Dear All
I have had issues with both rpy and rpy2 when it comes to using a library that
uses rJava. The error is below
using rpy
>>> r.library('GenePattern')
Loading required package: rJava
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
rpy.RPy_RException: Error: package 'rJava' could not be loaded
Using rpy2
>>> getexpression('/home/.../ArrayExpress/Tools/head.Fibro_Sz_Vs_Controls_Sample_Probe_Profile.txt.proc')
Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared library
'/home/.../R/i486-pc-linux-gnu-library/2.6/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
In addition: Warning messages:
1: In cbind(rep(names(exptable2)[i], dim(exptable2)[2]), probes, exptable2[, :
number of rows of result is not a multiple of vector length (arg 2)
2: In cbind(rep(names(exptable2)[i], dim(exptable2)[2]), probes, exptable2[, :
number of rows of result is not a multiple of vector length (arg 2)
3: In cbind(rep(names(exptable2)[i], dim(exptable2)[2]), probes, exptable2[, :
number of rows of result is not a multiple of vector length (arg 2)
4: In cbind(rep(names(exptable2)[i], dim(exptable2)[2]), probes, exptable2[, :
number of rows of result is not a multiple of vector length (arg 2)
Error: package 'rJava' could not be loaded
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 35, in getexpression
File "/usr/lib/python2.5/site-packages/rpy2/robjects/functions.py", line 83,
in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/usr/lib/python2.5/site-packages/rpy2/robjects/functions.py", line 35,
in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error: package 'rJava' could not be loaded
>>>
rJava is installed and at the address that is listed. When I run the script
through R it works correctly. Any advice?
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