RS4Auto_Type causes LookupError

Issue #301 resolved
Luca Beltrame
created an issue

"Minimal" example (requires the "graphite" package from Bioconductor)

from rpy2.robjects.packages import importr
from rpy2.robjects.methods import RS4Auto_Type

graphite = importr("graphite")

class PathwayList(six.with_metaclass(RS4Auto_Type)):
    __rpackagename__ = "graphite"

This causes

<ipython-input-10-35ad9a33f5e1> in <module>()
----> 1 class PathwayList(six.with_metaclass(RS4Auto_Type)):
      2     __rname__="PathwayList"
      3     __rpackagename__ = "graphite"

/usr/lib/python3.4/site-packages/ in __new__(cls, name, this_bases, d)
    776     class metaclass(meta):
    777         def __new__(cls, name, this_bases, d):
--> 778             return meta(name, bases, d)
    779     return type.__new__(metaclass, 'temporary_class', (), {})

/usr/lib64/python3.4/site-packages/rpy2/robjects/ in __new__(mcs, name, bases, cls_dict)
    202             # having the class we are considering somewhere in the signature
    203             # (the R/S4 systems allows multiple dispatch)
--> 204             for name, meth in zip(all_methods.do_slot("names"), all_methods):
    205                 # R/S4 is storing each method/signature as a string,
    206                 # with the argument type separated by the character '#'

LookupError: The object has no such attribute.

The object in question comes from all_generics and is actually Biobase. In this case all_methods is empty and thus triggers this error. I think Biobase got in there by "mistake" or the code should skip objects with no methods. Or is it more complex than my assessment?

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