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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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rpy2 exception rnaseqqc #109

Closed jscaber closed 4 years ago

jscaber commented 4 years ago

File "/***/***/***/cgat-developers-v2/cgat-flow/cgatpipelines/tasks/expression.py", line 69, in <module> from rpy2.rinterface import RRuntimeError ImportError: cannot import name 'RRuntimeError'

jscaber commented 4 years ago

RRutnime moved from rpy2.rinterface to rpy2.rinterface_lib.embedded Answer here: https://stackoverflow.com/questions/47306899/how-do-i-catch-an-rpy2-rinterface-rruntimeerror-in-python

jscaber commented 4 years ago

Hmm. Travis on the cluster runs a different (older) version of rpy2 that still supports the old import command, but not the new one. Have added exception handler, should hopefully work now.

Acribbs commented 4 years ago

Hi jakub, I think we had to pin the rpy2 version for travis testing but I could try when i have time to unpin it and see what the consequences for testing are. Whenever there are problems with this repo, they are usually rpy2 lol

jscaber commented 4 years ago

Hi, it's possible to deal with these using exception handling, so we could try. This pull has sucessfully fixed this particular issue.