From 90bb855ffa2d39d4cd861dd65f51acfa72d11ea4 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Fri, 11 Mar 2016 23:30:38 -0500 Subject: A new subclass StagedPackage(Package) is introduced. This PR should not change the behavior for existing packages that subclass from spack.Package. If a package subclasses spack.StagedPackage instead of spack.Package, the install() phase (run inside a forked process) is now separated into sub-stages: a) spconfig: Generate a script spconfig.py that will configure the package (eg by running CMake or ./configure) This is for use if the user wishes to build externally from Spack. Therefore, the Spack compiler wrappers are NOT used here. Currently, that means that RPATH support is up to the user. b) configure: Configure the project (eg: runs configure, CMake, etc). This will configure it for use within Spack, using the Spack wrapper. c) build: eg: "make" d) install: eg: "install" If one chooses to use StagedPackage instead of Package, then one must implement each of the install sub-stages as a separate method. StagedPackage.install() then calls each of the sub-stages as appropriate. StagedPackage can be configured to only run certain sub-stages. This is done by setting the optional kwarg install_phases when calling do_install(). Setting install_phases() ONLY has an effect on StagedPackage, not on any existing packages. By default, install_phases is set to make StagedPackage run the same stages that are normally run for any package: configure, build, install (and NOT spconfig). The ability for Spack to run stages selectively for StagedPackage instances will enable new functionality. For example, explicit CMake/Autotools helpers that allow Spack to help configure a user's project without fetching, building or installing it. ------------- One implementation of StagedPackage is provided, CMakePackage. This has the following advantage for CMake-based projects over using the standard Package class: a) By separating out the phases, it enables future new functionality for packages that use it. b) It provides an implementation of intall_spconfig(), which will help users configure their CMake-based projects. CMakePackage expects users to implement configure_args() and configure_env(). These methods provide the package-specific arguments and environment needed to properly configure the package. They are placed in separated functions because they are used in both the spconfig and configure stages. TODO: 1. Generate spconfig.py scripts that are more readable. This allows the users to understand how their project is configured. 2. Provide a practical way for the user to ACCESS the spconfig stage without building the project through Spack. 3. The CMAKE_TRANSITIVE_INCLUDE_PATH stuff needs to be reworked; it should be considered provisional for now. 4. User of Autotools might wish to make a similar ConfigurePackage subclass of StagedPackage. --------------- One package using CMakePackage is introduced. See ibmisc/package.py. --- var/spack/repos/builtin/packages/ibmisc/package.py | 47 ++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ibmisc/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py new file mode 100644 index 0000000000..9fadee7239 --- /dev/null +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -0,0 +1,47 @@ +from spack import * + +class Ibmisc(CMakePackage): + """Misc. reusable utilities used by IceBin.""" + + homepage = "https://github.com/citibeth/ibmisc" + url = "https://github.com/citibeth/ibmisc/tarball/123" + + version('0.1.0', '12f2a32432a11db48e00217df18e59fa') + + variant('everytrace', default=False, description='Report errors through Everytrace') + variant('proj', default=True, description='Compile utilities for PROJ.4 library') + variant('blitz', default=True, description='Compile utilities for Blitz library') + variant('netcdf', default=True, description='Compile utilities for NetCDF library') + variant('boost', default=True, description='Compile utilities for Boost library') + variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library') + variant('googletest', default=True, description='Compile utilities for Google Test library') + variant('python', default=True, description='Compile utilities for use with Python/Cython') + + extends('python') + + depends_on('eigen') + depends_on('everytrace', when='+everytrace') + depends_on('proj', when='+proj') + depends_on('blitz', when='+blitz') + depends_on('netcdf-cxx4', when='+netcdf') + depends_on('udunits2', when='+udunits2') + depends_on('googletest', when='+googletest') + depends_on('py-cython', when='+python') + depends_on('py-numpy', when='+python') + depends_on('boost', when='+boost') + + # Build dependencies + depends_on('cmake') + depends_on('doxygen') + + def configure_args(self): + spec = self.spec + return [ + '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'), + '-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'), + '-DUSE_BLITZ=%s' % ('YES' if '+blitz' in spec else 'NO'), + '-DUSE_NETCDF=%s' % ('YES' if '+netcdf' in spec else 'NO'), + '-DUSE_BOOST=%s' % ('YES' if '+boost' in spec else 'NO'), + '-DUSE_UDUNITS2=%s' % ('YES' if '+udunits2' in spec else 'NO'), + '-DUSE_GTEST=%s' % ('YES' if '+googletest' in spec else 'NO')] + -- cgit v1.2.3-70-g09d2 From c1a8574d8f67d6b4fdce109ecf4dd3a1cbe18488 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Sun, 13 Mar 2016 00:29:40 -0500 Subject: Fixed for Python 2.6 --- lib/spack/spack/package.py | 2 +- var/spack/repos/builtin/packages/ibmisc/package.py | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 3d8e098346..f815628bba 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -831,7 +831,7 @@ class Package(object): def do_install(self, keep_prefix=False, keep_stage=False, ignore_deps=False, skip_patch=False, verbose=False, make_jobs=None, fake=False, - install_phases = {'configure', 'build', 'install', 'provenance'}): + install_phases = set(['configure', 'build', 'install', 'provenance'])): """Called by commands to install a package and its dependencies. Package implementations should override install() to describe diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 9fadee7239..a3bd680655 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -1,4 +1,5 @@ from spack import * +import llnl.util.tty as tty class Ibmisc(CMakePackage): """Misc. reusable utilities used by IceBin.""" @@ -15,7 +16,7 @@ class Ibmisc(CMakePackage): variant('boost', default=True, description='Compile utilities for Boost library') variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library') variant('googletest', default=True, description='Compile utilities for Google Test library') - variant('python', default=True, description='Compile utilities for use with Python/Cython') + variant('python', default=True, description='Compile utilities fro use with Python/Cython') extends('python') @@ -26,16 +27,18 @@ class Ibmisc(CMakePackage): depends_on('netcdf-cxx4', when='+netcdf') depends_on('udunits2', when='+udunits2') depends_on('googletest', when='+googletest') +# depends_on('python', when='+python') depends_on('py-cython', when='+python') depends_on('py-numpy', when='+python') depends_on('boost', when='+boost') + + # Build dependencies depends_on('cmake') depends_on('doxygen') - def configure_args(self): - spec = self.spec + def config_args(self, spec, prefix): return [ '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'), '-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'), -- cgit v1.2.3-70-g09d2 From 003957a689b8d3d6e6da5408d61c45e73e01b575 Mon Sep 17 00:00:00 2001 From: citibeth Date: Sun, 13 Mar 2016 00:33:13 -0500 Subject: Reverted bad change --- var/spack/repos/builtin/packages/ibmisc/package.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index a3bd680655..8e6cf429a7 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -1,5 +1,4 @@ from spack import * -import llnl.util.tty as tty class Ibmisc(CMakePackage): """Misc. reusable utilities used by IceBin.""" @@ -16,7 +15,7 @@ class Ibmisc(CMakePackage): variant('boost', default=True, description='Compile utilities for Boost library') variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library') variant('googletest', default=True, description='Compile utilities for Google Test library') - variant('python', default=True, description='Compile utilities fro use with Python/Cython') + variant('python', default=True, description='Compile utilities for use with Python/Cython') extends('python') @@ -27,18 +26,16 @@ class Ibmisc(CMakePackage): depends_on('netcdf-cxx4', when='+netcdf') depends_on('udunits2', when='+udunits2') depends_on('googletest', when='+googletest') -# depends_on('python', when='+python') depends_on('py-cython', when='+python') depends_on('py-numpy', when='+python') depends_on('boost', when='+boost') - - # Build dependencies depends_on('cmake') depends_on('doxygen') - def config_args(self, spec, prefix): + def configure_args(self): + spec = self.spec return [ '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'), '-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'), @@ -47,4 +44,3 @@ class Ibmisc(CMakePackage): '-DUSE_BOOST=%s' % ('YES' if '+boost' in spec else 'NO'), '-DUSE_UDUNITS2=%s' % ('YES' if '+udunits2' in spec else 'NO'), '-DUSE_GTEST=%s' % ('YES' if '+googletest' in spec else 'NO')] - -- cgit v1.2.3-70-g09d2 From d3b0cb56b7ed1a545d0a13fbf20ece8bc89f0103 Mon Sep 17 00:00:00 2001 From: Tzanio Date: Thu, 30 Jun 2016 15:23:30 -0700 Subject: Updating MFEM package with v3.2 info. --- var/spack/repos/builtin/packages/mfem/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 504efb5e35..40e4906f8e 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -31,11 +31,13 @@ class Mfem(Package): homepage = 'http://www.mfem.org' url = 'https://github.com/mfem/mfem' -# version('3.1', git='https://github.com/mfem/mfem.git', -# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') + version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', + url='http://goo.gl/Y9T75B', expand=False) version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', expand=False) +# version('3.1', git='https://github.com/mfem/mfem.git', +# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') variant('metis', default=False, description='Activate support for metis') variant('hypre', default=False, description='Activate support for hypre') -- cgit v1.2.3-70-g09d2 From 137db14b75b63c9714e0eb5189bf074c828e2b30 Mon Sep 17 00:00:00 2001 From: Tzanio Kolev Date: Thu, 30 Jun 2016 15:40:02 -0700 Subject: Update package.py --- var/spack/repos/builtin/packages/mfem/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 40e4906f8e..1b4456380b 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -32,7 +32,7 @@ class Mfem(Package): url = 'https://github.com/mfem/mfem' version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', - url='http://goo.gl/Y9T75B', expand=False) + url='http://goo.gl/Y9T75B', expand=False, preferred=True) version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', expand=False) -- cgit v1.2.3-70-g09d2 From 729f23b43282d971365d66402fe0df67c4bd37a2 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Fri, 1 Jul 2016 22:13:40 -0500 Subject: Use Executable to set script Use `Executable("./install.sh")` to set `install_script`. This allows it to work when the current directory is not on the PATH. --- var/spack/repos/builtin/packages/intel/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index ec3192380a..56d9fabddf 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -73,7 +73,7 @@ CONTINUE_WITH_OPTIONAL_ERROR=yes COMPONENTS=%s """ % (self.intel_prefix, self.global_license_file, self.intel_components)) - install_script = which("install.sh") + install_script = Executable("./install.sh") install_script('--silent', silent_config_filename) -- cgit v1.2.3-70-g09d2 From 3e8391458c88c4a0ccb630769700d20133657437 Mon Sep 17 00:00:00 2001 From: alalazo Date: Mon, 4 Jul 2016 09:58:15 +0200 Subject: openssl : changed tag for system reserved versions fixes #1150 --- var/spack/repos/builtin/packages/openssl/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 377bffe723..b0b03503d7 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -57,11 +57,11 @@ class Openssl(Package): # Same idea, but just to avoid issuing the same message multiple times warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) if openssl_url is None: - if self.spec.satisfies('@external'): - # The version @external is reserved to system openssl. In that case return a fake url and exit - openssl_url = '@external (reserved version for system openssl)' + if self.spec.satisfies('@system'): + # The version @system is reserved to system openssl. In that case return a fake url and exit + openssl_url = '@system (reserved version for system openssl)' if not warnings_given_to_user.get(version, False): - tty.msg('Using openssl@external : the version @external is reserved for system openssl') + tty.msg('Using openssl@system : the version @system is reserved for system openssl') warnings_given_to_user[version] = True else: openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL -- cgit v1.2.3-70-g09d2 From 861f174f66b908aac2ac2d0245de8ef874cea00f Mon Sep 17 00:00:00 2001 From: alalazo Date: Mon, 4 Jul 2016 10:03:46 +0200 Subject: qa : fixed flake8 issues --- .../repos/builtin/packages/openssl/package.py | 36 ++++++++++++---------- 1 file changed, 20 insertions(+), 16 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index b0b03503d7..a0747f229d 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -35,7 +35,7 @@ class Openssl(Package): Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.""" homepage = "http://www.openssl.org" - url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" + url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1r', '1abd905e079542ccae948af37e393d28') @@ -50,21 +50,24 @@ class Openssl(Package): parallel = False def url_for_version(self, version): - # This URL is computed pinging the place where the latest version is stored. To avoid slowdown - # due to repeated pinging, we store the URL in a private class attribute to do the job only once per version + # This URL is computed pinging the place where the latest version is + # stored. To avoid slowdown due to repeated pinging, we store the URL + # in a private class attribute to do the job only once per version openssl_urls = getattr(Openssl, '_openssl_url', {}) openssl_url = openssl_urls.get(version, None) # Same idea, but just to avoid issuing the same message multiple times warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) if openssl_url is None: if self.spec.satisfies('@system'): - # The version @system is reserved to system openssl. In that case return a fake url and exit + # The version @system is reserved to system openssl. In that + # case return a fake url and exit openssl_url = '@system (reserved version for system openssl)' if not warnings_given_to_user.get(version, False): - tty.msg('Using openssl@system : the version @system is reserved for system openssl') + tty.msg('Using openssl@system : the version @system is reserved for system openssl') # NOQA: ignore=E501 warnings_given_to_user[version] = True else: - openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL + openssl_url = self.check_for_outdated_release( + version, warnings_given_to_user) # Store the computed URL openssl_urls[version] = openssl_url # Store the updated dictionary of URLS Openssl._openssl_url = openssl_urls @@ -75,22 +78,23 @@ class Openssl(Package): def check_for_outdated_release(self, version, warnings_given_to_user): latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' - older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' - # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then - # return the url for older format + older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' # NOQA: ignore=E501 + # Try to use the url where the latest tarballs are stored. + # If the url does not exist (404), then return the url for + # older format version_number = '.'.join([str(x) for x in version[:-1]]) try: openssl_url = latest.format(version=version) urllib.urlopen(openssl_url) except IOError: - openssl_url = older.format(version_number=version_number, version_full=version) - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version + openssl_url = older.format(version_number=version_number, version_full=version) # NOQA:ignore=E501 + # Checks if we already warned the user for this particular + # version of OpenSSL. If not we display a warning message + # and mark this version if not warnings_given_to_user.get(version, False): - tty.warn( - 'This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') # NOQA: ignore=E501 + tty.warn('Consider updating to the latest version of this package.') # NOQA: ignore=E501 + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) # NOQA: ignore=E501 warnings_given_to_user[version] = True return openssl_url -- cgit v1.2.3-70-g09d2 From 85982017b605f2c21bbe01149a92e512b8be27f7 Mon Sep 17 00:00:00 2001 From: Nicolas Date: Mon, 4 Jul 2016 18:19:09 +0200 Subject: Revert "Corrected the shared libraries and tests in mumps package" --- .../builtin/packages/mumps/mumps-shared.patch | 119 --------------- var/spack/repos/builtin/packages/mumps/package.py | 168 +++++++++------------ 2 files changed, 73 insertions(+), 214 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/mumps/mumps-shared.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch deleted file mode 100644 index 592f48037c..0000000000 --- a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch +++ /dev/null @@ -1,119 +0,0 @@ -diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile ---- MUMPS_5.0.1/libseq/Makefile 2015-07-23 19:08:32.000000000 +0200 -+++ MUMPS_5.0.1.new/libseq/Makefile 2016-06-07 10:41:16.585179151 +0200 -@@ -8,11 +8,15 @@ - - include ../Makefile.inc - --libmpiseq: libmpiseq$(PLAT)$(LIBEXT) -+libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT) - - libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o - $(AR)$@ mpi.o mpic.o elapse.o - $(RANLIB) $@ -+ -+libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o -+ $(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT) -+ - .f.o: - $(FC) $(OPTF) -c $*.f $(OUTF)$*.o - .c.o: -diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile ---- MUMPS_5.0.1/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/Makefile 2016-06-07 10:50:21.863281217 +0200 -@@ -51,7 +51,7 @@ - dexamples: d - (cd examples ; $(MAKE) d) - --requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) -+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT) - - # dummy MPI library (sequential version) - -@@ -62,16 +62,25 @@ - $(libdir)/libpord$(PLAT)$(LIBEXT): - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); \ -- $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \ -+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \ - fi; - if [ "$(LPORDDIR)" != "" ] ; then \ - cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ - fi; - -+$(libdir)/libpord$(PLAT)$(SHLIBEXT): -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cd $(LPORDDIR); \ -+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \ -+ fi; -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \ -+ fi; -+ - clean: - (cd src; $(MAKE) clean) - (cd examples; $(MAKE) clean) -- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT)) -+ (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT)) - (cd libseq; $(MAKE) clean) - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); $(MAKE) realclean; \ -diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile ---- MUMPS_5.0.1/PORD/lib/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/PORD/lib/Makefile 2016-06-07 10:49:48.889000958 +0200 -@@ -13,7 +13,7 @@ - - OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ - multisector.o gelim.o bucket.o tree.o \ -- symbfac.o interface.o sort.o minpriority.o -+ symbfac.o interface.o sort.o minpriority.o - - # Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c - # were not direcly used by MUMPS and have been removed from the -@@ -24,12 +24,15 @@ - .c.o: - $(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o - --libpord$(LIBEXT):$(OBJS) -+libpord$(PLAT)$(LIBEXT):$(OBJS) - $(AR)$@ $(OBJS) - $(RANLIB) $@ - -+libpord$(PLAT)$(SHLIBEXT): $(OBJS) -+ $(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT) -+ - clean: - rm -f *.o - - realclean: -- rm -f *.o libpord.a -+ rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT) -diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile ---- MUMPS_5.0.1/src/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/src/Makefile 2016-06-07 10:40:52.534703722 +0200 -@@ -24,7 +24,10 @@ - include $(topdir)/Makefile.inc - - mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \ -- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) -+ $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) -+ - - OBJS_COMMON_MOD = \ - ana_omp_m.o\ -@@ -162,6 +165,13 @@ - $(AR)$@ $? - $(RANLIB) $@ - -+$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -+ $(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) -+ -+ -+$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT): $(OBJS_MOD) $(OBJS_OTHER) -+ $(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) -+ - # Dependencies between modules: - $(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \ - $(ARITH)mumps_struc_def.o \ diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 8a90ef72d0..92c45c9b95 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -23,10 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os -import sys -import subprocess - +import os, sys, glob class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -47,6 +44,7 @@ class Mumps(Package): variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') variant('shared', default=True, description='Build shared libraries') + depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') depends_on('metis@5:', when='+metis') @@ -56,64 +54,49 @@ class Mumps(Package): depends_on('scalapack', when='+mpi') depends_on('mpi', when='+mpi') - patch('mumps-shared.patch', when='+shared') - # this function is not a patch function because in case scalapack # is needed it uses self.spec['scalapack'].fc_link set by the # setup_dependent_environment in scalapck. This happen after patch # end before install # def patch(self): def write_makefile_inc(self): - if (('+parmetis' in self.spec or - '+ptscotch' in self.spec)) and '+mpi' not in self.spec: - raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: E501 + if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: + raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') - makefile_conf = [ - "LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib - ] + makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] orderings = ['-Dpord'] if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') - makefile_conf.extend([ - "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, - "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, - join_lib, - join_lib.join(['esmumps', - 'scotch', - 'scotcherr'])) - ]) + makefile_conf.extend( + ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, + "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, + join_lib, + join_lib.join(['esmumps', 'scotch', 'scotcherr']))]) orderings.append('-Dscotch') if '+ptscotch' in self.spec: orderings.append('-Dptscotch') if '+parmetis' in self.spec and '+metis' in self.spec: - makefile_conf.extend([ - "IMETIS = -I%s" % self.spec['parmetis'].prefix.include, - "LMETIS = -L%s -l%s -L%s -l%s" % ( - self.spec['parmetis'].prefix.lib, 'parmetis', - self.spec['metis'].prefix.lib, 'metis') - ]) + libname = 'parmetis' if '+parmetis' in self.spec else 'metis' + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dparmetis') elif '+metis' in self.spec: - makefile_conf.extend([ - "IMETIS = -I%s" % self.spec['metis'].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, - 'metis') - ]) + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) - # when building shared libs need -fPIC, otherwise /usr/bin/ld: - # graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can - # not be used when making a shared object; recompile with - # -fPIC + # when building shared libs need -fPIC, otherwise + # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC fpic = '-fPIC' if '+shared' in self.spec else '' - # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers if '+idx64' in self.spec: @@ -121,7 +104,7 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501 + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), 'OPTL = %s -O ' % fpic, 'OPTC = %s -O -DINTSIZE64' % fpic]) else: @@ -130,47 +113,49 @@ class Mumps(Package): 'OPTL = %s -O ' % fpic, 'OPTC = %s -O ' % fpic]) + if '+mpi' in self.spec: makefile_conf.extend( - ["CC = %s" % self.spec['mpi'].mpicc, - "FC = %s" % self.spec['mpi'].mpifc, + ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), + "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), "SCALAP = %s" % self.spec['scalapack'].fc_link, "MUMPS_TYPE = par"]) else: makefile_conf.extend( ["CC = cc", "FC = fc", + "FL = fc", "MUMPS_TYPE = seq"]) # TODO: change the value to the correct one according to the # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER - makefile_conf.extend([ - 'CDEFS = -DAdd_', - 'FL = $(FC)', - ]) + makefile_conf.append("CDEFS = -DAdd_") if '+shared' in self.spec: - makefile_conf.append('SHLIBEXT = .%s' % dso_suffix) if sys.platform == 'darwin': - makefile_conf.append( - 'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501 - ) + # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + makefile_conf.extend([ + 'LIBEXT=.dylib', + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), + 'RANLIB=echo' + ]) else: - makefile_conf.append( - 'LDFLAGS = -shared {0}{1}'.format( - self.compiler.fc_rpath_arg, - prefix.lib) - ) - - makefile_conf.extend([ - 'LIBEXT = .a', - 'AR = ar vr ', - 'RANLIB = ranlib' - ]) - - makefile_inc_template = \ - join_path(os.path.dirname(self.module.__file__), - 'Makefile.inc') + makefile_conf.extend([ + 'LIBEXT=.so', + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT = .a', + 'AR = ar vr', + 'RANLIB = ranlib' + ]) + + + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), + 'Makefile.inc') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) @@ -179,53 +164,46 @@ class Mumps(Package): makefile_inc = '\n'.join(makefile_conf) fh.write(makefile_inc) + + def install(self, spec, prefix): make_libs = [] # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: - make_libs.append('s') + make_libs.append('sexamples') if '+complex' in spec: - make_libs.append('c') + make_libs.append('cexamples') if '+double' in spec: - make_libs.append('d') + make_libs.append('dexamples') if '+complex' in spec: - make_libs.append('z') + make_libs.append('zexamples') self.write_makefile_inc() - make('mumps_lib', parallel=False) - make(*make_libs) + # Build fails in parallel + make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) - if '~mpi' in spec: - install('libseq/libmpiseq.a', prefix.lib) - if '+shared' in spec: - install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib) - install('libseq/mpi.h', prefix.include) - install('libseq/mpif.h', prefix.include) - - # FIXME: extend the tests to mpirun -np 2 (or alike) when - # build with MPI - # FIXME: use something like numdiff to compare blessed output - # with the current - # TODO: test the installed mumps and not the one in stage - if '~mpi' in spec: - for t in make_libs: - make('{0}examples'.format(t)) - - with working_dir('examples'): - for t in make_libs: - input_file = 'input_simpletest_{0}'.format( - 'real' if t in ['s', 'd'] else 'cmplx') - with open(input_file) as input: - test = './{0}simpletest'.format(t) - ret = subprocess.call(test, - stdin=input) - if ret is not 0: - raise RuntimeError( - 'The test {0} did not pass'.format(test)) + if '~mpi' in spec: + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) + for f in glob.glob(join_path('libseq','*.h')): + install(f, prefix.include) + + # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI + # FIXME: use something like numdiff to compare blessed output with the current + with working_dir('examples'): + if '+float' in spec: + os.system('./ssimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./csimpletest < input_simpletest_real') + if '+double' in spec: + os.system('./dsimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./zsimpletest < input_simpletest_cmplx') -- cgit v1.2.3-70-g09d2 From 53bbbfbe21e795d3400f89e677ebc4edf33b07d4 Mon Sep 17 00:00:00 2001 From: "Robert D. French" Date: Mon, 4 Jul 2016 13:18:42 -0400 Subject: Require libffi, zlib; Make Openssl, readline optional --- var/spack/repos/builtin/packages/ruby/package.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index dd71913fc9..8dc314c171 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -35,9 +35,20 @@ class Ruby(Package): extendable = True version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852') + depends_on('libffi') + depends_on('zlib') + variant('openssl', default=False, description="Enable OpenSSL support") + depends_on('openssl', when='+openssl') + variant('readline', default=False, description="Enable Readline support") + depends_on('readline', when='+readline') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + options = ["--prefix=%s" % prefix] + if '+openssl' in spec: + options.append("--with-openssl-dir=%s" % spec['openssl'].prefix) + if '+readline' in spec: + options.append("--with-readline-dir=%s" % spec['readline'].prefix) + configure(*options) make() make("install") -- cgit v1.2.3-70-g09d2 From 519b760222d953b9c79793e7803526846a814607 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 4 Jul 2016 17:30:05 -0500 Subject: New package - RStan This PR creates the RStan package and its dependencies. --- var/spack/repos/builtin/packages/r-bh/package.py | 54 ++++++++++++++++++++ .../repos/builtin/packages/r-colorspace/package.py | 44 +++++++++++++++++ .../repos/builtin/packages/r-dichromat/package.py | 42 ++++++++++++++++ .../repos/builtin/packages/r-ggplot2/package.py | 54 ++++++++++++++++++++ .../repos/builtin/packages/r-gridextra/package.py | 44 +++++++++++++++++ .../repos/builtin/packages/r-gtable/package.py | 41 ++++++++++++++++ .../repos/builtin/packages/r-inline/package.py | 42 ++++++++++++++++ .../repos/builtin/packages/r-labeling/package.py | 41 ++++++++++++++++ .../repos/builtin/packages/r-lattice/package.py | 44 +++++++++++++++++ .../repos/builtin/packages/r-magrittr/package.py | 45 +++++++++++++++++ var/spack/repos/builtin/packages/r-mass/package.py | 42 ++++++++++++++++ .../repos/builtin/packages/r-matrix/package.py | 44 +++++++++++++++++ .../repos/builtin/packages/r-munsell/package.py | 47 ++++++++++++++++++ var/spack/repos/builtin/packages/r-plyr/package.py | 48 ++++++++++++++++++ .../builtin/packages/r-rcolorbrewer/package.py | 42 ++++++++++++++++ var/spack/repos/builtin/packages/r-rcpp/package.py | 49 +++++++++++++++++++ .../repos/builtin/packages/r-rcppeigen/package.py | 56 +++++++++++++++++++++ .../repos/builtin/packages/r-reshape2/package.py | 46 +++++++++++++++++ .../repos/builtin/packages/r-rstan/package.py | 57 ++++++++++++++++++++++ .../repos/builtin/packages/r-scales/package.py | 49 +++++++++++++++++++ .../builtin/packages/r-stanheaders/package.py | 55 +++++++++++++++++++++ .../repos/builtin/packages/r-stringi/package.py | 51 +++++++++++++++++++ .../repos/builtin/packages/r-stringr/package.py | 48 ++++++++++++++++++ 23 files changed, 1085 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-bh/package.py create mode 100644 var/spack/repos/builtin/packages/r-colorspace/package.py create mode 100644 