Additional r packages (#7892)

* Add r-bbmisc

* Add r-dicekriging

* Add r-lhs

* Add r-mco

* Add r-misc3d

* Add r-mlr

* Remove boilerplate from r-mlr package

* Add r-mlrMBO

* Add r-parallelmap

* Add r-paramhelpers

* Add r-plot3d

* Add r-rgenoud

* Add r-smoof

* Add r-rinside 0.2.14

* Fix flake8 issues

* Add specific required versions

* Add more up-to-date versions of r-{mco, mlr, mlrMBO, smoof}
This commit is contained in:
mcneish1 2018-04-25 18:59:46 -07:00 committed by Adam J. Stewart
parent 28901c8104
commit 94afb2430c
13 changed files with 509 additions and 3 deletions

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RBbmisc(RPackage):
"""Miscellaneous helper functions for and from B. Bischl and some other
guys, mainly for package development."""
homepage = "https://github.com/berndbischl/BBmisc"
url = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/BBmisc"
version('1.11', '681642628037406beb6088d5f773473d')
depends_on('r-checkmate@1.8.0:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RDicekriging(RPackage):
"""Estimation, validation and prediction of kriging models. Important
functions : km, print.km, plot.km, predict.km."""
homepage = "http://dice.emse.fr/"
url = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging"
version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844')

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RLhs(RPackage):
"""Provides a number of methods for creating and augmenting Latin Hypercube
Samples."""
homepage = "http://lhs.r-forge.r-project.org/"
url = "https://cran.r-project.org/src/contrib/lhs_0.16.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/lhs"
version('0.16', '088e593e5283414951e7e541a50ec2d1')

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMco(RPackage):
"""Functions for multiple criteria optimization using genetic algorithms
and related test problems"""
homepage = "https://github.com/cran/mco"
url = "https://cran.r-project.org/src/contrib/mco_1.0-15.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/mco"
version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa')
version('1.0-15', '0b444e085c59d919611224e86b5637f8')

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMisc3d(RPackage):
"""A collection of miscellaneous 3d plots, including isosurfaces."""
homepage = "http://www.example.com"
url = "https://cran.r-project.org/src/contrib/misc3d_0.8-4.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/misc3d"
version('0.8-4', 'aefa27e67a243c21a1046868540343fe')

