diff options
173 files changed, 238 insertions, 1213 deletions
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 771fc7b32a..1e38376f5e 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -159,7 +159,9 @@ from spack.package import Package from spack.build_systems.makefile import MakefilePackage from spack.build_systems.autotools import AutotoolsPackage from spack.build_systems.cmake import CMakePackage -__all__ += ['Package', 'CMakePackage', 'AutotoolsPackage', 'MakefilePackage'] +from spack.build_systems.r import RPackage +__all__ += ['Package', 'CMakePackage', 'AutotoolsPackage', 'MakefilePackage', + 'RPackage'] from spack.version import Version, ver __all__ += ['Version', 'ver'] diff --git a/lib/spack/spack/build_systems/r.py b/lib/spack/spack/build_systems/r.py new file mode 100644 index 0000000000..52b3d82c60 --- /dev/null +++ b/lib/spack/spack/build_systems/r.py @@ -0,0 +1,57 @@ +############################################################################## +# 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 +############################################################################## + +import inspect + +from spack.directives import extends +from spack.package import PackageBase + + +class RPackage(PackageBase): + """Specialized class for packages that are built using R + + This class provides a single phase that can be overridden: + * install + + It has sensible defaults and for many packages the only thing + necessary will be to add dependencies + """ + phases = ['install'] + + # To be used in UI queries that require to know which + # build-system class we are using + build_system_class = 'RPackage' + + extends('r') + + def install(self, spec, prefix): + """Install the R package""" + inspect.getmodule(self).R( + 'CMD', 'INSTALL', + '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) + + # Check that self.prefix is there after installation + PackageBase.sanity_check('install')(PackageBase.sanity_check_prefix) diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index f1a5bc5cdb..2607daaeb5 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -215,16 +215,11 @@ class PythonGuess(DefaultGuess): class RGuess(DefaultGuess): """Provides appropriate overrides for R extensions""" dependencies = """\ - extends('r') - - # FIXME: Add additional dependencies if required. + # FIXME: Add dependencies if required. # depends_on('r-foo', type=nolink)""" body = """\ - def install(self, spec, prefix): - # FIXME: Add logic to build and install here. - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path)""" + # FIXME: Override install() if necessary.""" def __init__(self, name, *args): name = 'r-{0}'.format(name) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index f691ae13ea..81fa319a90 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -25,7 +25,7 @@ from spack import * -class RAbind(Package): +class RAbind(RPackage): """Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and @@ -36,9 +36,3 @@ class RAbind(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/abind" version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index fe0c400aaa..97c29b4a99 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -25,7 +25,7 @@ from spack import * -class RAssertthat(Package): +class RAssertthat(RPackage): """assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what they've done @@ -35,9 +35,3 @@ class RAssertthat(Package): url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz" version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 2289f40e4f..698e27a29e 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -25,7 +25,7 @@ from spack import * -class RBase64enc(Package): +class RBase64enc(RPackage): """This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.""" @@ -34,9 +34,3 @@ class RBase64enc(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 4b2b4ca11d..683ba24d86 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -25,7 +25,7 @@ from spack import * -class RBh(Package): +class RBh(RPackage): """Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most @@ -46,9 +46,3 @@ class RBh(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/BH" version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py index ce93356541..654e7f1b2a 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -25,32 +25,16 @@ from spack import * -class RBiocgenerics(Package): +class RBiocgenerics(RPackage): """S4 generic functions needed by many Bioconductor packages.""" homepage = 'https://bioconductor.org/packages/BiocGenerics/' - version('bioc-3.3', + version('3.3', git='https://github.com/Bioconductor-mirror/BiocGenerics.git', branch='release-3.3') - version('bioc-3.2', + version('3.2', git='https://github.com/Bioconductor-mirror/BiocGenerics.git', branch='release-3.2') - extends('r') - - def validate(self, spec): - """ - Checks that the version of R is appropriate for the Bioconductor - version. - """ - if spec.satisfies('@bioc-3.3'): - if not spec.satisfies('^R@3.3.0:3.3.9'): - raise InstallError('Must use R-3.3 for Bioconductor-3.3') - elif spec.satisfies('@bioc-3.2'): - if not spec.satisfies('^R@3.2.0:3.2.9'): - raise InstallError('Must use R-3.2 for Bioconductor-3.2') - - def install(self, spec, prefix): - self.validate(spec) - R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.source_path) + depends_on('r@3.3.0:3.3.9', when='@3.3') + depends_on('r@3.2.0:3.2.9', when='@3.2') diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 7421ea4658..67bb0fe777 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -26,7 +26,7 @@ from spack import * -class RBitops(Package): +class RBitops(RPackage): """Functions for bitwise operations on integer vectors.""" homepage = "https://cran.r-project.org/package=bitops" @@ -34,9 +34,3 @@ class RBitops(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/bitops" version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index 0b78c202b8..1361920673 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -25,7 +25,7 @@ from spack import * -class RBoot(Package): +class RBoot(RPackage): """Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.""" @@ -35,9 +35,3 @@ class RBoot(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/boot" version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index 10bbccf1de..558d830a2b 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -25,7 +25,7 @@ from spack import * -class RBrew(Package): +class RBrew(RPackage): """brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.""" @@ -35,9 +35,3 @@ class RBrew(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/brew" version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index 6ce917521d..6fc5b60fdc 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -26,7 +26,7 @@ from spack import * -class RC50(Package): +class RC50(RPackage): """C5.0 decision trees and rule-based models for pattern recognition.""" homepage = "https://cran.r-project.org/package=C50" @@ -35,10 +35,4 @@ class RC50(Package): version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') - extends('r') - depends_on('r-partykit', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index fa2cc407b8..b6232d6297 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -25,7 +25,7 @@ from spack import * -class RCar(Package): +class RCar(RPackage): """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.""" @@ -35,14 +35,8 @@ class RCar(Package): version('2.1-2', '0f78ad74ef7130126d319acec23951a0') - extends('r') - depends_on('r-mass', type=nolink) depends_on('r-mgcv', type=nolink) depends_on('r-nnet', type=nolink) depends_on('r-pbkrtest', type=nolink) depends_on('r-quantreg', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index bfc2db5780..f98cebcff8 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -25,7 +25,7 @@ from spack import * -class RCaret(Package): +class RCaret(RPackage): """Misc functions for training and plotting classification and regression models.""" @@ -35,8 +35,6 @@ class RCaret(Package): version('6.0-70', '202d7abb6a679af716ea69fb2573f108') - extends('r') - depends_on('r-lattice', type=nolink) depends_on('r-ggplot2', type=nolink) depends_on('r-car', type=nolink) @@ -44,7 +42,3 @@ class RCaret(Package): depends_on('r-plyr', type=nolink) depends_on('r-nlme', type=nolink) depends_on('r-reshape2', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index b2daa14c6b..57e9c17f24 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -26,7 +26,7 @@ from spack import * -class RCatools(Package): +class RCatools(RPackage): """Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 @@ -38,10 +38,4 @@ class RCatools(Package): version('1.17.1', '5c872bbc78b177b306f36709deb44498') - extends('r') - depends_on('r-bitops', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 9393ac416f..e1731424b3 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -25,7 +25,7 @@ from spack import * -class RChron(Package): +class RChron(RPackage): """Chronological objects which can handle dates and times.""" homepage = "https://cran.r-project.org/package=chron" @@ -33,9 +33,3 @@ class RChron(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/chron" version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index 627cce808c..d455deb303 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -25,7 +25,7 @@ from spack import * -class RClass(Package): +class RClass(RPackage): """Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.""" @@ -35,10 +35,4 @@ class RClass(Package): version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') - extends('r') - depends_on('r-mass', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index 2deb053322..29e16c2271 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -25,7 +25,7 @@ from spack import * -class RCluster(Package): +class RCluster(RPackage): """Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".""" @@ -35,9 +35,3 @@ class RCluster(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 206e4c09a5..39186bf54a 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -25,7 +25,7 @@ from spack import * -class RCodetools(Package): +class RCodetools(RPackage): """Code analysis tools for R.""" homepage = "https://cran.r-project.org/web/packages/codetools/index.html" @@ -33,9 +33,3 @@ class RCodetools(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/codetools" version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index 48c50191ac..b7561ea360 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -25,7 +25,7 @@ from spack