var/spack/repos/builtin/packages/r-dichromat/package.py create mode 100644 var/spack/repos/builtin/packages/r-ggplot2/package.py create mode 100644 var/spack/repos/builtin/packages/r-gridextra/package.py create mode 100644 var/spack/repos/builtin/packages/r-gtable/package.py create mode 100644 var/spack/repos/builtin/packages/r-inline/package.py create mode 100644 var/spack/repos/builtin/packages/r-labeling/package.py create mode 100644 var/spack/repos/builtin/packages/r-lattice/package.py create mode 100644 var/spack/repos/builtin/packages/r-magrittr/package.py create mode 100644 var/spack/repos/builtin/packages/r-mass/package.py create mode 100644 var/spack/repos/builtin/packages/r-matrix/package.py create mode 100644 var/spack/repos/builtin/packages/r-munsell/package.py create mode 100644 var/spack/repos/builtin/packages/r-plyr/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcolorbrewer/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcpp/package.py create mode 100644 var/spack/repos/builtin/packages/r-rcppeigen/package.py create mode 100644 var/spack/repos/builtin/packages/r-reshape2/package.py create mode 100644 var/spack/repos/builtin/packages/r-rstan/package.py create mode 100644 var/spack/repos/builtin/packages/r-scales/package.py create mode 100644 var/spack/repos/builtin/packages/r-stanheaders/package.py create mode 100644 var/spack/repos/builtin/packages/r-stringi/package.py create mode 100644 var/spack/repos/builtin/packages/r-stringr/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py new file mode 100644 index 0000000000..a0f30b779f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 RBh(Package): + """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 + useful subset of Boost libraries for template use among CRAN package. By + placing these libraries in this package, we offer a more efficient + distribution system for CRAN as replication of this code in the sources of + other packages is avoided. As of release 1.60.0-2, the following Boost + libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' + 'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset' + 'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' + 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' + 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric' + 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' + 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.""" + + homepage = "https://cran.r-project.org/web/packages/BH/index.html" + url = "https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz" + 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-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py new file mode 100644 index 0000000000..a7622cad95 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-colorspace/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 RColorspace(Package): + """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 + are provided.""" + + homepage = "https://cran.r-project.org/web/packages/colorspace/index.html" + url = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz" + 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-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py new file mode 100644 index 0000000000..663e5295af --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDichromat(Package): + """Collapse red-green or green-blue distinctions to simulate the effects of + different types of color-blindness.""" + + homepage = "https://cran.r-project.org/web/packages/dichromat/index.html" + url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" + 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-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py new file mode 100644 index 0000000000..2d1f53af26 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 RGgplot2(Package): + """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 + from multiple data sources. It also implements a sophisticated + multidimensional conditioning system and a consistent interface to map data + to aesthetic attributes. See http://ggplot2.org for more information, + documentation and examples.""" + + homepage = "http://ggplot2.org/" + url = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2" + + version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') + + extends('R') + + depends_on('r-digest') + depends_on('r-gtable') + depends_on('r-mass') + depends_on('r-plyr') + depends_on('r-reshape2') + depends_on('r-scales') + + 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 new file mode 100644 index 0000000000..d215d10678 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridextra/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 RGridextra(Package): + """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.""" + + homepage = "https://github.com/baptiste/gridextra" + url = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtra" + + version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') + + extends('R') + + depends_on('r-gtable') + + 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 new file mode 100644 index 0000000000..74dee0b3d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gtable/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 RGtable(Package): + """Tools to make it easier to work with "tables" of 'grobs'.""" + + homepage = "https://cran.r-project.org/web/packages/gtable/index.html" + url = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz" + 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-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py new file mode 100644 index 0000000000..c972fe0ff0 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RInline(Package): + """Functionality to dynamically define R functions and S4 methods with + inlined C, C++ or Fortran code supporting .C and .Call calling conventions.""" + + homepage = "https://cran.r-project.org/web/packages/inline/index.html" + url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz" + 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-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py new file mode 100644 index 0000000000..02e5da9d85 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-labeling/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 RLabeling(Package): + """Provides a range of axis labeling algorithms.""" + + homepage = "https://cran.r-project.org/web/packages/labeling/index.html" + url = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz" + 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 new file mode 100644 index 0000000000..ba29feefc4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lattice/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 RLattice(Package): + """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 + handle most nonstandard requirements. See ?Lattice for an introduction.""" + + homepage = "http://lattice.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" + + version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e') + + 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-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py new file mode 100644 index 0000000000..11476c3d1e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -0,0 +1,45 @@ +############################################################################## +# 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 RMagrittr(Package): + """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 + support for the type of right-hand side expressions. For more information, + see package vignette.""" + + homepage = "https://cran.r-project.org/web/packages/magrittr/index.html" + url = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz" + 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-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py new file mode 100644 index 0000000000..1ab01d2256 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RMass(Package): + """Functions and datasets to support Venables and Ripley, "Modern Applied + Statistics with S" (4th edition, 2002).""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/MASS_7.3-45.tar.gz" + 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 new file mode 100644 index 0000000000..fbd8a7b4df --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matrix/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 RMatrix(Package): + """Classes and methods for dense and sparse matrices and operations on them + using 'LAPACK' and 'SuiteSparse'.""" + + homepage = "http://matrix.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/Matrix_1.2-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix" + + version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') + + extends('R') + + depends_on('r-lattice') + + 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 new file mode 100644 index 0000000000..3216c95e00 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-munsell/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 RMunsell(Package): + """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 + utilities to explore slices through the Munsell colour tree, to transform + Munsell colours and display colour palettes.""" + + homepage = "https://cran.r-project.org/web/packages/munsell/index.html" + url = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/munsell" + + version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') + + extends('R') + + depends_on('r-colorspace') + + 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 new file mode 100644 index 0000000000..e071050f4a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RPlyr(Package): + """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 + each spatial location or time point in your study, summarise data by panels + or collapse high-dimensional arrays to simpler summary statistics. The + development of 'plyr' has been generously supported by 'Becton Dickinson'.""" + + homepage = "http://had.co.nz/plyr" + url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/plyr" + + version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') + + 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-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py new file mode 100644 index 0000000000..b81ec2561c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRcolorbrewer(Package): + """Provides color schemes for maps (and other graphics) designed by Cynthia + Brewer as described at http://colorbrewer2.org""" + + homepage = "http://colorbrewer2.org" + url = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" + 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 new file mode 100644 index 