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-rw-r--r--etc/spack/modules.yaml2
-rw-r--r--lib/spack/docs/packaging_guide.rst43
-rw-r--r--lib/spack/spack/concretize.py6
-rw-r--r--lib/spack/spack/fetch_strategy.py9
-rw-r--r--lib/spack/spack/test/versions.py3
-rw-r--r--lib/spack/spack/version.py8
-rw-r--r--var/spack/repos/builtin/packages/R/package.py24
-rw-r--r--var/spack/repos/builtin/packages/dealii/package.py200
-rw-r--r--var/spack/repos/builtin/packages/libxml2/package.py6
-rw-r--r--var/spack/repos/builtin/packages/r-assertthat/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-dplyr/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-lazyeval/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-lubridate/package.py47
-rw-r--r--var/spack/repos/builtin/packages/r-tibble/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-tidyr/package.py49
15 files changed, 470 insertions, 109 deletions
diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml
index 5f31cdd5c0..9ae54a2d09 100644
--- a/etc/spack/modules.yaml
+++ b/etc/spack/modules.yaml
@@ -13,6 +13,8 @@ modules:
- PATH
man:
- MANPATH
+ share/man:
+ - MANPATH
lib:
- LIBRARY_PATH
- LD_LIBRARY_PATH
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 72559e47ce..0f549e2957 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -568,7 +568,7 @@ The package author is responsible for coming up with a sensible name
for each version to be fetched from a repository. For example, if
you're fetching from a tag like ``v1.0``, you might call that ``1.0``.
If you're fetching a nameless git commit or an older subversion
-revision, you might give the commit an intuitive name, like ``dev``
+revision, you might give the commit an intuitive name, like ``develop``
for a development version, or ``some-fancy-new-feature`` if you want
to be more specific.
@@ -578,6 +578,17 @@ branches move forward over time and you aren't guaranteed to get the
same thing every time you fetch a particular version. Life isn't
always simple, though, so this is not strictly enforced.
+When fetching from from the branch corresponding to the development version
+(often called ``master``,``trunk`` or ``dev``), it is recommended to
+call this version ``develop``. Spack has special treatment for this version so
+ that ``@develop`` will satisfy dependencies like
+``depends_on(abc, when="@x.y.z:")``. In other words, ``@develop`` is
+greater than any other version. The rationale is that certain features or
+options first appear in the development branch. Therefore if a package author
+wants to keep the package on the bleeding edge and provide support for new
+features, it is advised to use ``develop`` for such a version which will
+greatly simplify writing dependencies and version-related conditionals.
+
In some future release, Spack may support extrapolating repository
versions as it does for tarball URLs, but currently this is not
supported.
@@ -593,6 +604,7 @@ Git fetching is enabled with the following parameters to ``version``:
* ``tag``: name of a tag to fetch.
* ``branch``: name of a branch to fetch.
* ``commit``: SHA hash (or prefix) of a commit to fetch.
+ * ``submodules``: Also fetch submodules when checking out this repository.
Only one of ``tag``, ``branch``, or ``commit`` can be used at a time.
@@ -603,7 +615,7 @@ Default branch
class Example(Package):
...
- version('dev', git='https://github.com/example-project/example.git')
+ version('develop', git='https://github.com/example-project/example.git')
This is not recommended, as the contents of the default branch
change over time.
@@ -649,6 +661,17 @@ Commits
could just use the abbreviated commit hash. It's up to the package
author to decide what makes the most sense.
+Submodules
+
+ You can supply ``submodules=True`` to cause Spack to fetch submodules
+ along with the repository at fetch time.
+
+ .. code-block:: python
+
+ version('1.0.1', git='https://github.com/example-project/example.git',
+ tag='v1.0.1', submdoules=True)
+
+
Installing
^^^^^^^^^^^^^^
@@ -676,7 +699,7 @@ Default
.. code-block:: python
- version('hg-head', hg='https://jay.grs.rwth-aachen.de/hg/example')
+ version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example')
Note that this is not recommended; try to fetch a particular
revision instead.
@@ -708,7 +731,7 @@ Fetching the head
.. code-block:: python
- version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
+ version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
This is not recommended, as the head will move forward over time.
@@ -718,7 +741,7 @@ Fetching a revision
.. code-block:: python
- version('svn-head', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
+ version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
revision=128)
Subversion branches are handled as part of the directory structure, so
@@ -2712,15 +2735,15 @@ build process will start from scratch.