import * -class RColorspace(Package): +class RColorspace(RPackage): """Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors @@ -36,9 +36,3 @@ class RColorspace(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace" version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index f0578a7c81..2002ea5419 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -25,7 +25,7 @@ from spack import * -class RCrayon(Package): +class RCrayon(RPackage): """Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. @@ -37,9 +37,3 @@ class RCrayon(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/crayon" version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 4ae21947ae..918f8e9e3d 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -25,7 +25,7 @@ from spack import * -class RCubature(Package): +class RCubature(RPackage): """Adaptive multivariate integration over hypercubes""" homepage = "https://cran.r-project.org/package=cubature" @@ -33,9 +33,3 @@ class RCubature(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/cubature" version('1.1-2', '5617e1d82baa803a3814d92461da45c9') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 71f28d4609..7b62d1be60 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -25,7 +25,7 @@ from spack import * -class RCurl(Package): +class RCurl(RPackage): """The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, @@ -43,10 +43,4 @@ class RCurl(Package): version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') - extends('r') - depends_on('curl') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-datatable/package.py index f0d2247d36..fecde7ede2 100644 --- a/var/spack/repos/builtin/packages/r-datatable/package.py +++ b/var/spack/repos/builtin/packages/r-datatable/package.py @@ -25,7 +25,7 @@ from spack import * -class RDatatable(Package): +class RDatatable(RPackage): """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible @@ -37,10 +37,4 @@ class RDatatable(Package): version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372') - extends('r') - depends_on('r-chron', type='nolink') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index b0146ffb27..f00100bdf0 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -25,7 +25,7 @@ from spack import * -class RDbi(Package): +class RDbi(RPackage): """A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.""" @@ -35,9 +35,3 @@ class RDbi(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/DBI" version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 9f5302ce16..5334953d46 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -26,18 +26,12 @@ from spack import * -class RDeoptim(Package): +class RDeoptim(RPackage): """Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.""" homepage = "https://cran.r-project.org/package=DEoptim" url = "https://cran.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptim" - - version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') - - extends('r') - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) + version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 01adc6e327..4a8a8e3026 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -25,7 +25,7 @@ from spack import * -class RDevtools(Package): +class RDevtools(RPackage): """Collection of package development tools.""" homepage = "https://github.com/hadley/devtools" @@ -34,8 +34,6 @@ class RDevtools(Package): version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') - extends('r') - depends_on('r-httr', type=nolink) depends_on('r-memoise', type=nolink) depends_on('r-whisker', type=nolink) @@ -44,7 +42,3 @@ class RDevtools(Package): depends_on('r-jsonlite', type=nolink) depends_on('r-git2r', type=nolink) depends_on('r-withr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 420e4d803a..f99e146724 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -25,7 +25,7 @@ from spack import * -class RDiagrammer(Package): +class RDiagrammer(RPackage): """Create graph diagrams and flowcharts using R.""" homepage = "https://github.com/rich-iannone/DiagrammeR" @@ -34,8 +34,6 @@ class RDiagrammer(Package): version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') - extends('r') - depends_on('r-htmlwidgets', type=nolink) depends_on('r-igraph', type=nolink) depends_on('r-influencer', type=nolink) @@ -43,7 +41,3 @@ class RDiagrammer(Package): depends_on('r-stringr', type=nolink) depends_on('r-visnetwork', type=nolink) depends_on('r-scales', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index 240bfc3be7..ea465e2d6c 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -25,7 +25,7 @@ from spack import * -class RDichromat(Package): +class RDichromat(RPackage): """Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.""" @@ -34,9 +34,3 @@ class RDichromat(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat" version('2.0-0', '84e194ac95a69763d740947a7ee346a6') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index f573638b1b..7e077442f9 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -25,7 +25,7 @@ from spack import * -class RDigest(Package): +class RDigest(RPackage): """Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as @@ -48,9 +48,3 @@ class RDigest(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/digest" version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index c78624d6d8..f74b23aae0 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -25,7 +25,7 @@ from spack import * -class RDoparallel(Package): +class RDoparallel(RPackage): """Provides a parallel backend for the %dopar% function using the parallel package.""" @@ -35,11 +35,5 @@ class RDoparallel(Package): version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') - extends('r') - depends_on('r-foreach', type=nolink) depends_on('r-iterators', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index 2e0f43b726..77877a0e02 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -25,7 +25,7 @@ from spack import * -class RDplyr(Package): +class RDplyr(RPackage): """A fast, consistent tool for working with data frame like objects, both in memory and out of memory.""" @@ -35,8 +35,6 @@ class RDplyr(Package): version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef') - extends('r') - depends_on('r-assertthat', type=nolink) depends_on('r-r6', type=nolink) depends_on('r-rcpp', type=nolink) @@ -45,7 +43,3 @@ class RDplyr(Package): depends_on('r-lazyeval', type=nolink) depends_on('r-dbi', type=nolink) depends_on('r-bh', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py index 2612ce3a57..d5680bee99 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -25,7 +25,7 @@ from spack import * -class RDt(Package): +class RDt(RPackage): """Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an @@ -36,12 +36,6 @@ class RDt(Package): version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c') - extends('r') - depends_on('r-htmltools', type=nolink) depends_on('r-htmlwidgets', type=nolink) depends_on('r-magrittr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index 94441dd6d5..80aedda6d6 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -25,7 +25,7 @@ from spack import * -class RDygraphs(Package): +class RDygraphs(RPackage): """An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and @@ -38,13 +38,7 @@ class RDygraphs(Package): version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') - extends('r') - depends_on('r-magrittr', type=nolink) depends_on('r-htmlwidgets', type=nolink) depends_on('r-zoo', type=nolink) depends_on('r-xts', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index ef29cc3318..f9ba6854cc 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -25,7 +25,7 @@ from spack import * -class RE1071(Package): +class RE1071(RPackage): """Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...""" @@ -36,10 +36,4 @@ class RE1071(Package): version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') - extends('r') - depends_on('r-class', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index c9a980a2c5..5516cc8697 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -27,7 +27,7 @@ from spack import * -class REvaluate(Package): +class REvaluate(RPackage): """Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.""" @@ -37,10 +37,4 @@ class REvaluate(Package): version('0.9', '877d89ce8a9ef7f403b1089ca1021775') - extends('r') - depends_on('r-stringr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index 2b92013db8..b17335ed11 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -25,7 +25,7 @@ from spack import * -class RFilehash(Package): +class RFilehash(RPackage): """Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the @@ -41,9 +41,3 @@ class RFilehash(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/filehash" version('2.3', '01fffafe09b148ccadc9814c103bdc2f') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index 7f2b1e63a8..85f76b4779 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -25,7 +25,7 @@ from spack import * -class RForeach(Package): +class RForeach(RPackage): """Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used @@ -40,11 +40,5 @@ class RForeach(Package): version('1.4.3', 'ef45768126661b259f9b8994462c49a0') - extends('r') - depends_on('r-codetools', type=nolink) depends_on('r-iterators', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index a248518f58..b293f091c2 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -25,7 +25,7 @@ from spack import * -class RForeign(Package): +class RForeign(RPackage): """Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.""" @@ -35,9 +35,3 @@ class RForeign(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/foreign" version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 3935ee9000..db812b3eb6 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -26,7 +26,7 @@ from spack import * -class RFormatr(Package): +class RFormatr(RPackage): """Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more @@ -39,13 +39,7 @@ class RFormatr(Package): version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') - extends('r') - depends_on('r-codetools', type=nolink) depends_on('r-shiny', type=nolink) depends_on('r-testit', type=nolink) # depends_on('r-knitr', type=nolink) - mutual dependency - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index cd5b0b41e9..5515ca91a3 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -26,7 +26,7 @@ from spack import * -class RFormula(Package): +class RFormula(RPackage): """Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.""" @@ -35,9 +35,3 @@ class