0000000000..2428f4af3b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcpp/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 RRcpp(Package): + """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 + writing of new code as well as easier integration of third-party libraries. + Documentation about 'Rcpp' is provided by several vignettes included in + this package, via the 'Rcpp Gallery' site at , the + paper by Eddelbuettel and Francois (2011, JSS), and the book by + Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these + last two.""" + + homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + + 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 new file mode 100644 index 0000000000..3175628a73 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -0,0 +1,56 @@ +############################################################################## +# 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 RRcppeigen(Package): + """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, + floating point and complex numbers, decompositions of such matrices, and + solutions of linear systems. Its performance on many algorithms is + comparable with some of the best implementations based on 'Lapack' and + level-3 'BLAS'. The 'RcppEigen' package includes the header files from the + 'Eigen' C++ template library (currently version 3.2.8). Thus users do not + need to install 'Eigen' itself in order to use 'RcppEigen'. Since version + 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); + earlier version were licensed under the GNU LGPL version 3 or later. + 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the + GNU GPL version 2 or later, as is the rest of 'Rcpp'.""" + + homepage = "http://eigen.tuxfamily.org/" + url = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.8.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen" + + version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') + + extends('R') + + depends_on('r-matrix') + 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-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py new file mode 100644 index 0000000000..a96a314008 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-reshape2/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 RReshape2(Package): + """Flexibly restructure and aggregate data using just two functions: melt + and dcast (or acast).""" + + homepage = "https://github.com/hadley/reshape" + url = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2" + + version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') + + extends('R') + + depends_on('r-plyr') + depends_on('r-stringr') + 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-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py new file mode 100644 index 0000000000..00fd5116d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rstan/package.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 +############################################################################## +from spack import * + + +class RRstan(Package): + """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 + programming language that implements full Bayesian statistical inference + via Markov Chain Monte Carlo, rough Bayesian inference via variational + approximation, and (optionally penalized) maximum likelihood estimation via + optimization. In all three cases, automatic differentiation is used to + quickly and accurately evaluate gradients without burdening the user with + the need to derive the partial derivatives.""" + + homepage = "http://mc-stan.org/" + url = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rstan" + + version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') + + extends('R') + + depends_on('r-ggplot2') + depends_on('r-stanheaders') + depends_on('r-inline') + depends_on('r-gridextra') + depends_on('r-rcpp') + depends_on('r-rcppeigen') + 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-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py new file mode 100644 index 0000000000..046a05d48e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scales/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 RScales(Package): + """Graphical scales map data to aesthetics, and provide methods for + automatically determining breaks and labels for axes and legends.""" + + homepage = "https://github.com/hadley/scales" + url = "https://cran.r-project.org/src/contrib/scales_0.4.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/scales" + + version('0.4.0', '7b5602d9c55595901192248bca25c099') + + extends('R') + + depends_on('r-rcolorbrewer') + depends_on('r-dichromat') + depends_on('r-plyr') + depends_on('r-munsell') + depends_on('r-labeling') + 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-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py new file mode 100644 index 0000000000..c77b5aa8b6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -0,0 +1,55 @@ +############################################################################## +# 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 RStanheaders(Package): + """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 + accessible from R. StanHeaders is only useful for developers who want to + utilize the LinkingTo directive of their package's DESCRIPTION file to + build on the Stan library without incurring unnecessary dependencies. The + Stan project develops a probabilistic programming language that implements + full or approximate Bayesian statistical inference via Markov Chain Monte + Carlo or variational methods and implements (optionally penalized) maximum + likelihood estimation via optimization. The Stan library includes an + advanced automatic differentiation scheme, templated statistical and linear + algebra functions that can handle the automatically differentiable scalar + types (and doubles, ints, etc.), and a parser for the Stan language. The + 'rstan' package provides user-facing R functions to parse, compile, test, + estimate, and analyze Stan models.""" + + homepage = "http://mc-stan.org/" + url = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" + 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 new file mode 100644 index 0000000000..22774dedec --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stringi/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 RStringi(Package): + """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 + platform-independent functions known to Java, Perl, Python, PHP, and Ruby + programmers. Among available features there are: pattern searching (e.g., + with ICU Java-like regular expressions or the Unicode Collation Algorithm), + random string generation, case mapping, string transliteration, + concatenation, Unicode normalization, date-time formatting and parsing, + etc.""" + + homepage = "http://www.gagolewski.com/software/stringi/" + url = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/stringi" + + version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') + + extends('R') + + depends_on('icu') + + 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 new file mode 100644 index 0000000000..01fd969522 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RStringr(Package): + """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 + vectors in the same way, and the output from one function is easy to feed + into the input of another.""" + + homepage = "https://cran.r-project.org/web/packages/stringr/index.html" + url = "https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/stringr" + + version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') + + extends('R') + + depends_on('r-stringi') + depends_on('r-magrittr') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) -- cgit v1.2.3-70-g09d2 From d5abcc5c88a1aef31cba571a03966efded19c4ae Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 4 Jul 2016 17:55:10 -0500 Subject: Fix flake errors --- var/spack/repos/builtin/packages/r-inline/package.py | 3 ++- var/spack/repos/builtin/packages/r-plyr/package.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index c972fe0ff0..35eb8ca76f 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -27,7 +27,8 @@ from spack import * class RInline(Package): """Functionality to dynamically define R functions and S4 methods with - inlined C, C++ or Fortran code supporting .C and .Call calling conventions.""" + inlined C, C++ or Fortran code supporting .C and .Call calling + conventions.""" homepage = "https://cran.r-project.org/web/packages/inline/index.html" url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz" diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index e071050f4a..192e7e8b18 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -31,7 +31,8 @@ class RPlyr(Package): all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The - development of 'plyr' has been generously supported by 'Becton Dickinson'.""" + development of 'plyr' has been generously supported by 'Becton + Dickinson'.""" homepage = "http://had.co.nz/plyr" url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz" -- cgit v1.2.3-70-g09d2 From d687e332ad41cd7c84bf0007f8c331e56470da18 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 4 Jul 2016 22:59:02 -0700 Subject: Fix compile bugs for gcc on Mac OS X with macports. - add macports to things that are cleaned out of the environment. - linker incompatibilities cause issues with packages like OpenSSL. - also clean up NOQA stuff in OpenSSL --- lib/spack/spack/build_environment.py | 9 ++++++ .../repos/builtin/packages/openssl/package.py | 36 ++++++++++++++-------- 2 files changed, 32 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index ce0b91b718..fe5186a7d7 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -277,6 +277,15 @@ def set_build_environment_variables(pkg, env, dirty=False): env.unset('LD_RUN_PATH') env.unset('DYLD_LIBRARY_PATH') + # Remove any macports installs from the PATH. The macports ld can + # cause conflicts with the built-in linker on el capitan. Solves + # assembler issues, e.g.: + # suffix or operands invalid for `movq'" + path = get_path('PATH') + for p in path: + if '/macports/' in p: + env.remove_path('PATH', p) + # Add bin directories from dependencies to the PATH for the build. bin_dirs = reversed( filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index a0747f229d..e7c105d5f5 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -63,7 +63,8 @@ class Openssl(Package): # case return a fake url and exit openssl_url = '@system (reserved version for system openssl)' if not warnings_given_to_user.get(version, False): - tty.msg('Using