rpy2 import problems

[jcrow...@gmail.com]

Hi all,

I am just running the DaPars suite and the first step works perfectly.
When I try to run the DaPars_main.py script I keep getting conflicts with the import of the rpy2 libraries:

### Direct output from running $python DaPars_main.py
Traceback (most recent call last):
File "DaPars_main.py", line 11, in <module>
from rpy2.robjects.packages import importr
File "/user/leuven/307/vsc30711/.local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 15, in <module>
import rpy2.rinterface as rinterface
File "/user/leuven/307/vsc30711/.local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py", line 101, in <module>
from rpy2.rinterface._rinterface import *
ImportError: libR.so: cannot open shared object file: No such file or directory

I have installed rpy2 using the
$easy_install -user rpy2
and it runs fine, when I try to import rpy2 in python this works fine too (no conflicts)
because I am not a Root/Admin on the server.

Any help in additional installations to get past this would be great.

Thanks in advance,
Jonathan

[jcrow...@gmail.com]

I have figured out the problem.
If your R library is not installed correctly it does not locate the libR.so file and hence rpy2 has a conflict.
It is all resoved.

On an additional note beware if you are using deep coverage RNAseq data as genomecoveragebed will output any counts larger than 1,000,000 as 1e+06 whihc will also conflict with the software.
Maybe this would be a good bugfix for DaPars.


cheers

[Zheng Xia]

Hi, 

    Thanks for the feedback. 

     

    For 1e+06 issue, we have fixed it in the latest version. 

Many thanks,

Zheng

[jto...@rupskee.com]

Jonathan - I'm having the same problem, but I don't understand your solution. How can I make sure that my R library is installed correctly?

Best,

John