RFormula(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/Formula" version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index 2897ad922d..591d9cf18a 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -25,7 +25,7 @@ from spack import * -class RGdata(Package): +class RGdata(RPackage): """Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector @@ -50,10 +50,4 @@ class RGdata(Package): version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') - extends('r') - depends_on('r-gtools', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index dec9a3939e..5722fc1f31 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -25,7 +25,7 @@ from spack import * -class RGeosphere(Package): +class RGeosphere(RPackage): """Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.""" @@ -36,10 +36,4 @@ class RGeosphere(Package): version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') - extends('r') - depends_on('r-sp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index d6c6d53c21..be611e3562 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -25,7 +25,7 @@ from spack import * -class RGgmap(Package): +class RGgmap(RPackage): """A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for @@ -37,8 +37,6 @@ class RGgmap(Package): version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') - extends('r') - depends_on('r-ggplot2', type=nolink) depends_on('r-proto', type=nolink) depends_on('r-rgooglemaps', type=nolink) @@ -51,7 +49,3 @@ class RGgmap(Package): depends_on('r-geosphere', type=nolink) depends_on('r-digest', type=nolink) depends_on('r-scales', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index c0c37d9164..19da1eee9e 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -25,7 +25,7 @@ from spack import * -class RGgplot2(Package): +class RGgplot2(RPackage): """An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step @@ -40,15 +40,9 @@ class RGgplot2(Package): version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') - extends('r') - depends_on('r-digest', type=nolink) depends_on('r-gtable', type=nolink) depends_on('r-mass', type=nolink) depends_on('r-plyr', type=nolink) depends_on('r-reshape2', type=nolink) depends_on('r-scales', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 9c6720b4aa..3eb27d8483 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -25,7 +25,7 @@ from spack import * -class RGgvis(Package): +class RGgvis(RPackage): """An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework from 'shiny' and web graphics from 'vega'.""" @@ -36,8 +36,6 @@ class RGgvis(Package): version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') - extends('r') - depends_on('r-assertthat', type=nolink) depends_on('r-jsonlite', type=nolink) depends_on('r-shiny', type=nolink) @@ -45,7 +43,3 @@ class RGgvis(Package): depends_on('r-dplyr', type=nolink) depends_on('r-lazyeval', type=nolink) depends_on('r-htmltools', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index 08910b0fe1..b939fdfe5b 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -26,7 +26,7 @@ from spack import * -class RGistr(Package): +class RGistr(RPackage): """Work with 'GitHub' 'gists' from 'R'. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', @@ -40,8 +40,6 @@ class RGistr(Package): version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') - extends('r') - depends_on('r-jsonlite', type=nolink) depends_on('r-httr', type=nolink) depends_on('r-magrittr', type=nolink) @@ -49,7 +47,3 @@ class RGistr(Package): depends_on('r-knitr', type=nolink) depends_on('r-rmarkdown', type=nolink) depends_on('r-dplyr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index 1387581306..7c4ff3144b 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -25,7 +25,7 @@ from spack import * -class RGit2r(Package): +class RGit2r(RPackage): """Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.""" @@ -36,11 +36,5 @@ class RGit2r(Package): version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') - extends('r') - depends_on('zlib') depends_on('openssl') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index 895c066e57..1b56d9b5ef 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -25,7 +25,7 @@ from spack import * -class RGlmnet(Package): +class RGlmnet(RPackage): """Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two @@ -39,11 +39,5 @@ class RGlmnet(Package): version('2.0-5', '049b18caa29529614cd684db3beaec2a') - extends('r') - depends_on('r-matrix', type=nolink) depends_on('r-foreach', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 54e1d397a6..1d86dd7592 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -25,7 +25,7 @@ from spack import * -class RGooglevis(Package): +class RGooglevis(RPackage): """R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and @@ -38,10 +38,4 @@ class RGooglevis(Package): version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') - extends('r') - depends_on('r-jsonlite', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 1afc1af3ac..73d87c7e49 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -25,7 +25,7 @@ from spack import * -class RGridbase(Package): +class RGridbase(RPackage): """Integration of base and grid graphics.""" homepage = "https://cran.r-project.org/web/packages/gridBase/index.html" @@ -33,9 +33,3 @@ class RGridbase(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase" version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 582cd39b85..77808b5e4c 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -25,7 +25,7 @@ from spack import * -class RGridextra(Package): +class RGridextra(RPackage): """Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.""" @@ -35,10 +35,4 @@ class RGridextra(Package): version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') - extends('r') - depends_on('r-gtable', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index a633e8273f..236416755b 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -25,7 +25,7 @@ from spack import * -class RGtable(Package): +class RGtable(RPackage): """Tools to make it easier to work with "tables" of 'grobs'.""" homepage = "https://cran.r-project.org/web/packages/gtable/index.html" @@ -33,9 +33,3 @@ class RGtable(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/gtable" version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 6676ec1be3..632187b49e 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -25,7 +25,7 @@ from spack import * -class RGtools(Package): +class RGtools(RPackage): """Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse @@ -52,9 +52,3 @@ class RGtools(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/gtools" version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index b9a7e612c3..5e336c021a 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -26,7 +26,7 @@ from spack import * -class RHexbin(Package): +class RHexbin(RPackage): """Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.""" @@ -36,10 +36,4 @@ class RHexbin(Package): version('1.27.1', '7f380390c6511e97df10a810a3b3bb7c') - extends('r') - depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index e9fb7c34d5..13164f9c60 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -26,7 +26,7 @@ from spack import * -class RHighr(Package): +class RHighr(RPackage): """Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.""" @@ -36,9 +36,3 @@ class RHighr(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/highr" version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index aa776f3929..7da66f3314 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -25,7 +25,7 @@ from spack import * -class RHtmltools(Package): +class RHtmltools(RPackage): """Tools for HTML generation and output.""" homepage = "https://github.com/rstudio/htmltools" @@ -34,11 +34,5 @@ class RHtmltools(Package): version('0.3.5', '5f001aff4a39e329f7342dcec5139724') - extends('r') - depends_on('r-digest', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index 615936c585..69f64c2a31 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -25,7 +25,7 @@ from spack import * -class RHtmlwidgets(Package): +class RHtmlwidgets(RPackage): """A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.""" @@ -36,12 +36,6 @@ class RHtmlwidgets(Package): version('0.6', '7fa522d2eda97593978021bda9670c0e') - extends('r') - depends_on('r-htmltools', type=nolink) depends_on('r-jsonlite', type=nolink) depends_on('r-yaml', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index c353dacc5f..b700cd1510 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -25,7 +25,7 @@ from spack import * -class RHttpuv(Package): +class RHttpuv(RPackage): """Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy @@ -40,10 +40,4 @@ class RHttpuv(Package): version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') - extends('r') - depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index bf7ce4dccb..826e4a298b 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -25,7 +25,7 @@ from spack import * -class RHttr(Package): +class RHttr(RPackage): """Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).""" @@ -36,14 +36,8 @@ class RHttr(Package): version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') - extends('r') - depends_on('r-jsonlite', type=nolink) depends_on('r-mime', type=nolink) depends_on('r-curl', type=nolink) depends_on('r-openssl', type=nolink) depends_on('r-r6', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 8c1a6252ba..991cc424c0 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -25,7 +25,7 @@ from spack import * -class RIgraph(Package): +class RIgraph(RPackage): """Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.""" @@ -36,15 +36,9 @@ class RIgraph(Package): version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') - extends('r') - depends_on('r-matrix', type=nolink) depends_on('r-magrittr', type=nolink) depends_on('r-nmf', type=nolink) depends_on('r-irlba', type=nolink) depends_on('gmp') depends_on('libxml2') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index 8102954daa..04a7b27679 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -25,7 +25,7 @@ from spack import * -class RInfluencer(Package): +class RInfluencer(RPackage): """Provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's @@ -40,11 +40,5 @@ class RInfluencer(Package): version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') - extends('r') - depends_on('r-igraph', type=nolink) depends_on('r-matrix', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 0694af6d34..f30c87dc9b 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -25,7 +25,7 @@ from spack import * -class RInline(Package): +class RInline(RPackage): """Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.""" @@ -35,9 +35,3 @@ class RInline(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/inline" version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index 00de6b35ac..0c36be25c3 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -26,7 +26,7 @@ from spack import * -class RIrdisplay(Package): +class RIrdisplay(RPackage): """An interface to the rich display capabilities of Jupyter front-ends (e.g. 