``spack purge``
~~~~~~~~~~~~~~~~~
-Cleans up all of Spack's temporary and cached files. This can be used to
-recover disk space if temporary files from interrupted or failed installs
-accumulate in the staging area.
+Cleans up all of Spack's temporary and cached files. This can be used to
+recover disk space if temporary files from interrupted or failed installs
+accumulate in the staging area.
When called with ``--stage`` or ``--all`` (or without arguments, in which case
-the default is ``--all``) this removes all staged files; this is equivalent to
+the default is ``--all``) this removes all staged files; this is equivalent to
running ``spack clean`` for every package you have fetched or staged.
-When called with ``--cache`` or ``--all`` this will clear all resources
+When called with ``--cache`` or ``--all`` this will clear all resources
:ref:`cached <caching>` during installs.
Keeping the stage directory on success
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index f792008c49..d9992a5680 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -166,7 +166,11 @@ class DefaultConcretizer(object):
valid_versions.sort(key=prefer_key, reverse=True)
if valid_versions:
- spec.versions = ver([valid_versions[0]])
+ # Disregard @develop and take the next valid version
+ if ver(valid_versions[0]) == ver('develop') and len(valid_versions) > 1:
+ spec.versions = ver([valid_versions[1]])
+ else:
+ spec.versions = ver([valid_versions[0]])
else:
# We don't know of any SAFE versions that match the given
# spec. Grab the spec's versions and grab the highest
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 38133ee0ca..bcb33bd0e6 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -366,8 +366,8 @@ class CacheURLFetchStrategy(URLFetchStrategy):
try:
self.check()
except ChecksumError:
- # Future fetchers will assume they don't need to download if the
- # file remains
+ # Future fetchers will assume they don't need to
+ # download if the file remains
os.remove(self.archive_file)
raise
@@ -517,6 +517,7 @@ class GitFetchStrategy(VCSFetchStrategy):
super(GitFetchStrategy, self).__init__(
'git', 'tag', 'branch', 'commit', **forwarded_args)
self._git = None
+ self.submodules = kwargs.get('submodules', False)
@property
def git_version(self):
@@ -595,6 +596,10 @@ class GitFetchStrategy(VCSFetchStrategy):
self.git('pull', '--tags', ignore_errors=1)
self.git('checkout', self.tag)
+ # Init submodules if the user asked for them.
+ if self.submodules:
+ self.git('submodule', 'update', '--init')
+
def archive(self, destination):
super(GitFetchStrategy, self).archive(destination, exclude='.git')
diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py
index a3a328fb14..41d72e7c34 100644
--- a/lib/spack/spack/test/versions.py
+++ b/lib/spack/spack/test/versions.py
@@ -92,6 +92,9 @@ class VersionsTest(unittest.TestCase):
self.assert_ver_eq('1.0', '1.0')
self.assert_ver_lt('1.0', '2.0')
self.assert_ver_gt('2.0', '1.0')
+ self.assert_ver_eq('develop', 'develop')
+ self.assert_ver_lt('1.0', 'develop')
+ self.assert_ver_gt('develop', '1.0')
def test_three_segments(self):
self.assert_ver_eq('2.0.1', '2.0.1')
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index 6839643941..6f6c83b3d8 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -236,6 +236,14 @@ class Version(object):
if self.version == other.version:
return False
+ # dev is __gt__ than anything but itself.
+ if other.string == 'develop':
+ return True
+
+ # If lhs is dev then it can't be < than anything
+ if self.string == 'develop':
+ return False
+
for a, b in zip(self.version, other.version):
if a == b:
continue
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 001dde5329..07bb6b6b03 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -40,6 +40,7 @@ class R(Package):
extendable = True
+ version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
@@ -87,6 +88,29 @@ class R(Package):
make()
make('install')
+ self.filter_compilers(spec, prefix)
+
+ def filter_compilers(self, spec, prefix):
+ """Run after install to tell the configuration files and Makefiles
+ to use the compilers that Spack built the package with.
+
+ If this isn't done, they'll have CC and CXX set to Spack's generic
+ cc and c++. We want them to be bound to whatever compiler
+ they were built with."""
