Hi,

On our Ubuntu install stat packages and all that require rpy work fine.

On our CentOs install seeing this stubborn error that I did see from previous 
post to be difficult to fix.

At first suspected the SGE issue - environment not transferring to  compute 
nodes. After changing the app to run local had the same issue.

CentOs: 2.6.18-92.1.13.el5

rpy module is in:

/apps1/python/2.6.6/intel/lib/python2.6/site-packages

_rpy2122.so
_rpy2131.so

version:
[galaxy@compute-0-65 galaxy-dist]$ python -c "import rpy; print rpy.__version__"
1.5.1

path:

python -c 'import sys; print "\n".join( sys.path )'

/apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg
/apps1/python/2.6.6/intel/lib/python26.zip
/apps1/python/2.6.6/intel/lib/python2.6
/apps1/python/2.6.6/intel/lib/python2.6/plat-linux2
/apps1/python/2.6.6/intel/lib/python2.6/lib-tk
/apps1/python/2.6.6/intel/lib/python2.6/lib-old
/apps1/python/2.6.6/intel/lib/python2.6/lib-dynload
/apps1/python/2.6.6/intel/lib/python2.6/site-packages
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL


compiled against /R/2.13.1


env:

export PATH=.:\
/apps1/R/2.13.1/intel/bin:\
/apps1/python/2.6.6/intel/bin:\
/apps1/pipe/bowtie/0.12.7/intel:\
/apps1/pipe/bwa/0.5.9/intel:\
/apps1/samtools/0.1.13/intel/bin:\
/apps1/fastx_toolkit/0.0.13/intel/bin:\
/apps1/maq/maq-0.7.1:\
/apps1/maq/maq-0.7.1/scripts:\
/apps1/bfast/bfast-0.6.5a/butil:\
/apps1/bfast/bfast-0.6.5a/scripts:\
/apps1/abyss/1.2.7/intel/bin:\
/apps1/velvet/velvet_1.0.12:\
/apps1/pipe/tophat/1.3.0/intel/bin:\
/apps1/pipe/cufflinks/1.0.3/intel/bin:\
/apps1/blast/2.2.25/gnu/bin:\
/apps1/blast+/2.2.5/gnu/bin:\
/apps1/sputnik/intel/bin:\
/apps1/taxonomy/intel/bin:\
/apps1/add_scores/add_scores:\
/apps1/emboss/6.4.0/intel/bin:\
/apps1/hyphy/hyphy/HYPHY:\
/apps1/lastz/1.02.00:\
/apps1/perm/0.3.6/intel/bin:\
/apps1/beam2/intel/bin:\
/apps1/pass2/intel/bin:\
/apps1/plink/1.07/intel/bin:\
/apps1/fbat/2.0.3/bin:\
/apps1/eigensoft/3.0/intel/bin:\
/apps1/mosaik/Mosaik-1.1.0021-Linux-x64/bin:\
/apps1/freebayes/freebayes.git/bin:\
$PATH

export LD_LIBRARY_PATH=.:\
/apps1/python/2.6.6/intel/lib:\
/apps1/libgtextutils/0.6/intel/lib:\
/apps1/emboss/6.4.0/intel/lib:\
/apps1/intel/lib/intel64:\
/apps1/intel/mkl/lib/em64t:\
/apps1/tcltk/8.5.9/intel/lib:\
/apps1/zlib/1.2.5/intel/lib:\
/apps1/graphviz/2.26.3/intel/lib:\
/apps1/python/2.6.6/intel/lib/python2.6/site-packages/simtk/chem/openmm/OpenMM:\
/apps1/python/2.6.6/intel/lib/python2.6/site-packages:\
/apps1/libpng/1.5.0/intel/lib:\
/apps1/R/2.13.1/intel/lib64/R/lib:\
$LD_LIBRARY_PATH

export PKG_CONFIG_PATH=.:\
/apps1/R/2.13.1/intel/lib64/pkgconfig:\
/apps1/libgtextutils/0.6/intel/lib/pkgconfig:\
/apps1/sparsehash/1.11/intel/lib/pkgconfig:\
$PKG_CONFIG_PATH

export CLASSPATH=.:\
/apps1/gatk/gatk-git/dist:\
/apps1/gatk/gatk-git/lib:\
/apps1/srma/srma-0.1.13:\
/apps1/haploview/4.2:\
/apps1/picard/picard-tools-1.50:\
/apps1/fastqc/fastqc-0.9.5:\
$CLASSPATH


best,
joe


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