'Jupyter Notebook') Designed to be used from a running IRkernel session""" @@ -36,10 +36,4 @@ class RIrdisplay(Package): version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') - extends('r') - depends_on('r-repr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py index 4890d95b3e..68f62f2801 100644 --- a/var/spack/repos/builtin/packages/r-irkernel/package.py +++ b/var/spack/repos/builtin/packages/r-irkernel/package.py @@ -26,7 +26,7 @@ from spack import * -class RIrkernel(Package): +class RIrkernel(RPackage): """R kernel for Jupyter""" homepage = "https://irkernel.github.io/" @@ -35,8 +35,6 @@ class RIrkernel(Package): version('master', git='https://github.com/IRkernel/IRkernel.git', tag='0.7') - extends('r') - depends_on('r-repr', type=nolink) depends_on('r-irdisplay', type=nolink) depends_on('r-evaluate', type=nolink) @@ -45,7 +43,3 @@ class RIrkernel(Package): depends_on('r-devtools', type=nolink) depends_on('r-uuid', type=nolink) depends_on('r-digest', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index caae09930c..2028afcd34 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -25,7 +25,7 @@ from spack import * -class RIrlba(Package): +class RIrlba(RPackage): """Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principal component analysis of large sparse or dense matrices.""" @@ -36,10 +36,4 @@ class RIrlba(Package): version('2.0.0', '557674cf8b68fea5b9f231058c324d26') - extends('r') - depends_on('r-matrix', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index 7e6fb9890d..38dff8f9ac 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -25,7 +25,7 @@ from spack import * -class RIterators(Package): +class RIterators(RPackage): """Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.""" @@ -34,9 +34,3 @@ class RIterators(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/iterators" version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index 2ec11e744b..02c42b5ff1 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -25,7 +25,7 @@ from spack import * -class RJpeg(Package): +class RJpeg(RPackage): """This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.""" @@ -36,10 +36,4 @@ class RJpeg(Package): version('0.1-8', '696007451d14395b1ed1d0e9af667a57') - extends('r') - depends_on('jpeg') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index d01caf1f95..7368187af5 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -25,7 +25,7 @@ from spack import * -class RJsonlite(Package): +class RJsonlite(RPackage): """A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten in recent versions. The package offers flexible, robust, high performance @@ -43,9 +43,3 @@ class RJsonlite(Package): version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index 4ad22cf33f..7ed6562428 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -26,7 +26,7 @@ from spack import * -class RKnitr(Package): +class RKnitr(RPackage): """Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.""" @@ -35,9 +35,7 @@ class RKnitr(Package): list_url = "https://cran.rstudio.com/src/contrib/Archive/knitr" version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') - version('0.6' , 'c67d6db84cd55594a9e870c90651a3db') - - extends('r') + version('0.6', 'c67d6db84cd55594a9e870c90651a3db') depends_on('r-evaluate', type=nolink) depends_on('r-digest', type=nolink) @@ -46,7 +44,3 @@ class RKnitr(Package): depends_on('r-stringr', type=nolink) depends_on('r-markdown', type=nolink) depends_on('r-yaml', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index daf971bf44..7c288c63a4 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -25,7 +25,7 @@ from spack import * -class RLabeling(Package): +class RLabeling(RPackage): """Provides a range of axis labeling algorithms.""" homepage = "https://cran.r-project.org/web/packages/labeling/index.html" @@ -33,9 +33,3 @@ class RLabeling(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/labeling" version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index 9308a869a2..ed3c19f2e6 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -25,7 +25,7 @@ from spack import * -class RLattice(Package): +class RLattice(RPackage): """A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to @@ -36,9 +36,3 @@ class RLattice(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index 138691759f..ab41a39675 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -25,7 +25,7 @@ from spack import * -class RLazyeval(Package): +class RLazyeval(RPackage): """An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.""" @@ -35,9 +35,3 @@ class RLazyeval(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/lazyeval" version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index ab7fd2c48a..740c3f60bb 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -25,7 +25,7 @@ from spack import * -class RLeaflet(Package): +class RLeaflet(RPackage): """Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" @@ -36,8 +36,6 @@ class RLeaflet(Package): version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') - extends('r') - depends_on('r-base64enc', type=nolink) depends_on('r-htmlwidgets', type=nolink) depends_on('r-htmltools', type=nolink) @@ -48,7 +46,3 @@ class RLeaflet(Package): depends_on('r-raster', type=nolink) depends_on('r-scales', type=nolink) depends_on('r-sp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 2f9ee3e48f..bddc35fad2 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -25,7 +25,7 @@ from spack import * -class RLme4(Package): +class RLme4(RPackage): """Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for @@ -37,8 +37,6 @@ class RLme4(Package): version('1.1-12', 'da8aaebb67477ecb5631851c46207804') - extends('r') - depends_on('r-matrix', type=nolink) depends_on('r-mass', type=nolink) depends_on('r-lattice', type=nolink) @@ -47,7 +45,3 @@ class RLme4(Package): depends_on('r-nloptr', type=nolink) depends_on('r-rcpp', type=nolink) depends_on('r-rcppeigen', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index ff98eeadcf..b52bfd6861 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -25,7 +25,7 @@ from spack import * -class RLmtest(Package): +class RLmtest(RPackage): """A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.""" @@ -36,10 +36,4 @@ class RLmtest(Package): version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') - extends('r') - depends_on('r-zoo', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 125762de1e..8705ce805f 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -25,7 +25,7 @@ from spack import * -class RLubridate(Package): +class RLubridate(RPackage): """Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic @@ -39,10 +39,4 @@ class RLubridate(Package): version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') - extends('r') - depends_on('r-stringr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index ff32903125..d58ab5bacc 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -25,7 +25,7 @@ from spack import * -class RMagic(Package): +class RMagic(RPackage): """A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned @@ -37,10 +37,4 @@ class RMagic(Package): version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') - extends('r') - depends_on('r-abind', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index c41f4eff8f..915797e11d 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -25,7 +25,7 @@ from spack import * -class RMagrittr(Package): +class RMagrittr(RPackage): """Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible @@ -37,9 +37,3 @@ class RMagrittr(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr" version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index bace22a125..5aaac4fe11 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -25,7 +25,7 @@ from spack import * -class RMapproj(Package): +class RMapproj(RPackage): """Converts latitude/longitude into projected coordinates.""" homepage = "https://cran.r-project.org/package=mapproj" @@ -34,10 +34,4 @@ class RMapproj(Package): version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') - extends('r') - depends_on('r-maps', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 8cbb646643..c399bc52f3 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -25,7 +25,7 @@ from spack import * -class RMaps(Package): +class RMaps(RPackage): """Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').""" @@ -34,9 +34,3 @@ class RMaps(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/maps" version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index df9254e187..799125a7c9 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -25,7 +25,7 @@ from spack import * -class RMaptools(Package): +class RMaptools(RPackage): """Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for @@ -38,12 +38,6 @@ class RMaptools(Package): version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') - extends('r') - depends_on('r-sp', type=nolink) depends_on('r-foreign', type=nolink) depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index 9648412e50..544c002d52 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -25,7 +25,7 @@ from spack import * -class RMarkdown(Package): +class RMarkdown(RPackage): """Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See @@ -38,10 +38,4 @@ class RMarkdown(Package): version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') - extends('r') - depends_on('r-mime', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index eda7dccabf..25d3b5869b 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -25,7 +25,7 @@ from spack import * -class RMass(Package): +class RMass(RPackage): """Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).""" @@ -34,9 +34,3 @@ class RMass(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/MASS" version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index 02f193dd9b..12614014de 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -25,7 +25,7 @@ from spack import * -class RMatrix(Package): +class RMatrix(RPackage): """Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.""" @@ -35,10 +35,4 @@ class RMatrix(Package): version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') - extends('r') - depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index 62adab7f15..3b4d465132 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -25,7 +25,7 @@ from spack import * -class RMatrixmodels(Package): +class RMatrixmodels(RPackage): """Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.""" @@ -35,10 +35,4 @@ class RMatrixmodels(Package): version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') - extends('r') - depends_on('r-matrix', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index da93131554..c92daf6652 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -25,7 +25,7 @@ from spack import * -class RMemoise(Package): +class RMemoise(RPackage): """Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.""" @@ -35,10 +35,4 @@ class RMemoise(Package): version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') - extends('r') - depends_on('r-digest', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index 5b8f04a84c..5d5940129c 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -25,7 +25,7 @@ from spack import * -class RMgcv(Package): +class RMgcv(RPackage): """GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions @@ -37,11 +37,5 @@ class RMgcv(Package): version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') - extends('r') - depends_on('r-nlme', type=nolink) depends_on('r-matrix', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 55d40c5663..c4d2eb2b3e 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -25,7 +25,7 @@ from spack import * -class RMime(Package): +class RMime(RPackage): """Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.""" @@ -35,9 +35,3 @@ class RMime(Package): version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index a38f00f9ab..211694cc38 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -25,7 +25,7 @@ from spack import * -class RMinqa(Package): +class RMinqa(RPackage): """Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.""" @@ -35,10 +35,4 @@ class RMinqa(Package): version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') - extends('r') - depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index b32bea6249..c24f74de38 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -25,7 +25,7 @@ from spack import * -class RMultcomp(Package): +class RMultcomp(RPackage): """Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos @@ -38,14 +38,8 @@ class RMultcomp(Package): version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') - extends('r') - depends_on('r-mvtnorm', type=nolink) depends_on('r-survival', type=nolink) depends_on('r-thdata', type=nolink) depends_on('r-sandwich', type=nolink) depends_on('r-codetools', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 4250b00ec2..acc126a960 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -25,7 +25,7 @@ from spack import * -class RMunsell(Package): +class RMunsell(RPackage): """Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides @@ -38,10 +38,4 @@ class RMunsell(Package): version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') - extends('r') - depends_on('r-colorspace', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index 956ae6bc44..01e3aea91d 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -25,7 +25,7 @@ from spack import * -class RMvtnorm(Package): +class RMvtnorm(RPackage): """Computes multivariate normal and t probabilities, quantiles, random deviates and densities.""" @@ -34,9 +34,3 @@ class RMvtnorm(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm" version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 3949967022..597f4d903f 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -25,7 +25,7 @@ from spack import * -class RNcdf4(Package): +class RNcdf4(RPackage): """Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to @@ -47,10 +47,4 @@ class RNcdf4(Package): version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') - extends('r') - depends_on('netcdf') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 2374b78d7b..fafd3b3dde 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -25,7 +25,7 @@ from spack import * -class RNetworkd3(Package): +class RNetworkd3(RPackage): """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.""" @@ -35,12 +35,6 @@ class RNetworkd3(Package): version('0.2.12', '356fe4be59698e6fb052644bd9659d84') - extends('r') - depends_on('r-htmlwidgets', type=nolink) depends_on('r-igraph', type=nolink) depends_on('r-magrittr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 02a0836fd8..3c9056ec66 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -25,7 +25,7 @@ from spack import * -class RNlme(Package): +class RNlme(RPackage): """Fit and compare Gaussian linear and nonlinear mixed-effects models.""" homepage = "https://cran.r-project.org/package=nlme" @@ -34,10 +34,4 @@ class RNlme(Package): version('3.1-128', '3d75ae7380bf123761b95a073eb55008') - extends('r') - depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index 8b5e947710..8da84c5814 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -25,7 +25,7 @@ from spack import * -class RNloptr(Package): +class RNloptr(RPackage): """nloptr is an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original @@ -39,9 +39,3 @@ class RNloptr(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr" version('1.0.4', '9af69a613349b236fd377d0a107f484c') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index e33a9364d4..59defb441a 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -25,7 +25,7 @@ from spack import * -class RNmf(Package): +class RNmf(RPackage): """Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom @@ -39,8 +39,6 @@ class RNmf(Package): version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') - extends('r') - depends_on('r-pkgmaker', type=nolink) depends_on('r-registry', type=nolink) depends_on('r-rngtools', type=nolink) @@ -54,7 +52,3 @@ class RNmf(Package): depends_on('r-doparallel', type=nolink) depends_on('r-ggplot2', type=nolink) depends_on('r-reshape2', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index 6f5e7d6504..eeb6f91034 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -25,7 +25,7 @@ from spack import * -class RNnet(Package): +class RNnet(RPackage): """Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.""" @@ -34,9 +34,3 @@ class RNnet(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/nnet" version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index 1ee6105576..924472b526 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -25,7 +25,7 @@ from spack import * -class RNp(Package): +class RNp(RPackage): """This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support @@ -40,11 +40,5 @@ class RNp(Package): version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') - extends('r') - depends_on('r-boot', type=nolink) depends_on('r-cubature', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index f5442b102f..bf9f38be72 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -25,7 +25,7 @@ from spack import * -class ROpenssl(Package): +class ROpenssl(RPackage): """Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via @@ -43,10 +43,4 @@ class ROpenssl(Package): version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') - extends('r') - depends_on('openssl') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index f978b9f779..726a6640e8 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -25,7 +25,7 @@ from spack import * -class RPackrat(Package): +class RPackrat(RPackage): """Manage the R packages your project depends on in an isolated, portable, and reproducible way.""" @@ -34,9 +34,3 @@ class RPackrat(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/packrat" version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index ab994ce4d2..70dac90d99 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -26,7 +26,7 @@ from spack import * -class RPartykit(Package): +class RPartykit(RPackage): """A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from @@ -42,11 +42,5 @@ class RPartykit(Package): version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') - extends('r') - depends_on('r-survival', type=nolink) depends_on('r-formula', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index e6c546e921..02b1073ab4 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -26,7 +26,7 @@ from spack import * -class RPbdzmq(Package): +class RPbdzmq(RPackage): """'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus @@ -41,11 +41,5 @@ class RPbdzmq(Package): version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') - extends('r') - depends_on('r-r6', type=nolink) depends_on('zeromq') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 0bd749abe1..6910cad38b 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -25,7 +25,7 @@ from spack import * -class RPbkrtest(Package): +class RPbkrtest(RPackage): """Test in mixed effects models. Attention is on mixed effects models as implemented in the 'lme4' package. This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed @@ -38,12 +38,6 @@ class RPbkrtest(Package): version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') - extends('r') - depends_on('r-lme4', type=nolink) depends_on('r-matrix', type=nolink) depends_on('r-mass', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index 5c9e5496e7..4f193bc8e4 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -25,7 +25,7 @@ from spack import * -class RPkgmaker(Package): +class RPkgmaker(RPackage): """This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. @@ -40,14 +40,8 @@ class RPkgmaker(Package): version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') - extends('r') - depends_on('r-registry', type=nolink) depends_on('r-codetools', type=nolink) depends_on('r-digest', type=nolink) depends_on('r-stringr', type=nolink) depends_on('r-xtable', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index ec02193d40..8a17c72f91 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -25,7 +25,7 @@ from spack import * -class RPlotrix(Package): +class RPlotrix(RPackage): """Lots of plots, various labeling, axis and color scaling functions.""" homepage = "https://cran.r-project.org/package=plotrix" @@ -33,9 +33,3 @@ class RPlotrix(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix" version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index