+
+ etcdir = join_path(prefix, 'rlib', 'R', 'etc')
+
+ kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
+
+ filter_file(env['CC'], self.compiler.cc,
+ join_path(etcdir, 'Makeconf'), **kwargs)
+ filter_file(env['CXX'], self.compiler.cxx,
+ join_path(etcdir, 'Makeconf'), **kwargs)
+ filter_file(env['F77'], self.compiler.f77,
+ join_path(etcdir, 'Makeconf'), **kwargs)
+ filter_file(env['FC'], self.compiler.fc,
+ join_path(etcdir, 'Makeconf'), **kwargs)
+
# ========================================================================
# Set up environment to make install easy for R extensions.
# ========================================================================
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 068dbec10a..e7984466ba 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -37,7 +37,7 @@ class Dealii(Package):
version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
version('8.2.1', '71c728dbec14f371297cd405776ccf08')
version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d')
- version('dev', git='https://github.com/dealii/dealii.git')
+ version('develop', git='https://github.com/dealii/dealii.git')
variant('mpi', default=True, description='Compile with MPI')
variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)')
@@ -73,20 +73,21 @@ class Dealii(Package):
depends_on("doxygen+graphviz", when='+doc')
depends_on("graphviz", when='+doc')
depends_on("gsl", when='@8.5.0:+gsl')
- depends_on("gsl", when='@dev+gsl')
depends_on("hdf5+mpi", when='+hdf5+mpi')
depends_on("metis@5:", when='+metis')
depends_on("netcdf+mpi", when="+netcdf+mpi")
depends_on("netcdf-cxx", when='+netcdf+mpi')
depends_on("oce", when='+oce')
depends_on("p4est", when='+p4est+mpi')
- depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501
- depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi')
+ depends_on("petsc+mpi", when='@8.5.0:+petsc+mpi')
+ depends_on("slepc", when='@8.5.0:+slepc+petsc+mpi')
+ depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi')
+ depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi')
depends_on("trilinos", when='+trilinos+mpi')
# developer dependnecies
- depends_on("numdiff", when='@dev')
- depends_on("astyle@2.04", when='@dev')
+ depends_on("numdiff", when='@develop')
+ depends_on("astyle@2.04", when='@develop')
def install(self, spec, prefix):
options = []
@@ -119,6 +120,16 @@ class Dealii(Package):
'-DZLIB_DIR=%s' % spec['zlib'].prefix
])
+ # Set directory structure:
+ if spec.satisfies('@:8.2.1'):
+ options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF'])
+ else:
+ options.extend([
+ '-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples',
+ '-DDEAL_II_DOCREADME_RELDIR=share/deal.II/',
+ '-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc'
+ ])
+
# MPI
if '+mpi' in spec:
options.extend([
@@ -193,115 +204,118 @@ class Dealii(Package):
])
cmake('.', *options)
-
make()
- make("test")
+ if self.run_tests:
+ make("test")
make("install")
# run some MPI examples with different solvers from PETSc and Trilinos
- env['DEAL_II_DIR'] = prefix
- print('=====================================')
- print('============ EXAMPLES ===============')
- print('=====================================')
- # take bare-bones step-3
- print('=====================================')
- print('============ Step-3 =================')
- print('=====================================')
- with working_dir('examples/step-3'):
- cmake('.')
- make('release')
- make('run', parallel=False)
-
- # An example which uses Metis + PETSc
- # FIXME: switch step-18 to MPI
- with working_dir('examples/step-18'):
+ if self.run_tests:
+ env['DEAL_II_DIR'] = prefix
print('=====================================')
- print('============= Step-18 ===============')
+ print('============ EXAMPLES ===============')
print('=====================================')
- # list the number of cycles to speed up
- filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc')
- if '^petsc' in spec and '^metis' in spec:
- cmake('.')
- make('release')
- make('run', parallel=False)
-
- # take step-40 which can use both PETSc and Trilinos
- # FIXME: switch step-40 to MPI run
- with working_dir('examples/step-40'):
+ # take bare-bones step-3
print('=====================================')
- print('========== Step-40 PETSc ============')
+ print('============ Step-3 =================')
print('=====================================')
- # list the number of cycles to speed up
- filter_file(r'(const unsigned int n_cycles = 8;)',
- ('const unsigned int n_cycles = 2;'), 'step-40.cc')
- cmake('.')