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMlr(RPackage):
"""Interface to a large number of classification and regression techniques,
including machine-readable parameter descriptions. There is also an
experimental extension for survival analysis, clustering and general,
example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling.
Hyperparameter tuning with modern optimization techniques,
for single- and multi-objective problems. Filter and wrapper methods for
feature selection. Extension of basic learners with additional
operations common in machine learning, also allowing for easy nested
resampling. Most operations can be parallelized."""
homepage = "https://github.com/mlr-org/mlr/"
url = "https://cran.r-project.org/src/contrib/mlr_2.12.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/mlr"
version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec')
version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f')
depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
depends_on('r-bbmisc@1.11:', type=('build', 'run'))
depends_on('r-backports@1.1.0:', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-stringi', type=('build', 'run'))
depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r-parallelmap@1.3:', type=('build', 'run'))
depends_on('r-xml', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RMlrmbo(RPackage):
"""Flexible and comprehensive R toolbox for model-based optimization
('MBO'), also known as Bayesian optimization. It is designed for both
single- and multi-objective optimization with mixed continuous,
categorical and conditional parameters. The machine learning toolbox
'mlr' provide dozens of regression learners to model the performance of
the target algorithm with respect to the parameter settings. It provides
many different infill criteria to guide the search process. Additional
features include multi-point batch proposal, parallel execution as well
as visualization and sophisticated logging mechanisms, which is
especially useful for teaching and understanding of algorithm behavior.
'mlrMBO' is implemented in a modular fashion, such that single
components can be easily replaced or adapted by the user for specific
use cases."""
homepage = "https://github.com/mlr-org/mlrMBO/"
url = "https://cran.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/mlrMBO"
version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0')
version('1.1.0', '9e27ff8498225d24863b8da758d2918e')
depends_on('r-mlr@2.10:', type=('build', 'run'))
depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
depends_on('r-smoof@1.5.1:', type=('build', 'run'))
depends_on('r-backports@1.1.0:', type=('build', 'run'))
depends_on('r-bbmisc@1.11:', type=('build', 'run'))
depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r-lhs', type=('build', 'run'))
depends_on('r-parallelmap@1.3:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RParallelmap(RPackage):
"""Unified parallelization framework for multiple back-end, designed for
internal package and interactive usage. The main operation is a parallel
"map" over lists. Supports local, multicore, mpi and BatchJobs mode.
Allows "tagging" of the parallel operation with a level name that can be
later selected by the user to switch on parallel execution for exactly
this operation."""
homepage = "https://github.com/berndbischl/parallelMap"
url = "https://cran.r-project.org/src/contrib/parallelMap_1.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/parallelMap"
version('1.3', 'dd62866b395847b0bd5b13bed98c0081')
depends_on('r-bbmisc@1.8:', type=('build', 'run'))
depends_on('r-checkmate@1.5.1:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RParamhelpers(RPackage):
"""Functions for parameter descriptions and operations in black-box
optimization, tuning and machine learning. Parameters can be described
(type, constraints, defaults, etc.), combined to parameter sets and can
in general be programmed on. A useful OptPath object (archive) to log
function evaluations is also provided."""
homepage = "https://github.com/berndbischl/ParamHelpers"
url = "https://cran.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ParamHelpers"
version('1.10', '36e9060488ebd484d62cd991a4693332')
depends_on('r-bbmisc@1.10:', type=('build', 'run'))
depends_on('r-checkmate@1.8.1:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RPlot3d(RPackage):
"""Functions for viewing 2-D and 3-D data, including perspective plots,
slice plots, surface plots, scatter plots, etc. Includes data sets from
oceanography."""
homepage = "https://CRAN.R-project.org/package=plot3D"
url = "https://cran.r-project.org/src/contrib/plot3D_1.1.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/plot3D"
version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d')
depends_on('r-misc3d', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRgenoud(RPackage):
"""A genetic algorithm plus derivative optimizer."""
homepage = "http://sekhon.berkeley.edu/rgenoud/"
url = "https://cran.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/rgenoud"
version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f')

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@ -22,7 +22,6 @@
# License along with this program; if not, write to the Free Software # License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
############################################################################## ##############################################################################
from spack import * from spack import *
@ -43,9 +42,10 @@ class RRinside(RPackage):
available at the 'RInside' website as well.""" available at the 'RInside' website as well."""
homepage = "http://dirk.eddelbuettel.com/code/rinside.html" homepage = "http://dirk.eddelbuettel.com/code/rinside.html"
url = "https://cran.r-project.org/src/contrib/RInside_0.2.13.tar.gz" url = "https://cran.r-project.org/src/contrib/RInside_0.2.14.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/RInside" list_url = "https://cran.r-project.org/src/contrib/Archive/RInside"
version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff')
version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88')
depends_on('r-rcpp', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, 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/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RSmoof(RPackage):
"""Provides generators for a high number of both single- and
multi- objective test functions which are frequently used for the
benchmarking of (numerical) optimization algorithms. Moreover, it offers
a set of convenient functions to generate, plot and work with objective
functions."""
homepage = "http://github.com/jakobbossek/smoof"
url = "https://cran.r-project.org/src/contrib/smoof_1.5.1.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/smoof"
version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054')
version('1.5', 'b371bde2724eade5a6d4d808fa3ad269')
depends_on('r-paramhelpers@1.8:', type=('build', 'run'))
depends_on('r-bbmisc@1.6:', type=('build', 'run'))
depends_on('r-checkmate@1.1:', type=('build', 'run'))
depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-plot3d', type=('build', 'run'))
depends_on('r-plotly', type=('build', 'run'))
depends_on('r-mco', type=('build', 'run'))
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
depends_on('r-rjsonio', type=('build', 'run'))
depends_on('r-rcpparmadillo', type=('build', 'run'))