diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index 56c87c27a6d..9f99a4fb87d 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -36,8 +36,8 @@ class RCar(RPackage): version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565') version('2.1-2', '0f78ad74ef7130126d319acec23951a0') - depends_on('r-mass', type=('build', 'run')) - depends_on('r-mgcv', type=('build', 'run')) - depends_on('r-nnet', type=('build', 'run')) + # depends_on('r-mass', type=('build', 'run')) + # depends_on('r-mgcv', type=('build', 'run')) + # depends_on('r-nnet', type=('build', 'run')) depends_on('r-pbkrtest', type=('build', 'run')) depends_on('r-quantreg', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index de81e7588e0..be1e3c87776 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -35,4 +35,4 @@ class RClass(RPackage): version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') - depends_on('r-mass', type=('build','run')) + # depends_on('r-mass', type=('build','run')) diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py new file mode 100644 index 00000000000..3bde46b6f01 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDendextend(RPackage): + """dendextend: Extending 'Dendrogram' Functionality in R""" + + homepage = "https://CRAN.R-project.org/package=dendextend" + url = "https://cran.r-project.org/src/contrib/dendextend_1.5.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dendextend" + + version('1.5.2', '1134869d94005727c63cf3037e2f1bbf') + + depends_on('r@3.0.0:') + depends_on('r-magrittr@1.0.1:', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-fpc', type=('build', 'run')) + depends_on('r-whisker', type=('build', 'run')) + depends_on('r-viridis', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py new file mode 100644 index 00000000000..f9ce2dd7946 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -0,0 +1,35 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDiptest(RPackage): + """diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected""" + + homepage = "https://CRAN.R-project.org/package=diptest" + url = "https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/diptest" + + version('0.75-7', '1a4a958fda763f7c99cb485dbe5954ab') diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index 4d79fcccd72..f0326c4b2dc 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -36,4 +36,4 @@ class RE1071(RPackage): version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') - depends_on('r-class', type=('build', 'run')) + # depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py new file mode 100644 index 00000000000..44b39e73268 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RFactoextra(RPackage): + """factoextra: Extract and Visualize the Results of Multivariate Data + Analyses""" + + homepage = "http://www.sthda.com/english/rpkgs/factoextra" + url = "https://cran.r-project.org/src/contrib/factoextra_1.0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/factoextra" + + version('1.0.4', 'aa4c81ca610f17fdee0c9f3379e35429') + + depends_on('r@3.1.0:') + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-abind', type=('build', 'run')) + # depends_on('r-cluster', type=('build', 'run')) + depends_on('r-dendextend', type=('build', 'run')) + depends_on('r-factominer', type=('build', 'run')) + depends_on('r-ggpubr', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py new file mode 100644 index 00000000000..909e6871bf4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-factominer/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RFactominer(RPackage): + """FactoMineR: Multivariate Exploratory Data Analysis and Data Mining""" + + homepage = "http://factominer.free.fr" + url = "https://cran.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/FactoMineR" + + version('1.35', 'bef076181ce942016114dd7a6f5c2348') + + depends_on('r@3.3.0:') + depends_on('r-car', type=('build', 'run')) + # depends_on('r-cluster', type=('build', 'run')) + depends_on('r-ellipse', type=('build', 'run')) + depends_on('r-flashclust', type=('build', 'run')) + # depends_on('r-lattice', type=('build', 'run')) + depends_on('r-leaps', type=('build', 'run')) + # depends_on('r-mass', type=('build', 'run')) + depends_on('r-scatterplot3d', type=('build', 'run')) + depends_on('r-knitr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py new file mode 100644 index 00000000000..e8ea8c76e4e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RFlashclust(RPackage): + """flashClust: Implementation of optimal hierarchical clustering""" + + homepage = "https://CRAN.R-project.org/package=flashClust" + url = "https://cran.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/flashClust" + + version('1.01-2', '23409aeeef98bf35d0b3d5dd755fdeff') + + depends_on('r@2.3.0:') diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py new file mode 100644 index 00000000000..ebaed1ebd87 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RFlexmix(RPackage): + """flexmix: Flexible Mixture Modeling""" + + homepage = "https://CRAN.R-project.org/package=flexmix" + url = "https://cran.r-project.org/src/contrib/flexmix_2.3-14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/flexmix" + + version('2.3-14', '5be4f7764e6a697f4586e60c2bf6e960') + + depends_on('r@2.15.0:') + # depends_on('r-lattice', type=('build', 'run')) + depends_on('r-modeltools@0.2-16:', type=('build', 'run')) + # depends_on('r-nnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 011111af07b..7abb0240744 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -39,7 +39,7 @@ class RFormatr(RPackage): version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') - depends_on('r-codetools', type=('build', 'run')) + # depends_on('r-codetools', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) depends_on('r-testit', type=('build', 'run')) # depends_on('r-knitr', type=('build', 'run')) - mutual dependency diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py new file mode 100644 index 00000000000..8a50a984f4c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RFpc(RPackage): + """fpc: Flexible Procedures for Clustering""" + + homepage = "http://www.homepages.ucl.ac.uk/~ucakche" + url = "https://cran.r-project.org/src/contrib/fpc_2.1-10.