openssl@system : the version @system is reserved for system openssl') # NOQA: ignore=E501 + tty.msg('Using openssl@system: ' + 'the version @system is reserved for system openssl') warnings_given_to_user[version] = True else: openssl_url = self.check_for_outdated_release( @@ -87,37 +88,46 @@ class Openssl(Package): openssl_url = latest.format(version=version) urllib.urlopen(openssl_url) except IOError: - openssl_url = older.format(version_number=version_number, version_full=version) # NOQA:ignore=E501 + openssl_url = older.format( + version_number=version_number, version_full=version) # Checks if we already warned the user for this particular # version of OpenSSL. If not we display a warning message # and mark this version if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') # NOQA: ignore=E501 - tty.warn('Consider updating to the latest version of this package.') # NOQA: ignore=E501 - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) # NOQA: ignore=E501 + tty.warn( + 'This installation depends on an old version of OpenSSL, ' + 'which may have known security issues. ') + tty.warn( + 'Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format( + homepage=Openssl.homepage)) warnings_given_to_user[version] = True return openssl_url + def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set # in the environment, then this will override what is set in the # Makefile, leading to build errors. env.pop('APPS', None) - if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"): + + if spec.satisfies('target=x86_64') or spec.satisfies('target=ppc64'): # This needs to be done for all 64-bit architectures (except Linux, # where it happens automatically?) env['KERNEL_BITS'] = '64' - config = Executable("./config") - config("--prefix=%s" % prefix, - "--openssldir=%s" % join_path(prefix, 'etc', 'openssl'), - "zlib", - "no-krb5", - "shared") + + options = ['zlib', 'no-krb5', 'shared'] + + config = Executable('./config') + config('--prefix=%s' % prefix, + '--openssldir=%s' % join_path(prefix, 'etc', 'openssl'), + *options) + # Remove non-standard compiler options if present. These options are # present e.g. on Darwin. They are non-standard, i.e. most compilers # (e.g. gcc) will not accept them. filter_file(r'-arch x86_64', '', 'Makefile') make() - make("install") + make('install') -- cgit v1.2.3-70-g09d2 From 79b3ef0362beba8dba260bdb023518f8c77c62bd Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Tue, 5 Jul 2016 10:58:11 -0400 Subject: Don't enforce `hdf5~mpi` --- var/spack/repos/builtin/packages/py-h5py/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index 0180b658f5..67461babe7 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -43,8 +43,8 @@ class PyH5py(Package): # Build dependencies depends_on('py-cython@0.19:') depends_on('pkg-config') - depends_on('hdf5@1.8.4:+mpi', when='+mpi') - depends_on('hdf5@1.8.4:~mpi', when='~mpi') + depends_on('hdf5@1.8.4:') + depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') # Build and runtime dependencies -- cgit v1.2.3-70-g09d2 From 976b2b4d250c88f9668c7e4cf4f6c7bdb8324a2c Mon Sep 17 00:00:00 2001 From: Greg Lee Date: Tue, 5 Jul 2016 13:45:22 -0700 Subject: added suitesparse version 4.5.3 --- var/spack/repos/builtin/packages/suite-sparse/package.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index dd0dfa3e23..4135c7dd72 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -33,6 +33,7 @@ class SuiteSparse(Package): url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + version('4.5.3', '8ec57324585df3c6483ad7f556afccbd') # FIXME: (see below) # variant('tbb', default=True, description='Build with Intel TBB') @@ -41,6 +42,7 @@ class SuiteSparse(Package): depends_on('lapack') depends_on('metis@5.1.0', when='@4.5.1') + depends_on('metis@5.1.0', when='@4.5.3') # FIXME: # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags # does not seem to be used, which leads to linking errors on Linux. @@ -79,9 +81,10 @@ class SuiteSparse(Package): # BLAS arguments require path to libraries # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make_args.extend([ - 'BLAS=-lblas', - 'LAPACK=-llapack' - ]) + if '@4.5.1' in spec: + make_args.extend([ + 'BLAS=-lblas', + 'LAPACK=-llapack' + ]) make('install', *make_args) -- cgit v1.2.3-70-g09d2 From 4c063c60556d714fd7fe4792b6aa137fd7d3f45e Mon Sep 17 00:00:00 2001 From: Greg Lee Date: Tue, 5 Jul 2016 13:48:32 -0700 Subject: kludge to get suite-sparse-4.5.1 to link with -lstdc++ --- var/spack/repos/builtin/packages/suite-sparse/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 4135c7dd72..bc25fa8c6c 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -82,8 +82,10 @@ class SuiteSparse(Package): # BLAS arguments require path to libraries # FIXME : (blas / lapack always provide libblas and liblapack as aliases) if '@4.5.1' in spec: + # adding -lstdc++ is clearly an ugly way to do this, but it follows suit + # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk make_args.extend([ - 'BLAS=-lblas', + 'BLAS=-lblas -lstdc++', 'LAPACK=-llapack' ]) -- cgit v1.2.3-70-g09d2 From f5f7abd71f04b08a454c0a83dd87d2f806dcc23a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 10:56:16 +0200 Subject: arpack-ng: add 3.4.0 with cmake build --- .../builtin/packages/arpack-ng/make_install.patch | 24 ++++++++++++++ .../repos/builtin/packages/arpack-ng/package.py | 38 +++++++++++++++++++--- .../builtin/packages/arpack-ng/parpack_cmake.patch | 17 ++++++++++ 3 files changed, 75 insertions(+), 4 deletions(-) create mode 100644 var/spack/repos/builtin/packages/arpack-ng/make_install.patch create mode 100644 var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/make_install.patch b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch new file mode 100644 index 0000000000..ad5cffcc19 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch @@ -0,0 +1,24 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..50426c3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) + add_test(bug_1323 Tests/bug_1323) + + add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323) ++ ++############################ ++# install ++############################ ++# 'make install' to the correct location ++install(TARGETS arpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++ ++if (MPI) ++ install(TARGETS parpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++endif () diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index fcd5171a7d..c7501b5a6d 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -54,6 +54,7 @@ class ArpackNg(Package): homepage = 'https://github.com/opencollab/arpack-ng' url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz' + version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4') version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') variant('shared', default=True, description='Enables the build of shared libraries') @@ -61,16 +62,45 @@ class ArpackNg(Package): # The function pdlamch10 does not set the return variable. This is fixed upstream # see https://github.com/opencollab/arpack-ng/issues/34 - patch('pdlamch10.patch', when='@3.3:') + patch('pdlamch10.patch', when='@3.3.0') + + patch('make_install.patch', when='@3.4.0') + patch('parpack_cmake.patch', when='@3.4.0') depends_on('blas') depends_on('lapack') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool@2.4.2:') + depends_on('automake', when='@3.3.0') + depends_on('autoconf', when='@3.3.0') + depends_on('libtool@2.4.2:', when='@3.3.0') + depends_on('cmake@2.8.6:', when='@3.4.0:') depends_on('mpi', when='+mpi') + @when('@3.4.0:') + def install(self, spec, prefix): + + options = ['-DEXAMPLES=ON'] + options.extend(std_cmake_args) + + # Arpack do directly find_package(BLAS REQUIRED) and + # find_package(LAPACK REQUIRED). + + if '+mpi' in spec: + options.append('-DMPI=ON') + + # TODO: -DINTERFACE64=ON + + if '+shared' in spec: + options.append('-DBUILD_SHARED_LIBS=ON') + + cmake('.', *options) + make() + # TODO: make test does not work + # make('test') + + make('install') + + @when('@3.3.0') def install(self, spec, prefix): # Apparently autotools are not bootstrapped # TODO: switch to use the CMake build in the next version diff --git a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch new file mode 100644 index 0000000000..0ba8600046 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch @@ -0,0 +1,17 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..345b7fc 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX}) + + if (MPI) + # add_library(parpack SHARED +- add_library(parpack ++ add_library(parpack + ${parpacksrc_STAT_SRCS} + ${parpackutil_STAT_SRCS}) + + target_link_libraries(parpack ${MPI_Fortran_LIBRARIES}) ++ target_link_libraries(parpack arpack) + set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX}) + endif () -- cgit v1.2.3-70-g09d2 From a47b3ba01bc3f93795c0702c3858784a64d3bd91 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 13:23:51 +0200 Subject: arpack-ng: use spec['mpi'].mpif77 --- var/spack/repos/builtin/packages/arpack-ng/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index c7501b5a6d..5adc8c0b8c 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -113,7 +113,7 @@ class ArpackNg(Package): if '+mpi' in spec: options.extend([ '--enable-mpi', - 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + 'F77=%s' % spec['mpi'].mpif77 ]) if '~shared' in spec: -- cgit v1.2.3-70-g09d2 From 63e45c586c93da209590c31e7185084af87fa316 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 13:27:02 +0200 Subject: arpack-ng: flake8 fixes and minor update of incode comments --- .../repos/builtin/packages/arpack-ng/package.py | 31 ++++++++++++---------- 1 file changed, 17 insertions(+), 14 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 5adc8c0b8c..97f6ca3218 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -27,7 +27,8 @@ from spack import * class ArpackNg(Package): """ - ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. + ARPACK-NG is a collection of Fortran77 subroutines designed to solve large + scale eigenvalue problems. Important Features: @@ -38,16 +39,17 @@ class ArpackNg(Package): Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. - * Example driver routines that may be used as templates to implement numerous - Shift-Invert strategies for all problem types, data types and precision. + * Example driver routines that may be used as templates to implement + numerous Shift-Invert strategies for all problem types, data types and + precision. - This project is a joint project between Debian, Octave and Scilab in order to - provide a common and maintained version