Amanda Miotto <a.miotto <at> griffith.edu.au> writes:
>
> 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_Pro
be_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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>
I'm not sure why it happens, but here's a quick workaround.
1.) Find out where libjvm.so is actually located. On my Debian system, it's
located here:
$ locate libjvm.so
...
/usr/lib/jvm/java-6-sun-1.6.0.21/jre/lib/amd64/server/libjvm.so
...
This will vary based on your system and how you have Java installed.
2.) Link it to a global library path, like /usr/lib
$ sudo ln -s /path/to/libjvm.so /usr/lib
3.) Ensure rJava.so can find it:
$ ldd /path/to/rJava.so
...
libjvm.so => /usr/lib/libjvm.so (0x00007fead1f8e000)
...
For reference, before I symlinked libjvm.so, the output was the following:
$ ldd /path/to/rJava.so
...
libjvm.so => not found
...
4.) Ensure rpy2 finds it:
$ python -c "from rpy2 import robjects; robjects.r('library(rJava)')"
(should return nothing)
Hope that helps!
Yacin
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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