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/fpc" + + version('2.1-10', '75e5340e416cd13d7751e06f1c07866b') + + depends_on('r@2.0.0:') + # depends_on('r-mass', type=('build', 'run')) + # depends_on('r-cluster', type=('build', 'run')) + depends_on('r-mclust', type=('build', 'run')) + depends_on('r-flexmix', type=('build', 'run')) + depends_on('r-prabclus', type=('build', 'run')) + # depends_on('r-class', type=('build', 'run')) + depends_on('r-diptest', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-robustbase', type=('build', 'run')) + depends_on('r-kernlab', type=('build', 'run')) + depends_on('r-trimcluster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index e5c80e4b799..ee74f21fbc4 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -45,7 +45,7 @@ class RGgplot2(RPackage): depends_on('r-digest', type=('build', 'run')) depends_on('r-gtable@0.1.1:', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) + # depends_on('r-mass', type=('build', 'run')) depends_on('r-plyr@1.7.1:', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-scales@0.4.1', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py new file mode 100644 index 00000000000..52184b73070 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGgpubr(RPackage): + """ggpubr: 'ggplot2' Based Publication Ready Plots""" + + homepage = "http://www.sthda.com/english/rpkgs/ggpubr" + url = "https://cran.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggpubr" + + version('0.1.2', '42a5749ae44121597ef511a7424429d1') + + depends_on('r@3.1.0:') + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggrepel', type=('build', 'run')) + depends_on('r-ggsci', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py new file mode 100644 index 00000000000..c1547655c0c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGgrepel(RPackage): + """ggrepel: Repulsive Text and Label Geoms for 'ggplot2'""" + + homepage = "http://github.com/slowkow/ggrepel" + url = "https://cran.r-project.org/src/contrib/ggrepel_0.6.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggrepel" + + version('0.6.5', '7e2732cd4840efe2dc9e4bc689cf1ee5') + + depends_on('r@3.0.0:') + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-scales@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py new file mode 100644 index 00000000000..fb811ff2fe5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGgsci(RPackage): + """ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for + 'ggplot2'""" + + homepage = "https://github.com/road2stat/ggsci" + url = "https://cran.r-project.org/src/contrib/ggsci_2.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggsci" + + version('2.4', '8e5dc2fcf84352cacbb91363e26c7175') + + depends_on('r@3.0.2:') + depends_on('r-scales', type=('build', 'run')) + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py new file mode 100644 index 00000000000..077ea282baa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -0,0 +1,35 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RLeaps(RPackage): + """leaps: Regression Subset Selection""" + + homepage = "https://CRAN.R-project.org/package=leaps" + url = "https://cran.r-project.org/src/contrib/leaps_3.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/leaps" + + version('3.0', '30823138890680e0493d1491c8f43edc') diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 0ca545ced90..712deb37f36 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -37,10 +37,10 @@ class RLme4(RPackage): version('1.1-12', 'da8aaebb67477ecb5631851c46207804') - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-lattice', type=('build', 'run')) - depends_on('r-nlme', type=('build', 'run')) + # depends_on('r-matrix', type=('build', 'run')) + # depends_on('r-mass', type=('build', 'run')) + # depends_on('r-lattice', type=('build', 'run')) + # depends_on('r-nlme', type=('build', 'run')) depends_on('r-minqa', type=('build', 'run')) depends_on('r-nloptr', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index ba1323a7372..cf945f0657d 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -36,4 +36,4 @@ class RMatrix(RPackage): version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5') version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') - depends_on('r-lattice', type=('build', 'run')) + # depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index 0958de49a3f..4a89d41e66b 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -35,4 +35,4 @@ class RMatrixmodels(RPackage): version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') - depends_on('r-matrix', type=('build', 'run')) + # depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py new file mode 100644 index 00000000000..5bf58c02cd6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMclust(RPackage): + """mclust: Gaussian Mixture Modelling for Model-Based Clustering, + Classification, and Density Estimation""" + + homepage = "http://www.stat.washington.edu/mclust" + url = "https://cran.r-project.org/src/contrib/mclust_5.