of arpack. + This project is a joint project between Debian, Octave and Scilab in order + to provide a common and maintained version of arpack. - Indeed, no single release has been published by Rice university for the last - few years and since many software (Octave, Scilab, R, Matlab...) forked it and - implemented their own modifications, arpack-ng aims to tackle this by providing - a common repository and maintained versions. + Indeed, no single release has been published by Rice university for the + last few years and since many software (Octave, Scilab, R, Matlab...) + forked it and implemented their own modifications, arpack-ng aims to tackle + this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere. """ @@ -60,7 +62,8 @@ class ArpackNg(Package): variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') - # The function pdlamch10 does not set the return variable. This is fixed upstream + # The function pdlamch10 does not set the return variable. + # This is fixed upstream # see https://github.com/opencollab/arpack-ng/issues/34 patch('pdlamch10.patch', when='@3.3.0') @@ -82,8 +85,10 @@ class ArpackNg(Package): options = ['-DEXAMPLES=ON'] options.extend(std_cmake_args) - # Arpack do directly find_package(BLAS REQUIRED) and - # find_package(LAPACK REQUIRED). + # TODO: + # Arpack calls directly find_package(BLAS REQUIRED) and + # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are + # picked up. if '+mpi' in spec: options.append('-DMPI=ON') @@ -103,8 +108,6 @@ class ArpackNg(Package): @when('@3.3.0') def install(self, spec, prefix): # Apparently autotools are not bootstrapped - # TODO: switch to use the CMake build in the next version - # rather than bootstrapping. which('libtoolize')() bootstrap = Executable('./bootstrap') -- cgit v1.2.3-70-g09d2 From c8fc56686cbab2f7f9d2dd76740604d2daeb9783 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 13:42:59 +0200 Subject: arpack-ng: fix corrupted parpack_cmake.patch --- var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch index 0ba8600046..9b11bea6ac 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch +++ b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch @@ -3,15 +3,16 @@ index 607d221..345b7fc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX}) - + if (MPI) # add_library(parpack SHARED -- add_library(parpack +- add_library(parpack + add_library(parpack ${parpacksrc_STAT_SRCS} ${parpackutil_STAT_SRCS}) - + target_link_libraries(parpack ${MPI_Fortran_LIBRARIES}) + target_link_libraries(parpack arpack) set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX}) endif () + -- cgit v1.2.3-70-g09d2 From 3d755a148b1940218a3c990b1d8342ea88ae8012 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 18:29:56 +0200 Subject: arpack-ng: fix binaries for macOS --- var/spack/repos/builtin/packages/arpack-ng/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 97f6ca3218..d9021f8043 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -84,6 +84,7 @@ class ArpackNg(Package): options = ['-DEXAMPLES=ON'] options.extend(std_cmake_args) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) # TODO: # Arpack calls directly find_package(BLAS REQUIRED) and -- cgit v1.2.3-70-g09d2 From 61fe89bda0d5690a4851cde5baa7d55f6a43a6bd Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Wed, 6 Jul 2016 18:29:54 +0100 Subject: Add ucs4 unicode variant to Python package --- var/spack/repos/builtin/packages/python/package.py | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 8033c52b91..d019133585 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -47,6 +47,8 @@ class Python(Package): extendable = True + variant('ucs4', default=False, description='Enable UCS4 unicode strings') + depends_on("openssl") depends_on("bzip2") depends_on("readline") @@ -82,6 +84,9 @@ class Python(Package): "LDFLAGS=-L{0}".format(ldflags) ] + if '+ucs4' in spec: + config_args.append('--enable-unicode=ucs4') + if spec.satisfies('@3:'): config_args.append('--without-ensurepip') -- cgit v1.2.3-70-g09d2 From 57eaea2e8c23a2533fa5235e97f1e3ca3f517dab Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 20:34:05 +0200 Subject: oce: add 0.17.2; fix running tests --- var/spack/repos/builtin/packages/oce/package.py | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 0f0fcfb733..b93f1317ef 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -33,6 +33,7 @@ class Oce(Package): homepage = "https://github.com/tpaviot/oce" url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" + version('0.17.2', 'bf2226be4cd192606af677cf178088e5') version('0.17.1', '36c67b87093c675698b483454258af91') version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') @@ -77,15 +78,8 @@ class Oce(Package): '-DOCE_OSX_USE_COCOA:BOOL=ON', ]) - cmake('.', *options) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + cmake('.', *options) make("install/strip") - - # OCE tests build is brocken at least on Darwin. - # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib - # see https://github.com/tpaviot/oce/issues/612 - # make("test") - - # The shared libraries are not installed correctly on Darwin; correct this - if (sys.platform == 'darwin'): - fix_darwin_install_name(prefix.lib) + make("test") -- cgit v1.2.3-70-g09d2 From 4e27d91351f1f2f29adec9d1be44e25cbb79bb9f Mon Sep 17 00:00:00 2001 From: Greg Lee Date: Tue, 5 Jul 2016 14:28:24 -0700 Subject: flake 8 fixes --- .../repos/builtin/packages/suite-sparse/package.py | 31 +++++++++++----------- 1 file changed, 16 insertions(+), 15 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index bc25fa8c6c..1dc64f385f 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -44,32 +44,33 @@ class SuiteSparse(Package): depends_on('metis@5.1.0', when='@4.5.1') depends_on('metis@5.1.0', when='@4.5.3') # FIXME: - # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags - # does not seem to be used, which leads to linking errors on Linux. + # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng + # flags does not seem to be used, which leads to linking errors on Linux. # Try re-enabling in future versions. # depends_on('tbb', when='+tbb') def install(self, spec, prefix): - # The build system of SuiteSparse is quite old-fashioned - # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) - # with a lot of convoluted logic in it. - # Any kind of customization will need to go through filtering of that file + # The build system of SuiteSparse is quite old-fashioned. + # It's basically a plain Makefile which include an header + # (SuiteSparse_config/SuiteSparse_config.mk)with a lot of convoluted + # logic in it. Any kind of customization will need to go through + # filtering of that file make_args = ['INSTALL=%s' % prefix] # inject Spack compiler wrappers make_args.extend([ - 'AUTOCC=no', - 'CC=cc', - 'CXX=c++', - 'F77=f77', + 'AUTOCC=no', + 'CC=cc', + 'CXX=c++', + 'F77=f77', ]) # use Spack's metis in CHOLMOD/Partition module, # otherwise internal Metis will be compiled make_args.extend([ - 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, - 'MY_METIS_INC=%s' % spec['metis'].prefix.include, + 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, + 'MY_METIS_INC=%s' % spec['metis'].prefix.include, ]) # Intel TBB in SuiteSparseQR @@ -80,10 +81,10 @@ class SuiteSparse(Package): ]) # BLAS arguments require path to libraries - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) + # FIXME: (blas/lapack always provide libblas and liblapack as aliases) if '@4.5.1' in spec: - # adding -lstdc++ is clearly an ugly way to do this, but it follows suit - # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk + # adding -lstdc++ is clearly an ugly way to do this, but it follows + # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk make_args.extend([ 'BLAS=-lblas -lstdc++', 'LAPACK=-llapack' -- cgit v1.2.3-70-g09d2 From 3df0f1902d84223dba02692d80439ee928f28285 Mon Sep 17 00:00:00 2001 From: Greg Lee Date: Wed, 6 Jul 2016 12:15:20 -0700 Subject: clean up suitesparse deps --- var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 1dc64f385f..2cc89b843f 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -41,8 +41,7 @@ class SuiteSparse(Package): depends_on('blas') depends_on('lapack') - depends_on('metis@5.1.0', when='@4.5.1') - depends_on('metis@5.1.0', when='@4.5.3') + depends_on('metis@5.1.0', when='@4.5.1:') # FIXME: # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng # flags does not seem to be used, which leads to linking errors on Linux. -- cgit v1.2.3-70-g09d2 From c096bb332a7710a0618049f0e2df1800771bd3f9 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 22:45:43 +0200 Subject: petsc: fix unit tests --- var/spack/repos/builtin/packages/petsc/package.py | 30 ++++++++++++----------- 1 file changed, 16 insertions(+), 14 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 6a7bee9788..90afdbdb90 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -149,20 +149,22 @@ class Petsc(Package): make("install") # solve Poisson equation in 2D to make sure nothing is broken: - with working_dir('src/ksp/ksp/examples/tutorials'): - cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc # NOQA: ignore=E501 - os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % ( - cc, prefix.include, prefix.lib)) - ex50 = Executable('./ex50') - ex50('-da_grid_x', '4', '-da_grid_y', '4') - if 'superlu-dist' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 - - if 'mumps' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 - - if 'hypre' in spec: - ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 + if ('mpi' in spec) and self.run_tests: + with working_dir('src/ksp/ksp/examples/tutorials'): + env['PETSC_DIR'] = self.prefix + cc = Executable(spec['mpi'].mpicc) + cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib, + '-lpetsc', '-o', 'ex50') + run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun')) + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4') + if 'superlu-dist' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 + + if 'mumps' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 + + if 'hypre' in spec: + run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up PETSC_DIR for everyone using PETSc package -- cgit v1.2.3-70-g09d2 From 14cef6eab8a29ac8cb93c6d528b0e62201a7f0d3 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Jul 2016 22:51:20 +0200 Subject: oce: flake8 fixes --- var/spack/repos/builtin/packages/oce/package.