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-rw-r--r--var/spack/repos/builtin/packages/gts/package.py53
-rw-r--r--var/spack/repos/builtin/packages/hmmer/package.py76
-rw-r--r--var/spack/repos/builtin/packages/python/package.py25
-rw-r--r--var/spack/repos/builtin/packages/r-ggvis/package.py51
-rw-r--r--var/spack/repos/builtin/packages/r-htmltools/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-httpuv/package.py49
-rw-r--r--var/spack/repos/builtin/packages/r-shiny/package.py52
-rw-r--r--var/spack/repos/builtin/packages/r-xtable/package.py41
-rw-r--r--var/spack/repos/builtin/packages/swiftsim/package.py1
9 files changed, 389 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py
new file mode 100644
index 0000000000..2b3d4dd4f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gts/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Gts(Package):
+ """GTS stands for the GNU Triangulated Surface Library.
+
+ It is an Open Source Free Software Library intended to provide a set of
+ useful functions to deal with 3D surfaces meshed with interconnected
+ triangles. The source code is available free of charge under the Free
+ Software LGPL license.
+
+ The code is written entirely in C with an object-oriented approach
+ based mostly on the design of GTK+. Careful attention is paid to
+ performance related issues as the initial goal of GTS is to provide a
+ simple and efficient library to scientists dealing with 3D computational
+ surface meshes.
+ """
+
+ homepage = "http://gts.sourceforge.net/index.html"
+ url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz"
+
+ version('121130', '023ebb6b13b8707534182a3ef0d12908')
+
+ depends_on('glib')
+
+ def install(self, spec, prefix):
+ configure('--prefix={0}'.format(prefix))
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py
new file mode 100644
index 0000000000..6a236e9fc9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hmmer/package.py
@@ -0,0 +1,76 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Hmmer(Package):
+ """HMMER is used for searching sequence databases for sequence homologs,
+ and for making sequence alignments. It implements methods using
+ probabilistic models called profile hidden Markov models (profile HMMs).
+ """
+ homepage = 'http://www.hmmer.org'
+ url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+
+ version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
+ version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588')
+ version('2.4i', 'dab234c87e026ac1de942450750acd20')
+ version('2.3.2', '5f073340c0cf761288f961a73821228a')
+ version('2.3.1', 'c724413e5761c630892506698a4716e2')
+
+ variant('mpi', default=True, description='Compile with MPI')
+ variant('gsl', default=False, description='Compile with GSL')
+
+ depends_on('mpi', when='+mpi')
+ depends_on('gsl', when='+gsl')
+
+ def url_for_version(self, version):
+ base_url = 'http://eddylab.org/software'
+
+ if version >= Version('3.0'):
+ return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+ else:
+ return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
+
+ def install(self, spec, prefix):
+ configure_args = [
+ '--prefix={0}'.format(prefix)
+ ]
+
+ if '+gsl' in self.spec:
+ configure_args.extend([
+ '--with-gsl',
+ 'LIBS=-lgsl -lgslcblas'
+ ])
+
+ if '+mpi' in self.spec:
+ configure_args.append('--enable-mpi')
+
+ configure(*configure_args)
+ make()
+
+ if self.run_tests:
+ make('check')
+
+ make('install')
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index dafafabb05..516b5c6cfe 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -38,16 +38,29 @@ class Python(Package):
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
+ version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72')
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
- version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
+ version('3.4.3', '4281ff86778db65892c05151d5de738d')
+ version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
+ version('3.2.6', '23815d82ae706e9b781ca65865353d39')
+ version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
+ version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True)
+ version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
extendable = True
- variant('ucs4', default=False, description='Enable UCS4 unicode strings')
+ variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
+ # From https://docs.python.org/2/c-api/unicode.html: Python's default
+ # builds use a 16-bit type for Py_UNICODE and store Unicode values
+ # internally as UCS2. It is also possible to build a UCS4 version of Python
+ # (most recent Linux distributions come with UCS4 builds of Python). These
+ # builds then use a 32-bit type for Py_UNICODE and store Unicode data
+ # internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary
+ # compatible.
depends_on("openssl")
depends_on("bzip2")
@@ -85,7 +98,13 @@ class Python(Package):
]
if '+ucs4' in spec:
- config_args.append('--enable-unicode=ucs4')
+ if spec.satisfies('@:2.7'):
+ config_args.append('--enable-unicode=ucs4')
+ elif spec.satisfies('@3.0:3.2'):
+ config_args.append('--with-wide-unicode')
+ elif spec.satisfies('@3.3:'):
+ # https://docs.python.org/3.3/whatsnew/3.3.html
+ raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501
if spec.satisfies('@3:'):
config_args.append('--without-ensurepip')
diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py
new file mode 100644
index 0000000000..8fc1f397c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggvis/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGgvis(Package):
+ """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'."""
+
+ homepage = "http://ggvis.rstudio.com/"
+ url = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis"
+
+ version('0.4.2', '039f45e5c7f1e0652779163d7d99f922')
+
+ extends('R')
+
+ depends_on('r-assertthat')
+ depends_on('r-jsonlite')
+ depends_on('r-shiny')
+ depends_on('r-magrittr')
+ depends_on('r-dplyr')
+ depends_on('r-lazyeval')
+ depends_on('r-htmltools')
+
+ 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
new file mode 100644
index 0000000000..0aea564372
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-htmltools/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RHtmltools(Package):
+ """Tools for HTML generation and output."""
+
+ homepage = "https://github.com/rstudio/htmltools"
+ url = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools"
+
+ version('0.3.5', '5f001aff4a39e329f7342dcec5139724')
+
+ extends('R')
+
+ depends_on('r-digest')
+ depends_on('r-rcpp')
+
+ 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
new file mode 100644
index 0000000000..6ab12bcf9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-httpuv/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RHttpuv(Package):
+ """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
+ to create complete web applications using httpuv alone. httpuv is built on
+ top of the libuv and http-parser C libraries, both of which were developed
+ by Joyent, Inc. (See LICENSE file for libuv and http-parser license
+ information.)"""
+
+ homepage = "https://github.com/rstudio/httpuv"
+ url = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv"
+
+ version('1.3.3', 'c78ae068cf59e949b9791be987bb4489')
+
+ extends('R')
+
+ depends_on('r-rcpp')
+
+ 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
new file mode 100644
index 0000000000..a9a9532910
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-shiny/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RShiny(Package):
+ """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
+ powerful applications with minimal effort."""
+
+ homepage = "http://shiny.rstudio.com/"
+ url = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/shiny"
+
+ version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611')
+
+ extends('R')
+
+ depends_on('r-httpuv')
+ depends_on('r-mime')
+ depends_on('r-jsonlite')
+ depends_on('r-xtable')
+ depends_on('r-digest')
+ depends_on('r-htmltools')
+ depends_on('r-R6')
+
+ 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
new file mode 100644
index 0000000000..46434b4842
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-xtable/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RXtable(Package):
+ """Coerce data to LaTeX and HTML tables."""
+
+ homepage = "http://xtable.r-forge.r-project.org/"
+ url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz"
+ 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/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py
index 37862a73a9..620d658a10 100644
--- a/var/spack/repos/builtin/packages/swiftsim/package.py
+++ b/var/spack/repos/builtin/packages/swiftsim/package.py
@@ -71,6 +71,7 @@ class Swiftsim(Package):
# Configure and install
options = ['--prefix=%s' % prefix,
'--enable-mpi' if '+mpi' in spec else '--disable-mpi',
+ '--with-metis={0}'.format(spec['metis'].prefix),
'--enable-optimization']
configure(*options)
make()
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-12 05:02:55 +0000