cc9c19b98a..229d5177c0 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -25,7 +25,7 @@ from spack import * -class RPlyr(Package): +class RPlyr(RPackage): """A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to @@ -40,10 +40,4 @@ class RPlyr(Package): version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') - extends('r') - depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index aa3d4f3c69..38b7ae5138 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -25,7 +25,7 @@ from spack import * -class RPng(Package): +class RPng(RPackage): """This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.""" @@ -36,10 +36,4 @@ class RPng(Package): version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') - extends('r') - depends_on('libpng') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index dba2289311..ff23594af9 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -25,7 +25,7 @@ from spack import * -class RPraise(Package): +class RPraise(RPackage): """Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.""" @@ -33,9 +33,3 @@ class RPraise(Package): url = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz" version('1.0.0', '9318724cec0454884b5f762bee2da6a1') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 109ea5fe4f..2553e325f3 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -25,7 +25,7 @@ from spack import * -class RProto(Package): +class RProto(RPackage): """An object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.""" @@ -34,9 +34,3 @@ class RProto(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/proto" version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index e9cbab3878..703a6f788f 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -26,7 +26,7 @@ from spack import * -class RPryr(Package): +class RPryr(RPackage): """Useful tools to pry back the covers of R and understand the language at a deeper level.""" @@ -36,11 +36,5 @@ class RPryr(Package): version('0.1.2', '66b597a762aa15a3b7037779522983b6') - extends('r') - depends_on('r-stringr', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index bf27e1a41b..e0276ef6d8 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -25,7 +25,7 @@ from spack import * -class RQuantmod(Package): +class RQuantmod(RPackage): """Specify, build, trade, and analyse quantitative financial trading strategies.""" @@ -35,12 +35,6 @@ class RQuantmod(Package): version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') - extends('r') - depends_on('r-xts', type=nolink) depends_on('r-zoo', type=nolink) depends_on('r-ttr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index 81aa242ee8..248ab28e41 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -25,7 +25,7 @@ from spack import * -class RQuantreg(Package): +class RQuantreg(RPackage): """Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response @@ -39,12 +39,6 @@ class RQuantreg(Package): version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') - extends('r') - depends_on('r-sparsem', type=nolink) depends_on('r-matrix', type=nolink) depends_on('r-matrixmodels', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index cb5593f6fc..e64a8a6532 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -25,7 +25,7 @@ from spack import * -class RR6(Package): +class RR6(RPackage): """The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 @@ -38,9 +38,3 @@ class RR6(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/R6" version('2.1.2', 'b6afb9430e48707be87638675390e457') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index 4d56210c99..bc7798695d 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -25,7 +25,7 @@ from spack import * -class RRandomforest(Package): +class RRandomforest(RPackage): """Classification and regression based on a forest of trees using random inputs.""" @@ -34,9 +34,3 @@ class RRandomforest(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest" version('4.6-12', '071c03af974198e861f1475c5bab9e7a') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index 017838428c..02b121566e 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -25,7 +25,7 @@ from spack import * -class RRaster(Package): +class RRaster(RPackage): """Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.""" @@ -36,11 +36,5 @@ class RRaster(Package): version('2.5-8', '2a7db931c74d50516e82d04687c0a577') - extends('r') - depends_on('r-sp', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index c410acaba2..168e8bf765 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -26,7 +26,7 @@ from spack import * -class RRbokeh(Package): +class RRbokeh(RPackage): """R interface for creating plots in Bokeh. Bokeh by Continuum Analytics.""" @@ -36,8 +36,6 @@ class RRbokeh(Package): version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') - extends('r') - depends_on('r-htmlwidgets', type=nolink) depends_on('r-maps', type=nolink) depends_on('r-jsonlite', type=nolink) @@ -49,7 +47,3 @@ class RRbokeh(Package): depends_on('r-ggplot2', type=nolink) depends_on('r-scales', type=nolink) depends_on('r-gistr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index 4734a1674f..59f134caad 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -25,7 +25,7 @@ from spack import * -class RRcolorbrewer(Package): +class RRcolorbrewer(RPackage): """Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org""" @@ -34,9 +34,3 @@ class RRcolorbrewer(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer" version('1.1-2', '66054d83eade4dff8a43ad4732691182') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 1637faca03..b447dea8bd 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -25,7 +25,7 @@ from spack import * -class RRcpp(Package): +class RRcpp(RPackage): """The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both @@ -42,9 +42,3 @@ class RRcpp(Package): version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index f0aebb54f0..d407a99b48 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -25,7 +25,7 @@ from spack import * -class RRcppeigen(Package): +class RRcppeigen(RPackage): """R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, @@ -46,11 +46,5 @@ class RRcppeigen(Package): version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') - extends('r') - depends_on('r-matrix', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index 89402cfbff..479250cac6 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -25,7 +25,7 @@ from spack import * -class RRegistry(Package): +class RRegistry(RPackage): """Provides a generic infrastructure for creating and using registries.""" homepage = "https://cran.r-project.org/web/packages/registry/index.html" @@ -33,9 +33,3 @@ class RRegistry(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/registry" version('0.3', '85345b334ec81eb3da6edcbb27c5f421') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index 11d43cf7ea..47720327de 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -26,7 +26,7 @@ from spack import * -class RRepr(Package): +class RRepr(RPackage): """String and binary representations of objects for several formats and mime types.""" @@ -35,9 +35,3 @@ class RRepr(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/repr" version('0.9', 'db5ff74893063b492f684e42283070bd') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index 1fd8067bbe..129198d14f 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -25,7 +25,7 @@ from spack import * -class RReshape2(Package): +class RReshape2(RPackage): """Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).""" @@ -35,12 +35,6 @@ class RReshape2(Package): version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') - extends('r') - depends_on('r-plyr', type=nolink) depends_on('r-stringr', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 0e0d94a3d3..4dd2cd9867 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -25,7 +25,7 @@ from spack import * -class RRgooglemaps(Package): +class RRgooglemaps(RPackage): """This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate @@ -37,11 +37,5 @@ class RRgooglemaps(Package): version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') - extends('r') - depends_on('r-png', type=nolink) depends_on('r-rjsonio', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index e18fc2499c..8e2a802eec 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -26,7 +26,7 @@ from spack import * -class RRinside(Package): +class RRinside(RPackage): """C++ classes to embed R in C++ applications The 'RInside' packages makes it easier to have "R inside" your C++ application by providing a C++ wrapperclass providing the R interpreter. As R itself is embedded into @@ -48,10 +48,4 @@ class RRinside(Package): version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') - extends('r') - depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index e1de4b77ff..440b93ff1f 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -25,7 +25,7 @@ from spack import * -class RRjava(Package): +class RRjava(RPackage): """Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.""" @@ -35,10 +35,4 @@ class RRjava(Package): version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') - extends('r') - depends_on('jdk') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index db25a92916..f37b574323 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -25,7 +25,7 @@ from spack import * -class RRjson(Package): +class RRjson(RPackage): """Converts R object into JSON objects and vice-versa.""" homepage = "https://cran.r-project.org/package=rjson" @@ -33,9 +33,3 @@ class RRjson(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/rjson" version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index a62f17abf7..4d5ffa6ddf 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -25,7 +25,7 @@ from spack import * -class RRjsonio(Package): +class RRjsonio(RPackage): """This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read @@ -47,9 +47,3 @@ class RRjsonio(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO" version('1.3-0', '72c395622ba8d1435ec43849fd32c830') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index c65ff7df9b..2200ee18ec 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -26,7 +26,7 @@ from spack import * -class RRmarkdown(Package): +class RRmarkdown(RPackage): """Convert R Markdown documents into a variety of formats.""" homepage = "http://rmarkdown.rstudio.com/" @@ -35,8 +35,6 @@ class