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mclust" + + version('5.3', '74aac9fccdfc78373ce733c1a09176ef') + + depends_on('r@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index 611abfd47c1..ee5b7075930 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -38,5 +38,5 @@ class RMgcv(RPackage): version('1.8-16', '4c1d85e0f80b017bccb4b63395842911') version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') - depends_on('r-nlme', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + # depends_on('r-nlme', type=('build', 'run')) + # depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 32fa484f60a..183891981ab 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -35,4 +35,4 @@ class RNlme(RPackage): version('3.1-130', '1935d6e308a8018ed8e45d25c8731288') version('3.1-128', '3d75ae7380bf123761b95a073eb55008') - depends_on('r-lattice', type=('build', 'run')) + # depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 2a2edc50ce5..d45970ad598 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -42,5 +42,5 @@ class RPbkrtest(RPackage): depends_on('r@3.2.3:') depends_on('r-lme4@1.1.10:', type=('build', 'run')) - depends_on('r-matrix@1.2.3:', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) + # depends_on('r-matrix@1.2.3:', type=('build', 'run')) + # depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py new file mode 100644 index 00000000000..424d75274d7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPrabclus(RPackage): + """prabclus: Functions for Clustering of Presence-Absence, Abundance and + Multilocus Genetic Data""" + + homepage = "http://www.homepages.ucl.ac.uk/~ucakche" + url = "https://cran.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/prabclus" + + version('2.2-6', '7f835dcc113243e1db74aad28ce93d11') + + depends_on('r@2.1.0:') + # depends_on('r-mass', type=('build', 'run')) + depends_on('r-mclust', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index c9bdaefa44e..b48e65988df 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -41,5 +41,5 @@ class RQuantreg(RPackage): version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') depends_on('r-sparsem', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + # depends_on('r-matrix', type=('build', 'run')) depends_on('r-matrixmodels', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index b33e938d5bf..2210be32125 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -47,5 +47,5 @@ class RRcppeigen(RPackage): version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318') version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') - depends_on('r-matrix', type=('build', 'run')) + # depends_on('r-matrix', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py new file mode 100644 index 00000000000..edb92a08208 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RScatterplot3d(RPackage): + """scatterplot3d: 3D Scatter Plot""" + + homepage = "https://CRAN.R-project.org/package=scatterplot3d" + url = "https://cran.r-project.org/src/contrib/scatterplot3d_0.3-40.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/scatterplot3d" + + version('0.3-40', '67b9ab6131d244d7fc1db39dcc911dfe') + + depends_on('r@2.7.0:') diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py new file mode 100644 index 00000000000..770718ae009 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RTrimcluster(RPackage): + """trimcluster: Cluster analysis with trimming""" + + homepage = "http://www.homepages.ucl.ac.uk/~ucakche" + url = "https://cran.r-project.org/src/contrib/trimcluster_0.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/trimcluster" + + version('0.1-2', '7617920e224bd18f5b87db38a3116ec2') + + depends_on('r@1.9.0:') diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py new file mode 100644 index 00000000000..55f879e90e7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RViridis(RPackage): + """viridis: Default Color Maps from 'matplotlib'""" + + homepage = "https://github.com/sjmgarnier/viridis" + url = "https://cran.r-project.org/src/contrib/viridis_0.4.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/viridis" + + version('0.4.0', 'f874384cbedf459f6c309ddb40b354ea') + + depends_on('r@2.1.0:') + depends_on('r-viridislite@0.2.0:', type=('build', 'run')) + depends_on('r-ggplot2@1.0.1:', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py new file mode 100644 index 00000000000..fc65b7f3931 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -0,0 +1,37 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RViridislite(RPackage): + """viridisLite: Default Color Maps from 'matplotlib' (Lite Version)""" + + homepage = "https://github.com/sjmgarnier/viridisLite" + url = "https://cran.r-project.org/src/contrib/viridisLite_0.2.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/viridisLite" + + version('0.2.0', '04a04415cf651a2b5f964b261896c0fb') + + depends_on('r@2.1.0:') diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 7418d36a64d..49f29042cf8 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -39,4 +39,4 @@ class RZoo(RPackage): version('1.7-14', '8c577a7c1e535c899ab14177b1039c32') version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') - depends_on('r-lattice', type=('build', 'run')) + # depends_on('r-lattice', type=('build', 'run'))