danpos2 error messages

Hello everybody,

i try to run danpos2, but only get error messages i cannot solve on my own.

$ danpos.py
cannot find system Renviron
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error in identical(env, as.environment(i)) : 
  2 arguments passed to .Internal(identical) which requires 7

  warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
  File "/bin/danpos.py", line 6, in <module>
    from functions import danpos
  File "/bin/functions.py", line 4, in <module>
    from wigs import Wigs
  File "/bin/wigs.py", line 3, in <module>
    from wig import Wig
  File "/bin/wig.py", line 4, in <module>
    from rpy2.robjects import r,FloatVector
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 19, in <module>
    from rpy2.robjects.robject import RObjectMixin, RObject
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 58, in <module>
    class RObjectMixin(object):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 71, in RObjectMixin
    __show = rpy2.rinterface.baseenv.get("show")
LookupError: 'show' not found

I tried to remove rpy2 and reinstall it again, but installing does not work at all due to some compilation problem: i asked for help in another post:

https://stackoverflow.com/questions/44331415/pip-install-rpy2-does-not-work-and-produces-error-message-concening-compilation

I though the error messages might mean i need to install wigs or functions or rpy2, but I'm not really into python and 'pip install wigs' resulted in the announcement that there is nothing like a wigs package. I'd be happy if someone could please tell me how i can handle these error messages. Do i have to install packages or may it be a wrong version of a program? I use Python 2.7.8 Thanks a lot

danpos2 python rpy2 unix mac

• 3,751 views • link

written 9.2 years ago by ChIP-Tease •

At least i found out that all these errors occur because rpy2 is missing. But i still don't know how to fix this.

• 0 views • link

written 9.2 years ago by ChIP-Tease •

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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written 9.2 years ago by GenoMax

OK, i could fix the rpy2 problem, now other problems occur.

Line 186 in __init__.py is 

185 def consoleWarn(x):
186    warnings.warn(x, RRuntimeWarning)
187 set_writeconsole_warnerror(consoleWarn)


$ danpos.py

    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Warnmeldung:

      warnings.warn(x, RRuntimeWarning)
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: 
In local({ :
      warnings.warn(x, RRuntimeWarning)
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning:  
not fitting Bytecode Versions; use eval

      warnings.warn(x, RRuntimeWarning)
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: 
At start - 
      warnings.warn(x, RRuntimeWarning)
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: There were 13 warnings (show with warnings())
      warnings.warn(x, RRuntimeWarning)
    /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: 

      warnings.warn(x, RRuntimeWarning)
    Traceback (most recent call last):
      File "/Volumes/AlexEverything/1_Alex_alles_SD/Bioanalytics/2_NGS_course/bin/danpos.py", line 6, in <module>
        from functions import danpos
      File "/Volumes/AlexEverything/1_Alex_alles_SD/Bioanalytics/2_NGS_course/bin/functions.py", line 4, in <module>
        from wigs import Wigs
      File "/Volumes/AlexEverything/1_Alex_alles_SD/Bioanalytics/2_NGS_course/bin/wigs.py", line 3, in <module>
        from wig import Wig
      File "/Volumes/AlexEverything/1_Alex_alles_SD/Bioanalytics/2_NGS_course/bin/wig.py", line 4, in <module>
        from rpy2.robjects import r,FloatVector
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 19, in <module>
        from rpy2.robjects.robject import RObjectMixin, RObject
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 58, in <module>
        class RObjectMixin(object):
      File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/rpy2/robjects/robject.py", line 71, in RObjectMixin
        __show = rpy2.rinterface.baseenv.get("show")

• 0 views • link

updated 9.2 years ago by WouterDeCoster

• written 9.2 years ago by ChIP-Tease •

1 answer

How did you install rpy2? I've found the most convenient method is to use anaconda python and use conda to install R and rpy2.

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written 9.2 years ago by WouterDeCoster

Before I used $pip install rpy2.

Thanks a lot for your hint!!! Now I installed anaconda2 for the command line, used $conda install rpy2, which installed rpy2 and i guess dependencies and now danpos works. I didn't even had to change anything about R. Thanks a lot again :)

• 0 views • link

written 9.2 years ago by ChIP-Tease •

I have moved my comment to an answer so it can get accepted.

• 0 views • link

written 9.2 years ago by WouterDeCoster