RRmarkdown(Package): version('1.0', '264aa6a59e9680109e38df8270e14c58') - extends('r') - depends_on('r-knitr', type=nolink) depends_on('r-yaml', type=nolink) depends_on('r-htmltools', type=nolink) @@ -44,7 +42,3 @@ class RRmarkdown(Package): depends_on('r-evaluate', type=nolink) depends_on('r-base64enc', type=nolink) depends_on('r-jsonlite', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 4164dd3721..fd38647220 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -25,7 +25,7 @@ from spack import * -class RRmysql(Package): +class RRmysql(RPackage): """Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.""" homepage = "https://github.com/rstats-db/rmysql" @@ -34,11 +34,5 @@ class RRmysql(Package): version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') - extends('r') - depends_on('r-dbi', type=nolink) depends_on('mariadb') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index 2c06306f31..b2b5e52861 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -25,7 +25,7 @@ from spack import * -class RRngtools(Package): +class RRngtools(RPackage): """This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects @@ -38,12 +38,6 @@ class RRngtools(Package): version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') - extends('r') - depends_on('r-pkgmaker', type=nolink) depends_on('r-stringr', type=nolink) depends_on('r-digest', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index af142c841a..70e477bcb1 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -25,7 +25,7 @@ from spack import * -class RRodbc(Package): +class RRodbc(RPackage): """An ODBC database interface.""" homepage = "https://cran.rstudio.com/web/packages/RODBC/" @@ -34,10 +34,4 @@ class RRodbc(Package): version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') - extends('r') - depends_on('unixodbc') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index 1c017d7898..1d3b3fa1f6 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -25,7 +25,7 @@ from spack import * -class RRoxygen2(Package): +class RRoxygen2(RPackage): """A 'Doxygen'-like in-source documentation system for Rd, collation, and 'NAMESPACE' files.""" @@ -35,14 +35,8 @@ class RRoxygen2(Package): version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') - extends('r') - depends_on('r-stringr', type=nolink) depends_on('r-stringi', type=nolink) depends_on('r-brew', type=nolink) depends_on('r-digest', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 3f7b64693f..227f7e9ce5 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -25,7 +25,7 @@ from spack import * -class RRpostgresql(Package): +class RRpostgresql(RPackage): """Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. In order to build and install this package from source, @@ -42,11 +42,5 @@ class RRpostgresql(Package): version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') - extends('r') - depends_on('r-dbi', type=nolink) depends_on('postgresql') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index fad75827d4..d707f5f542 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -26,7 +26,7 @@ from spack import * -class RRsnns(Package): +class RRsnns(RPackage): """The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS @@ -41,10 +41,4 @@ class RRsnns(Package): version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') - extends('r') - depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index a22421ed87..f090405408 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -25,7 +25,7 @@ from spack import * -class RRsqlite(Package): +class RRsqlite(RPackage): """This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.""" @@ -36,10 +36,4 @@ class RRsqlite(Package): version('1.0.0', 'e6cbe2709612b687c13a10d30c7bad45') - extends('r') - depends_on('r-dbi', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 4f580d7853..26a040c363 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -25,7 +25,7 @@ from spack import * -class RRstan(Package): +class RRstan(RPackage): """User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic @@ -42,8 +42,6 @@ class RRstan(Package): version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') - extends('r') - depends_on('r-ggplot2', type=nolink) depends_on('r-stanheaders', type=nolink) depends_on('r-inline', type=nolink) @@ -51,7 +49,3 @@ class RRstan(Package): depends_on('r-rcpp', type=nolink) depends_on('r-rcppeigen', type=nolink) depends_on('r-bh', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 1a20fc226b..2558a5c3f6 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -25,7 +25,7 @@ from spack import * -class RRstudioapi(Package): +class RRstudioapi(RPackage): """Access the RStudio API (if available) and provide informative error messages when it's not.""" @@ -35,9 +35,3 @@ class RRstudioapi(Package): version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index d013c8889c..f385a13901 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -26,7 +26,7 @@ from spack import * -class RRzmq(Package): +class RRzmq(RPackage): """Interface to the ZeroMQ lightweight messaging kernel.""" homepage = "http://github.com/armstrtw/rzmq" @@ -36,9 +36,3 @@ class RRzmq(Package): version('0.7.7', '8ba18fd1c222d1eb25bb622ccd2897e0') depends_on('zeromq') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index a9d39d37f9..248f09c614 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -25,7 +25,7 @@ from spack import * -class RSandwich(Package): +class RSandwich(RPackage): """Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.""" @@ -35,10 +35,4 @@ class RSandwich(Package): version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') - extends('r') - depends_on('r-zoo', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index 0072de8f5f..174b7d7d6e 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -25,7 +25,7 @@ from spack import * -class RScales(Package): +class RScales(RPackage): """Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.""" @@ -35,15 +35,9 @@ class RScales(Package): version('0.4.0', '7b5602d9c55595901192248bca25c099') - extends('r') - depends_on('r-rcolorbrewer', type=nolink) depends_on('r-dichromat', type=nolink) depends_on('r-plyr', type=nolink) depends_on('r-munsell', type=nolink) depends_on('r-labeling', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index 4617e8a0b2..4c357bdc30 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -25,7 +25,7 @@ from spack import * -class RShiny(Package): +class RShiny(RPackage): """Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and @@ -37,8 +37,6 @@ class RShiny(Package): version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') - extends('r') - depends_on('r-httpuv', type=nolink) depends_on('r-mime', type=nolink) depends_on('r-jsonlite', type=nolink) @@ -46,7 +44,3 @@ class RShiny(Package): depends_on('r-digest', type=nolink) depends_on('r-htmltools', type=nolink) depends_on('r-r6', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index ecb75203bb..19ce2ee912 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -25,7 +25,7 @@ from spack import * -class RSp(Package): +class RSp(RPackage): """Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as @@ -37,10 +37,4 @@ class RSp(Package): version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') - extends('r') - depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index 1bd8835d5a..370497e395 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -25,7 +25,7 @@ from spack import * -class RSparsem(Package): +class RSparsem(RPackage): """Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.""" @@ -35,9 +35,3 @@ class RSparsem(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index 681969f18d..322356e347 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -25,7 +25,7 @@ from spack import * -class RStanheaders(Package): +class RStanheaders(RPackage): """The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not @@ -47,9 +47,3 @@ class RStanheaders(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders" version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 5a5f4ee18a..d89238f3d7 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -25,7 +25,7 @@ from spack import * -class RStringi(Package): +class RStringi(RPackage): """Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with @@ -42,10 +42,4 @@ class RStringi(Package): version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') - extends('r') - depends_on('icu4c') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 43bae9bbf0..5f9f05df31 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -25,7 +25,7 @@ from spack import * -class RStringr(Package): +class RStringr(RPackage): """A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length @@ -38,11 +38,5 @@ class RStringr(Package): version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') - extends('r') - depends_on('r-stringi', type=nolink) depends_on('r-magrittr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index 619f22cb59..249cad8178 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -25,7 +25,7 @@ from spack import * -class RSurvey(Package): +class RSurvey(RPackage): """Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, @@ -39,9 +39,3 @@ class RSurvey(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/survey" version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index 71652c2bcc..44d5043189 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -25,7 +25,7 @@ from spack import * -class RSurvival(Package): +class RSurvival(RPackage): """Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.""" @@ -36,10 +36,4 @@ class RSurvival(Package): version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') - extends('r') - depends_on('r-matrix', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index a6b5fbddd3..0703c0f5f0 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -25,7 +25,7 @@ from spack import * -class RTarifx(Package): +class RTarifx(RPackage): """A collection of various utility and convenience functions.""" homepage = "https://cran.r-project.org/package=taRifx" @@ -34,11 +34,5 @@ class RTarifx(Package): version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') - extends('r') - depends_on('r-reshape2', type=nolink) depends_on('r-plyr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index 2f2b0f3c4f..4d99c388e6 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -26,7 +26,7 @@ from spack import * -class RTestit(Package): +class RTestit(RPackage): """Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.""" @@ -35,9 +35,3 @@ class