I am getting an error when using rpy2 under a Debian operating system. It
seems to be some kind of problem with R_LIBS enviromental variable but I
cannot get it completly. Can someone please explain me better the problem
so I can try to fix.
I have tried to export a varible R_LIBS but the problem persist.
Here is the detailed information:
run phasingBinomial.py xp 0.002 21 11
Error in strsplit(Sys.getenv("R_LIBS"), ":") :
5 arguments passed to .Internal(strsplit) which requires 6
Error in strsplit(x[ok], "[.-]") :
5 arguments passed to .Internal(strsplit) which requires 6
Error in strsplit(x[ok], "[.-]") :
5 arguments passed to .Internal(strsplit) which requires 6
.
.
.
Error in eval(expr, envir, enclos) : object 'phyper' not found
---------------------------------------------------------------------------
RRuntimeError Traceback (most recent call last)
/export/home/bacms2/AtillaChlamy/phasingBinomial.py in <module>()
236 for signature in dtSignatures.values():
237 #Defines the loci object
--> 238 loc = loci(nWindow*2,nSize)
239 #Test if read is on the Watson strand
240 if signature.nStrand == 1:
/export/home/bacms2/AtillaChlamy/phasingBinomial.py in __init__(self,
length, nSize)
112 self.__aux_ls__ = []
113 self.__printValue__ = False
--> 114 self.phyper = robjects.r('phyper')
115
116 def addRead(self,name,pos=0):
/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.pyc in
__call__(self, string)
534 def __call__(self, string):
535 p = self.parse(text=string)
--> 536 res = self.eval(p)
537 return res
538
/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.pyc in
__call__(self, *args, **kwargs)
421 for k, v in kwargs.iteritems():
422 new_kwargs[k] = conversion.py2ri(v) --> 423 res = super(RFunction,
self).__call__(*new_args, **new_kwargs)
424 res = conversion.ri2py(res)
425 return res
RRuntimeError: Error in eval(expr, envir, enclos) : object 'phyper' not
found
WARNING: Failure executing file: <phasingBinomial.py>
------------------------------------------------------------------------------
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