correctly configure R for BLAS/LAPACK & check configure output

easybuild/easyblocks/r/r.py

@@ -26,12 +26,15 @@
 EasyBuild support for building and installing R, implemented as an easyblock
 
 @author: Jens Timmerman (Ghent University)
+@author: Kenneth Hoste (Ghent University)
 """
 import os
+import re
 from distutils.version import LooseVersion
 
+import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
-from easybuild.tools import environment
+from easybuild.tools.build_log import print_warning
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.systemtools import get_shared_lib_ext
 
@@ -55,19 +58,39 @@ def prepare_for_extensions(self):
         self.cfg['exts_filter'] = EXTS_FILTER_R_PACKAGES
 
     def configure_step(self):
-        """Configuration step, we set FC, F77 is already set by EasyBuild to the right compiler,
-        FC is used for Fortan90"""
-        environment.setvar('FC', self.toolchain.get_variable('F90'))
+        """Custom configuration for R."""
+
+        # define $BLAS_LIBS to build R correctly against BLAS/LAPACK library
+        # $LAPACK_LIBS should *not* be specified since that may lead to using generic LAPACK
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1435
+        env.setvar('BLAS_LIBS', os.getenv('LIBBLAS_MT'))
+        self.cfg.update('configopts', "--with-blas --with-lapack")
 
         # make sure correct config script is used for Tcl/Tk
         for dep in ['Tcl', 'Tk']:
             root = get_software_root(dep)
             if root:
                 dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower())
-                self.cfg.update('configopts', '-with-%s-config=%s' % (dep.lower(), dep_config))
+                self.cfg.update('configopts', '--with-%s-config=%s' % (dep.lower(), dep_config))
+
+        out = ConfigureMake.configure_step(self)
+
+        # check output of configure command to verify BLAS/LAPACK settings
+        ext_libs_regex = re.compile("External libraries:.*BLAS\((?P<BLAS>.*)\).*LAPACK\((?P<LAPACK>.*)\)")
+        res = ext_libs_regex.search(out)
+        if res:
+            for lib in ['BLAS', 'LAPACK']:
+                if res.group(lib) == 'generic':
+                    warn_msg = "R will be built with generic %s, which will result in poor performance." % lib
+                    self.log.warning(warn_msg)
+                    print_warning(warn_msg)
+                else:
+                    self.log.info("R is configured to use non-generic %s: %s", lib, res.group(lib))
+        else:
+            warn_msg = "R is configured to be built without BLAS/LAPACK, which will result in (very) poor performance"
+            self.log.warning(warn_msg)
+            print_warning(warn_msg)
 
-        ConfigureMake.configure_step(self)
-
     def make_module_req_guess(self):
         """
         Add extra paths to modulefile