add flag to specify custom R library instead of /usr/lib/R/lib

kforeman · Apr 8, 2015 · ef0694d · ef0694d
1 parent 4aa5c5c
commit ef0694d
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/magic/PyMB_magic.py b/magic/PyMB_magic.py
@@ -40,6 +40,11 @@ def __init__(self, shell):
                         location of R shared library
                         Note: R must be built with shared libraries
                         See http://stackoverflow.com/a/13224980/1028347''')
+        @argument('-LR', '--R_LIB', type=str, default='/usr/share/R/include',
+                  help='''R_LIB : str, default '/usr/lib/R/lib'
+                        location of R library
+                        Note: R must be built with shared libraries
+                        See http://stackoverflow.com/a/13224980/1028347''')
         @argument('-CC', '--CCOMPILER', type=str, default='g++',
                   help='''CCOMPILER : str, default 'g++'
                         C++ compiler to use''')
@@ -95,7 +100,7 @@ def PyMB(self, line, cell):
                 code += '}\n'
 
             # compile model
-            model.compile(codestr=code, output_dir=args.OUTPUT_DIR, cc=args.CCOMPILER, R=args.R_DIR, TMB=args.TMB_DIR, verbose=args.VERBOSE)
+            model.compile(codestr=code, output_dir=args.OUTPUT_DIR, cc=args.CCOMPILER, R=args.R_DIR, TMB=args.TMB_DIR, LR=args.R_LIB, verbose=args.VERBOSE)
 
             # print if verbose
             if args.VERBOSE == True:

diff --git a/model.py b/model.py
@@ -59,7 +59,7 @@ def __init__(self, name=None, filepath=None, codestr=None, **kwargs):
 
     def compile(self, filepath=None, codestr=None, output_dir='tmb_tmp',
         cc='g++', R='/usr/share/R/include',
-        TMB='/usr/local/lib/R/site-library/TMB/include', verbose=False):
+        TMB='/usr/local/lib/R/site-library/TMB/include', LR='/usr/lib/R/lib', verbose=False):
         '''
         Compile TMB C++ code and load into R
 
@@ -137,7 +137,7 @@ def compile(self, filepath=None, codestr=None, output_dir='tmb_tmp',
             options='-shared',
             so='{output_dir}/{name}.so'.format(output_dir=output_dir, name=self.name),
             o='{output_dir}/{name}.o'.format(output_dir=output_dir, name=self.name),
-            link='-L/usr/lib/R/lib -lR')
+            link='-L{LR} -lR'.format(LR=LR))
         try:
             cmnd_output = subprocess.check_output(link, stderr=subprocess.STDOUT, shell=True)
         except subprocess.CalledProcessError as exc: