The error message refers to undefined symbols in shared C libraries for
R recommended packages, not about whether can be found or written into.
Did you reinstall rpy2 after the more recent R was installed ?
L.
On 12/8/09 1:15 PM, B.A.D.C.M.D Santos wrote:
> I managed to ask our Systems Administrator to install a new version of
> R. I know have R2.10.0 installed but rpy2 is still not very happy with it.
>
> When I try to import robjects I get the following errors:
>
> Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32) [GCC 4.3.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import rpy2.robjects
> Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared
> library '/applications/R-2.10.0/library/methods/libs/methods.so':
> /applications/R-2.10.0/library/methods/libs/methods.so: undefined
> symbol: Rf_allocS4Object Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library
> '/applications/R-2.10.0/library/grDevices/libs/grDevices.so':
> /applications/R-2.10.0/library/grDevices/libs/grDevices.so: undefined
> symbol: R_ClassSymbol In addition: Warning message: package "methods" in
> options("defaultPackages") was not found Error in dyn.load(file, DLLpath
> = DLLpath, ...) :
> unable to load shared library
> '/applications/R-2.10.0/library/grDevices/libs/grDevices.so':
> /applications/R-2.10.0/library/grDevices/libs/grDevices.so: undefined
> symbol: R_ClassSymbol In addition: Warning message: package grDevices in
> options("defaultPackages") was not found Error in dyn.load(file, DLLpath
> = DLLpath, ...) :
> unable to load shared library
> '/applications/R-2.10.0/library/grDevices/libs/grDevices.so':
> /applications/R-2.10.0/library/grDevices/libs/grDevices.so: undefined
> symbol: R_ClassSymbol In addition: Warning message: package graphics in
> options("defaultPackages") was not found Error in dyn.load(file, DLLpath
> = DLLpath, ...) :
> unable to load shared library
> '/applications/R-2.10.0/library/methods/libs/methods.so':
> /applications/R-2.10.0/library/methods/libs/methods.so: undefined
> symbol: Rf_allocS4Object In addition: Warning message: package stats in
> options("defaultPackages") was not found During startup - Warning
> message: package methods in options("defaultPackages") was not found
>
> I checked the path for the files and they are there. I even tried with
> write permissions but I get the same error. Is this a but with rpy2?
>
> Many thanks,
> Bruno
>
> 2009/12/7 Laurent Gautier <lgaut...@gmail.com>
>
> rpy2 will be happier with R >= 2.8
> (as bugs in R were fixed)
>
>
> L.
>
>
>
>
> On 12/7/09 12:33 PM, B.A.D.C.M.D Santos wrote:
> The problem is that I get the error when import robjects. When I tried
> to replicate your instructions I got the following error: In [5]:
> print(rpy2.robjects.r['search']())
> ---------------------------------------------------------------------------
> AttributeError Traceback (most recent call last)
>
> /export/home/bacms2/<ipython console> in <module>()
>
> /usr/lib/python2.5/site-packages/rpy2/robjects/__init__.pyc in
> __str__(self)
> 125 tmp = baseNameSpaceEnv["fifo"]("")
> 126 baseNameSpaceEnv["sink"](tmp)
> --> 127 r.show(self)
> 128 baseNameSpaceEnv["sink"]()
> 129 if sys.platform == 'win32':
>
> /usr/lib/python2.5/site-packages/rpy2/robjects/__init__.pyc in
> __getattribute__(self, attr)
> 511 return self[attr]
> 512 except LookupError, le:
> --> 513 raise orig_ae
> 514
> 515 def __getitem__(self, item):
>
> AttributeError: 'R' object has no attribute 'show'
>
> I am using the following versions:
> R version 2.7.1 (2008-06-23)
> Python 2.5.2 (r252:60911, Jan 4 2009, 21:59:32)
> rpy2 version 2.0.8
>
> Many Thanks,
> Bruno
>
>
> 2009/12/7 Laurent Gautier <lgaut...@gmail.com>
>
>
> phyper is part of "stats", which should be loaded by defaults.
>
> Check what returns:
> print(robjects.r["search"]())
>
> If not attached, you'll have to load it.
>
> L.
>
> PS: The R version, Python version, and rpy2 version is generally a good
> thing to tell us.
>
>
>
> On 12/7/09 11:06 AM, B.A.D.C.M.D Santos wrote:
>
> 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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