build', 'run'))
      depends_on('r-nlme', type=('build', 'run'))
      depends_on('r-lattice', type=('build', 'run'))
      depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
  
subject: add version 5.4-1 to r-ape (#20804)