I am trying to build R (tried 2.14.2 and 2.15) and rpy2 (2.2.6, python 2.7.1) on ubuntu (11.04, natty narwhal), to deploy it to a custom directory (in the following called /home/me/lib/R), since I do not have root access, but need a newer version than available on the server.
Details of build etc further down, but even when running the tests of rpy2, I always get the following error:
/home/me/lib/pythonlib/lib/python/rpy2/rinterface/__init__.py in <module>()
---> 87 from rpy2.rinterface._rinterface import *
ImportError: libRblas.so: cannot open shared object file: No such file or directory
WARNING: Failure executing file: <experiments/arrangement/test_smacof_arrange.py>
I am sure I am calling the right rpy2 module (my custom built one) which has been built against custom built R version. To do this I am doing the following:
I first Build R-base on ubuntu
wget http://cran.r-project.org/bin/linux/ubuntu/natty/r-base_2.14.2.orig.tar.gz
# untar and go to directory
# enable-R-shblib flag is needed for rpy2 linking, enable-BLAS-shlib was included
# because I hoped to solve the problem, which doesnt change anything however
./configure --enable-R-shlib --enable-BLAS-shlib --prefix=/home/me/lib/R
make
make install
I then build rpy2 against this R build
wget http://pypi.python.org/packages/source/r/rpy2/rpy2-2.2.6.tar.gz
# untar and go to directory
# build rpy2, by providing the r-home-lib and r-home flags, and deploy to custom dir
python setup.py build --r-home /home/me/lib/R --r-home-lib /home/me/lib/R/lib64/R/lib install --home /home/me/lib/pythonlib
I also have adapted my pythonpath to find modules in /home/me/lib/pythonlib, so the problem isn't there. The python build returns the correct configuration (note that Rblas appears here!)
Configuration for R as a library:
include_dirs: ('/home/me/lib/R/lib64/R/include',)
libraries: ('R', 'Rblas', 'Rlapack')
library_dirs: ('/home/me/lib/R/lib64/R/lib',)
extra_link_args: ()
I have tried to track down the error, but to no end. /home/me/lib/R/lib64/R/lib contains libRblas.so, but there is one thing which seems strange however, which is that libRblas.so is not linked correctly from libR.so, but I am not sure wether this causes the error, nor do I know how to fix it.
>> ldd -d libR.so
linux-vdso.so.1 => (0x00007fffcec58000)
libRblas.so => not found
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fe63d21d000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe63cf97000)
...
Any help would be greatly appreciated!
For others running into this issue, I was able to solve it by making sure to add the R libraries to my library path in bashrc:
export LD_LIBRARY_PATH="R-install-location/lib65/R/lib:$LD_LIBRARY_PATH"