I have been trying to use the function in an ubuntu server but got some errors...
First I got a message indicating that the function was not able to open file 'CS/CS_resistances.out': file or directory does not exist.....
I modified the function by clipping the last part of the run statement
from CS_run <- paste("csrun.py", paste("CS/myini.ini"), paste("&> /dev/null"))
to CS_run <- paste("csrun.py", paste("CS/myini.ini"))
to check is there was something wrong with circuitscape and got this long string of messages
--- Reading maps ---
--- Processing maps ---
--- Resistance/conductance map has 436477 nodes ---
Traceback (most recent call last):
File "/usr/local/bin/csrun.py", line 13, in
resistances = cs.compute()
File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper
return func(*args)
File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 31, in compute
return self.compute_raster()
File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper
return func(*args)
File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 152, in compute_raster
resistances, solver_failed = self.pairwise_module(self.state.g_map, self.state.poly_map, self.state.points_rc)
File "/usr/local/lib/python2.7/dist-packages/circuitscape/profiler.py", line 144, in wrapper
return func(*args)
File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute.py", line 367, in pairwise_module
g_habitat = HabitatGraph(g_map=g_map, poly_map=poly_map, connect_using_avg_resistances=self.options.connect_using_avg_resistances, connect_four_neighbors_only=self.options.connect_four_neighbors_only)
File "/usr/local/lib/python2.7/dist-packages/circuitscape/compute_base.py", line 510, in init
if None != g_map:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Any idea or suggestion about what could be wrong in runCS.

Thanks in advance Marcelo