- if '^petsc' in spec:
+ with working_dir('examples/step-3'):
+ cmake('.')
make('release')
make('run', parallel=False)
- print('=====================================')
- print('========= Step-40 Trilinos ==========')
- print('=====================================')
- # change Linear Algebra to Trilinos
- # The below filter_file should be different for versions
- # before and after 8.4.0
- if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'):
- filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
- ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
- else:
- filter_file(r'(#define USE_PETSC_LA.*)',
- ('// #define USE_PETSC_LA'), 'step-40.cc')
- if '^trilinos+hypre' in spec:
- make('release')
- make('run', parallel=False)
+ # An example which uses Metis + PETSc
+ # FIXME: switch step-18 to MPI
+ with working_dir('examples/step-18'):
+ print('=====================================')
+ print('============= Step-18 ===============')
+ print('=====================================')
+ # list the number of cycles to speed up
+ filter_file(r'(end_time = 10;)', ('end_time = 3;'),
+ 'step-18.cc')
+ if '^petsc' in spec and '^metis' in spec:
+ cmake('.')
+ make('release')
+ make('run', parallel=False)
- # the rest of the tests on step 40 only works for
- # dealii version 8.4.0 and after
- if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'):
+ # take step-40 which can use both PETSc and Trilinos
+ # FIXME: switch step-40 to MPI run
+ with working_dir('examples/step-40'):
print('=====================================')
- print('=== Step-40 Trilinos SuperluDist ====')
+ print('========== Step-40 PETSc ============')
print('=====================================')
- # change to direct solvers
- filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501
- filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
- (''), 'step-40.cc')
- filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501
- (''), 'step-40.cc')
- filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501
- (''), 'step-40.cc')
- filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501
- filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
- if '^trilinos+superlu-dist' in spec:
+ # list the number of cycles to speed up
+ filter_file(r'(const unsigned int n_cycles = 8;)',
+ ('const unsigned int n_cycles = 2;'), 'step-40.cc')
+ cmake('.')
+ if '^petsc' in spec:
make('release')
- make('run', paralle=False)
+ make('run', parallel=False)
print('=====================================')
- print('====== Step-40 Trilinos MUMPS =======')
+ print('========= Step-40 Trilinos ==========')
print('=====================================')
- # switch to Mumps
- filter_file(r'(Amesos_Superludist)',
- ('Amesos_Mumps'), 'step-40.cc')
- if '^trilinos+mumps' in spec:
+ # change Linear Algebra to Trilinos
+ # The below filter_file should be different for versions
+ # before and after 8.4.0
+ if spec.satisfies('@8.4.0:'):
+ filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
+ ('#define FORCE_USE_OF_TRILINOS'),
+ 'step-40.cc')
+ else:
+ filter_file(r'(#define USE_PETSC_LA.*)',
+ ('// #define USE_PETSC_LA'), 'step-40.cc')
+ if '^trilinos+hypre' in spec:
make('release')
make('run', parallel=False)
- print('=====================================')
- print('============ Step-36 ================')
- print('=====================================')
- with working_dir('examples/step-36'):
- if 'slepc' in spec:
- cmake('.')
- make('release')
- make('run', parallel=False)
+ # the rest of the tests on step 40 only works for
+ # dealii version 8.4.0 and after
+ if spec.satisfies('@8.4.0:'):
+ print('=====================================')
+ print('=== Step-40 Trilinos SuperluDist ====')
+ print('=====================================')
+ # change to direct solvers
+ filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501
+ filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
+ (''), 'step-40.cc')
+ filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501
+ (''), 'step-40.cc')
+ filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501
+ (''), 'step-40.cc')
+ filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501
+ filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
+ if '^trilinos+superlu-dist' in spec:
+ make('release')
+ make('run', paralle=False)
- print('=====================================')
- print('============ Step-54 ================')
- print('=====================================')
- with working_dir('examples/step-54'):
- if 'oce' in spec:
- cmake('.')
- make('release')
- make('run', parallel=False)
+ print('=====================================')
+ print('====== Step-40 Trilinos MUMPS =======')
+ print('=====================================')
+ # switch to Mumps
+ filter_file(r'(Amesos_Superludist)',
+ ('Amesos_Mumps'), 'step-40.cc')
+ if '^trilinos+mumps' in spec:
+ make('release')
+ make('run', parallel=False)
+
+ print('=====================================')
+ print('============ Step-36 ================')
+ print('=====================================')
+ with working_dir('examples/step-36'):
+ if 'slepc' in spec:
+ cmake('.')
+ make('release')
+ make('run', parallel=False)
+
+ print('=====================================')
+ print('============ Step-54 ================')
+ print('=====================================')
+ with working_dir('examples/step-54'):
+ if 'oce' in spec:
+ cmake('.')
+ make('release')
+ make('run', parallel=False)
def setup_environment(self, spack_env, env):
env.set('DEAL_II_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index baaa2fc83d..a6dabd2c05 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -23,7 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
-import os
+
class Libxml2(Package):
"""Libxml2 is the XML C parser and toolkit developed for the Gnome
@@ -42,8 +42,8 @@ class Libxml2(Package):
def install(self, spec, prefix):
if '+python' in spec:
- site_packages_dir = os.path.join(prefix, 'lib/python%s.%s/site-packages' %(spec['python'].version[:2]))
- python_args = ["--with-python=%s" % spec['python'].prefix, "--with-python-install-dir=%s" % site_packages_dir]
+ python_args = ["--with-python=%s" % spec['python'].prefix,
+ "--with-python-install-dir=%s" % site_packages_dir]
else:
python_args = ["--without-python"]
diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py
new file mode 100644
index 0000000000..4070b6fe8d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-assertthat/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 RAssertthat(Package):
+ """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
+ wrong."""
+
+ homepage = "https://cran.r-project.org/web/packages/assertthat/index.html"
+ 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-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py
new file mode 100644
index 0000000000..b065e0b817
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dplyr/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 RDplyr(Package):
+ """A fast, consistent tool for working with data frame like objects, both
+ in memory and out of memory."""
+
+ homepage = "https://github.com/hadley/dplyr"
+ url = "https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr"
+
+ version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef')
+
+ extends('R')
+ depends_on('r-assertthat')
+ depends_on('r-R6')
+ depends_on('r-rcpp')
+ depends_on('r-tibble')
+ depends_on('r-magrittr')
+ depends_on('r-lazyeval')
+ depends_on('r-dbi')
+ depends_on('r-bh')
+
+ 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
new file mode 100644
index 0000000000..f80fb4d272
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 RLazyeval(Package):
+ """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."""
+
+ homepage = "https://cran.r-project.org/web/packages/lazyeval/index.html"
+ url = "https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz"
+ 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-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py
new file mode 100644
index 0000000000..88576911f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lubridate/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLubridate(Package):
+ """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
+ manipulation on date-time and timespan objects. The 'lubridate' package has
+ a consistent and memorable syntax that makes working with dates easy and
+ fun."""
+
+ homepage = "https://cran.r-project.org/web/packages/lubridate/index.html"
+ url = "https://cran.r-project.org/src/contrib/lubridate_1.5.6.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate"
+
+ version('1.5.6', 'a5dc44817548ee219d26a10bae92e611')
+
+ extends('R')
+ depends_on('r-stringr')
+
+ 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
new file mode 100644
index 0000000000..837c3df603
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tibble/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTibble(Package):
+ """Provides a 'tbl_df' class that offers better checking and printing
+ capabilities than traditional data frames."""
+
+ homepage = "https://github.com/hadley/tibble"
+ url = "https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/tibble"
+
+ version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8')
+
+ extends('R')
+
+ depends_on('r-assertthat')
+ depends_on('r-lazyeval')
+ 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-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py
new file mode 100644
index 0000000000..2db7b174c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidyr/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 RTidyr(Package):
+ """An evolution of 'reshape2'. It's designed specifically for data tidying
+ (not general reshaping or aggregating) and works well with 'dplyr' data
+ pipelines."""
+
+ homepage = "https://github.com/hadley/tidyr"
+ url = "https://cran.r-project.org/src/contrib/tidyr_0.5.1.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr"
+
+ version('0.5.1', '3cadc869510c054ed93d374ab44120bd')
+
+ extends('R')
+ depends_on('r-tibble')
+ depends_on('r-dplyr')
+ depends_on('r-stringi')
+ depends_on('r-lazyeval')
+ depends_on('r-magrittr')
+ depends_on('r-rcpp')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-08 20:51:36 +0000