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index b93f1317ef..06b6b7cbb0 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -23,21 +23,22 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import platform, sys +import platform + class Oce(Package): - """ - Open CASCADE Community Edition: - patches/improvements/experiments contributed by users over the official Open CASCADE library. + """Open CASCADE Community Edition: + patches/improvements/experiments contributed by users over the official + Open CASCADE library. """ homepage = "https://github.com/tpaviot/oce" url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" version('0.17.2', 'bf2226be4cd192606af677cf178088e5') version('0.17.1', '36c67b87093c675698b483454258af91') - version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.17', 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') - version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.16', '7a4b4df5a104d75a537e25e7dd387eca') variant('tbb', default=True, description='Build with Intel Threading Building Blocks') @@ -50,8 +51,7 @@ class Oce(Package): # http://tracker.dev.opencascade.org/view.php?id=26042 # https://github.com/tpaviot/oce/issues/605 # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch - patch('null.patch',when='@0.16:0.17.1') - + patch('null.patch', when='@0.16:0.17.1') def install(self, spec, prefix): options = [] @@ -64,7 +64,8 @@ class Oce(Package): '-DOCE_DISABLE_X11:BOOL=ON', '-DOCE_DRAW:BOOL=OFF', '-DOCE_MODEL:BOOL=ON', - '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'), + '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ( + 'TBB' if '+tbb' in spec else 'NONE'), '-DOCE_OCAF:BOOL=ON', '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', '-DOCE_VISUALISATION:BOOL=OFF', -- cgit v1.2.3-70-g09d2 From 1b53452618154b47caa5a4d8493ff025c9a3aa10 Mon Sep 17 00:00:00 2001 From: Stephen Herbein Date: Thu, 7 Jul 2016 17:41:53 -0700 Subject: docbook-xml: replace 'cp -t' with install_tree '-t' is not supported by the default cp on Mac OS X replace with install/install_tree cannot just use install_tree since shutil.copytree insists that the dst directory not exist --- var/spack/repos/builtin/packages/docbook-xml/package.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py index 9c22174610..87137168f3 100644 --- a/var/spack/repos/builtin/packages/docbook-xml/package.py +++ b/var/spack/repos/builtin/packages/docbook-xml/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os -import glob from spack import * @@ -35,9 +34,10 @@ class DocbookXml(Package): version('4.5', '03083e288e87a7e829e437358da7ef9e') def install(self, spec, prefix): - cp = which('cp') - - install_args = ['-a', '-t', prefix] - install_args.extend(glob.glob('*')) - - cp(*install_args) + for item in os.listdir('.'): + src = os.path.abspath(item) + dst = os.path.join(prefix, item) + if os.path.isdir(item): + install_tree(src, dst, symlinks=True) + else: + install(src, dst) -- cgit v1.2.3-70-g09d2 From 1a1bf31032fca3d61d1ae9209f9c77a4822eb733 Mon Sep 17 00:00:00 2001 From: Stephen Herbein Date: Thu, 7 Jul 2016 18:54:34 -0700 Subject: lua: switch self.version[:2] to .up_to(2) Previous package would not install correctly, would throw: return os.path.join('share', 'lua', '%d.%d' % self.version[:2]) TypeError: %d format: a number is required, not Version --- var/spack/repos/builtin/packages/lua/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 761932361b..48c1c6a919 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -140,11 +140,11 @@ class Lua(Package): @property def lua_lib_dir(self): - return os.path.join('lib', 'lua', '%d.%d' % self.version[:2]) + return os.path.join('lib', 'lua', self.version.up_to(2)) @property def lua_share_dir(self): - return os.path.join('share', 'lua', '%d.%d' % self.version[:2]) + return os.path.join('share', 'lua', self.version.up_to(2)) def setup_dependent_package(self, module, ext_spec): """ -- cgit v1.2.3-70-g09d2 From bb8a8ecda33bebe1dd19f84ded752432ab5855bf Mon Sep 17 00:00:00 2001 From: Stephen Herbein Date: Fri, 8 Jul 2016 10:14:02 -0700 Subject: json-c: fix build by running serially --- var/spack/repos/builtin/packages/libjson-c/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libjson-c/package.py b/var/spack/repos/builtin/packages/libjson-c/package.py index 75f3e130ad..662ed3cb5a 100644 --- a/var/spack/repos/builtin/packages/libjson-c/package.py +++ b/var/spack/repos/builtin/packages/libjson-c/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class LibjsonC(Package): """ A JSON implementation in C """ homepage = "https://github.com/json-c/json-c/wiki" @@ -34,5 +35,5 @@ class LibjsonC(Package): def install(self, spec, prefix): configure('--prefix=%s' % prefix) - make() + make(parallel=False) make("install") -- cgit v1.2.3-70-g09d2 From c8137194f0f09c594cafd417ef820c3ecf5ead85 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 8 Jul 2016 15:20:09 -0400 Subject: Update Cereal to 1.2.0 --- var/spack/repos/builtin/packages/cereal/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index c53c667efb..80198fa224 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -31,6 +31,7 @@ class Cereal(Package): homepage = "http://uscilab.github.io/cereal/" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" + version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b') version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9') version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27') version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f') -- cgit v1.2.3-70-g09d2 From e482994a1505bf7b8e506872c8ac205fce68b217 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 9 Jul 2016 08:12:34 +0200 Subject: petsc: add -lm when building example --- var/spack/repos/builtin/packages/petsc/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 90afdbdb90..11f5c36c22 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -154,7 +154,7 @@ class Petsc(Package): env['PETSC_DIR'] = self.prefix cc = Executable(spec['mpi'].mpicc) cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib, - '-lpetsc', '-o', 'ex50') + '-lpetsc', '-lm', '-o', 'ex50') run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun')) run('ex50', '-da_grid_x', '4', '-da_grid_y', '4') if 'superlu-dist' in spec: -- cgit v1.2.3-70-g09d2 From 38550bbc1b5a61c5c7a2869297642627fd598035 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 11 Jul 2016 10:17:09 +0200 Subject: slepc: fix install_name for binaries on macOS for 3.7.1 --- .../builtin/packages/slepc/install_name_371.patch | 32 ++++++++++++++++++++++ var/spack/repos/builtin/packages/slepc/package.py | 15 ++++++---- 2 files changed, 42 insertions(+), 5 deletions(-) create mode 100644 var/spack/repos/builtin/packages/slepc/install_name_371.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/slepc/install_name_371.patch b/var/spack/repos/builtin/packages/slepc/install_name_371.patch new file mode 100644 index 0000000000..d02ca88657 --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/install_name_371.patch @@ -0,0 +1,32 @@ +From 7489a3f3d569e2fbf5513ac9dcd769017d9f7eb7 Mon Sep 17 00:00:00 2001 +From: Lisandro Dalcin +Date: Thu, 2 Jun 2016 21:57:38 +0300 +Subject: [PATCH] OS X: Fix library path in invocation of install_name_tool + +--- + config/install.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/config/install.py b/config/install.py +index 09acd03..6ce98ae 100755 +--- a/config/install.py ++++ b/config/install.py +@@ -25,6 +25,7 @@ class Installer: + + def setupDirectories(self): + self.installDir = self.destDir ++ self.archDir = os.path.join(self.rootDir, self.arch) + self.rootIncludeDir = os.path.join(self.rootDir, 'include') + self.archIncludeDir = os.path.join(self.rootDir, self.arch, 'include') + self.rootConfDir = os.path.join(self.rootDir, 'lib','slepc','conf') +@@ -220,7 +221,7 @@ for dir in dirs: + if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'): + (result, output) = commands.getstatusoutput('otool -D '+src) + oldname = output[output.find("\n")+1:] +- installName = oldname.replace(self.destDir, self.installDir) ++ installName = oldname.replace(self.archDir, self.installDir) + (result, output) = commands.getstatusoutput('/usr/bin/install_name_tool -id ' + installName + ' ' + dst) + # preserve the original timestamps - so that the .a vs .so time order is preserved + shutil.copystat(src,dst) +-- +2.7.4.1.g5468f9e diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index d3739bf6a6..fd6c42d9fc 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -28,7 +28,7 @@ from spack import * class Slepc(Package): """ - Scalable Library for Eigenvalue Computations. + Scalable Library for Eigenvalue Problem Computations. """ homepage = "http://www.grycap.upv.es/slepc" @@ -45,9 +45,13 @@ class Slepc(Package): depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') + patch('install_name_371.patch', when='@3.7.1') + def install(self, spec, prefix): # set SLEPC_DIR for installation - os.environ['SLEPC_DIR'] = self.stage.source_path + # Note that one should set the current (temporary) directory instead + # its symlink in spack/stage/ ! + os.environ['SLEPC_DIR'] = os.getcwd() options = [] @@ -67,9 +71,10 @@ class Slepc(Package): configure('--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) - # FIXME: - # make('test') - make('install') + if self.run_tests: + make('test', parallel=False) + + make('install', parallel=False) def setup_dependent_environment(self, spack_env, run_env, dependent_spec): # set up SLEPC_DIR for everyone using SLEPc package -- cgit v1.2.3-70-g09d2 From 0d3a52ae29c501c2259370d79a480630be4c7268 Mon Sep 17 00:00:00 2001 From: Paul Hopkins Date: Mon, 11 Jul 2016 16:00:19 +0100 Subject: Fix typo in Octave variant suitesparse --- var/spack/repos/builtin/packages/octave/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index f97bfc7d12..6535f528ee 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -61,7 +61,7 @@ class Octave(Package): variant('qrupdate', default=False) variant('qscintilla', default=False) variant('qt', default=False) - variant('suiteparse', default=False) + variant('suitesparse', default=False) variant('zlib', default=False) # Required dependencies -- cgit v1.2.3-70-g09d2 From 664bdd359fc0421cc2327a4dbfdf50e739361664 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 11 Jul 2016 13:29:43 -0500 Subject: Filter compilers for R This adds a filter_compilers function to have the Makeconf file for R point to the actual compilers rather than the spack wrappers. Also added version 3.3.1. --- var/spack/repos/builtin/packages/R/package.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'var') 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. # ======================================================================== -- cgit v1.2.3-70-g09d2