RTestit(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/testit" version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index 8d4d174128..7589909b3b 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -25,7 +25,7 @@ from spack import * -class RTestthat(Package): +class RTestthat(RPackage): """A unit testing system designed to be fun, flexible and easy to set up.""" @@ -35,14 +35,8 @@ class RTestthat(Package): version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') - extends('r') - depends_on('r-digest', type=nolink) depends_on('r-crayon', type=nolink) depends_on('r-praise', type=nolink) depends_on('r-magrittr', type=nolink) depends_on('r-r6', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py index a389da3045..4639b7f5ae 100644 --- a/var/spack/repos/builtin/packages/r-thdata/package.py +++ b/var/spack/repos/builtin/packages/r-thdata/package.py @@ -25,7 +25,7 @@ from spack import * -class RThdata(Package): +class RThdata(RPackage): """Contains data sets used in other packages Torsten Hothorn maintains.""" homepage = "https://cran.r-project.org/package=TH.data" @@ -34,11 +34,5 @@ class RThdata(Package): version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') - extends('r') - depends_on('r-survival', type=nolink) depends_on('r-mass', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index e3aa271b3e..a525425fa3 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -25,7 +25,7 @@ from spack import * -class RThreejs(Package): +class RThreejs(RPackage): """Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ("http://threejs.org").""" @@ -35,13 +35,7 @@ class RThreejs(Package): version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') - extends('r') - depends_on('r-htmlwidgets', type=nolink) depends_on('r-base64enc', type=nolink) depends_on('r-matrix', type=nolink) depends_on('r-jsonlite', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 6d59a40147..47355cc451 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -25,7 +25,7 @@ from spack import * -class RTibble(Package): +class RTibble(RPackage): """Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.""" @@ -35,12 +35,6 @@ class RTibble(Package): version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') - extends('r') - depends_on('r-assertthat', type=nolink) depends_on('r-lazyeval', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index c83d75b6fd..c7ac3d3225 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -25,7 +25,7 @@ from spack import * -class RTidyr(Package): +class RTidyr(RPackage): """An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.""" @@ -36,14 +36,9 @@ class RTidyr(Package): version('0.5.1', '3cadc869510c054ed93d374ab44120bd') - extends('r') depends_on('r-tibble', type=nolink) depends_on('r-dplyr', type=nolink) depends_on('r-stringi', type=nolink) depends_on('r-lazyeval', type=nolink) depends_on('r-magrittr', type=nolink) depends_on('r-rcpp', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index 355ba6ca3c..98f4a0e450 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -25,7 +25,7 @@ from spack import * -class RTtr(Package): +class RTtr(RPackage): """Functions and data to construct technical trading rules with R.""" homepage = "https://github.com/joshuaulrich/TTR" @@ -34,11 +34,5 @@ class RTtr(Package): version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') - extends('r') - depends_on('r-xts', type=nolink) depends_on('r-zoo', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index 9a2455017b..b9dcc12629 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -26,7 +26,7 @@ from spack import * -class RUuid(Package): +class RUuid(RPackage): """Tools for generating and handling of UUIDs (Universally Unique Identifiers).""" @@ -35,9 +35,3 @@ class RUuid(Package): list_url = "https://cran.rstudio.com/src/contrib/Archive/uuid" version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index f7c0b25369..0e16260d0f 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -25,7 +25,7 @@ from spack import * -class RVcd(Package): +class RVcd(RPackage): """Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired @@ -39,12 +39,6 @@ class RVcd(Package): version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') - extends('r') - depends_on('r-mass', type=nolink) depends_on('r-colorspace', type=nolink) depends_on('r-lmtest', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index 6cce369325..81be9fb5c2 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -25,7 +25,7 @@ from spack import * -class RVisnetwork(Package): +class RVisnetwork(RPackage): """Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.""" @@ -35,13 +35,7 @@ class RVisnetwork(Package): version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') - extends('r') - depends_on('r-htmlwidgets', type=nolink) depends_on('r-htmltools', type=nolink) depends_on('r-jsonlite', type=nolink) depends_on('r-magrittr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 8edea7e840..17f904f5c3 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -25,7 +25,7 @@ from spack import * -class RWhisker(Package): +class RWhisker(RPackage): """logicless templating, reuse templates in many programming languages including R""" @@ -34,9 +34,3 @@ class RWhisker(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/whisker" version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index 92b941b32f..785050ed87 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -25,7 +25,7 @@ from spack import * -class RWithr(Package): +class RWithr(RPackage): """A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited @@ -36,9 +36,3 @@ class RWithr(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/withr" version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 586a99f76f..dfa9928ee3 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -26,7 +26,7 @@ from spack import * -class RXgboost(Package): +class RXgboost(RPackage): """Extreme Gradient Boosting, which is an efficient implementation of gradient boosting framework. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The @@ -42,13 +42,7 @@ class RXgboost(Package): version('0.4-4', 'c24d3076058101a71de4b8af8806697c') - extends('r') - depends_on('r-matrix', type=nolink) depends_on('r-datatable', type=nolink) depends_on('r-magrittr', type=nolink) depends_on('r-stringr', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 64b95f84e0..cdb8dbce3f 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -25,7 +25,7 @@ from spack import * -class RXlconnect(Package): +class RXlconnect(RPackage): """Provides comprehensive functionality to read, write and format Excel data.""" @@ -36,11 +36,5 @@ class RXlconnect(Package): version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') - extends('r') - depends_on('r-xlconnectjars', type=nolink) depends_on('r-rjava', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index 37dbed2783..4606847512 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -25,7 +25,7 @@ from spack import * -class RXlconnectjars(Package): +class RXlconnectjars(RPackage): """Provides external JAR dependencies for the XLConnect package.""" homepage = "http://miraisolutions.wordpress.com/" @@ -35,10 +35,4 @@ class RXlconnectjars(Package): version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') - extends('r') - depends_on('r-rjava', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index 4c7b8ee15d..e7a8b28204 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -25,7 +25,7 @@ from spack import * -class RXlsx(Package): +class RXlsx(RPackage): """Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.""" @@ -35,11 +35,5 @@ class RXlsx(Package): version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') - extends('r') - depends_on('r-rjava', type=nolink) depends_on('r-xlsxjars', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 22bda6e83f..972ac4b557 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -25,7 +25,7 @@ from spack import * -class RXlsxjars(Package): +class RXlsxjars(RPackage): """The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.""" @@ -35,10 +35,4 @@ class RXlsxjars(Package): version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') - extends('r') - depends_on('r-rjava', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index 416491cbe6..2fe2a8a05b 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -25,7 +25,7 @@ from spack import * -class RXml(Package): +class RXml(RPackage): """Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".""" @@ -37,10 +37,4 @@ class RXml(Package): version('3.98-1.5', 'd1cfcd56f7aec96a84ffca91aea507ee') version('3.98-1.4', '1a7f3ce6f264eeb109bfa57bedb26c14') - extends('r') - depends_on('libxml2') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 8c675e1b3b..66d8687b6d 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -25,7 +25,7 @@ from spack import * -class RXtable(Package): +class RXtable(RPackage): """Coerce data to LaTeX and HTML tables.""" homepage = "http://xtable.r-forge.r-project.org/" @@ -33,9 +33,3 @@ class RXtable(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/xtable" version('1.8-2', '239e4825cd046156a67efae3aac01d86') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index 678a9f4bf4..47b3a60720 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -25,7 +25,7 @@ from spack import * -class RXts(Package): +class RXts(RPackage): """Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying @@ -37,10 +37,4 @@ class RXts(Package): version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') - extends('r') - depends_on('r-zoo', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index d8a3c9bacc..c812ea8ca2 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -25,7 +25,7 @@ from spack import * -class RYaml(Package): +class RYaml(RPackage): """This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.""" @@ -34,9 +34,3 @@ class RYaml(Package): list_url = "https://cran.r-project.org/src/contrib/Archive/yaml" version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') - - extends('r') - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 27295c7afc..ade0e762df 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -25,7 +25,7 @@ from spack import * -class RZoo(Package): +class RZoo(RPackage): """An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular @@ -38,10 +38,4 @@ class RZoo(Package): version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') - extends('r') - depends_on('r-lattice', type=nolink) - - def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), - self.stage.source_path) |