cannot import edger from rpy2-bioconductor-extensions

Issue #288 wontfix
yardenkatz created an issue


I installed rpy2-bioconductor-extensions. When I try to import edger from bioc, I get this error:

>>> from bioc import edger
Error in as.environment(where) : no item called "None" on the search list
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/yarden/anaconda/lib/python2.7/site-packages/bioc/", line 69, in <module>
    class DeDGEList(vectors.Vector):
  File "/Users/yarden/anaconda/lib/python2.7/site-packages/rpy2/robjects/", line 154, in __new__
    cls_def = getclassdef(cls_rname, cls_rpackagename)
  File "/Users/yarden/anaconda/lib/python2.7/site-packages/rpy2/robjects/", line 80, in getclassdef
    StrSexpVector((cls_packagename, )))
rpy2.rinterface.RRuntimeError: Error in as.environment(where) : no item called "None" on the search list

I'm using this Python version on Mac OS X:

Python 2.7.8 |Anaconda 2.1.0 (x86_64)| (default, Aug 21 2014, 15:21:46) 
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin

Is this a known bug? I'm using the latest rpy2-bioconductor-extensions and rpy2-2.5.6. Thank you.

Comments (4)

  1. Laurent Gautier

    That's not an rpy2 bug. The bioconductor extension was a proof-of-concept using rpy2, but with bioconductor packages being moving targets the extension are quite possibly no longer working with it.

    The upside is that in the same time rpy2 has become even better and rolling out your own mapping of bioconductor packages is rather simple.

  2. Laurent Gautier

    Not an issue with rpy2 itself.

    However, start from the following:

    from rpy2.robjects.packages import importr
    edger = importr("edgeR")
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