I reinstalled everything, reset all my paths and my weird error went away.
Whoosh...like a ghost.
The errors I get now are all related to pickling attempts so I'll look
closer at this tomorrow. I'm getting 8 failures out of 24 tests.
On Tue, Sep 9, 2008 at 7:37 PM, C. Titus Brown <[EMAIL PROTECTED]> wrote:
>
> On Tue, Sep 09, 2008 at 01:14:29PM -0700, Rob Kirkpatrick wrote:
> -> AFAIK this is only on my machine. I'll do some cleanup and see if I can
> get
> -> things to go more smoothly. I only asked about the indentation because
> most
> -> of that code is pretty greek to me and I needed a starting point to
> -> understand the error. I'll look at it again with your explanation and
> see
> -> if can grok it a bit more.
>
> Hi, Rob,
>
> using
>
> % nosetests --with-doctest
>
> everything works for me with the latest version of pygr.
>
> cheers,
> --titus
>
> -> > > I've run into this error when trying to run some of Jenny's
> -> > > doctests. When I look in the code of sqlgraph.py", line 269 seems
> -> > > to be at the wrong indentation level. I get a new set of errors
> -> > > when I indent that line, so I'm not sure if this is part of my
> -> > > problem or not... Comments?
> -> >
> -> > Hi Rob,
> -> > what makes you think line 269 is mis-indented? It looks right to me;
> -> > __init__() must always bind its itemClass as a subclass, which is what
> -> > self.objclass() does... Note that if itemClass is None,
> -> > self.objclass() just uses self.itemClass (typically provided by the
> -> > class definition).
> -> >
> -> > more comments below...
> -> >
> -> > >
> -> > >
> -> > >
> **********************************************************************
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py",
> -> > > line 274, in ensembl.adaptor.ExonAdaptor
> -> > > Failed example:
> -> > > slice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1',
> -> > > end=100000, strand = -1)
> -> > > Exception raised:
> -> > > Traceback (most recent call last):
> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> -> > > python2.5/doctest.py", line 1212, in __run
> -> > > compileflags, 1) in test.globs
> -> > > File "<doctest ensembl.adaptor.ExonAdaptor[5]>", line 1, in
> -> > > <module>
> -> > > slice = coreDBAdaptor.fetch_slice_by_region('chromosome',
> -> > > '1', end=100000, strand = -1)
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> -> > > adaptor.py", line 688, in fetch_slice_by_region
> -> > > sr = self._get_seqregion()
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> -> > > adaptor.py", line 584, in _get_seqregion
> -> > > seqRegion = self._create_seqregion()
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> -> > > adaptor.py", line 565, in _create_seqregion
> -> > > dnaAdaptor = self.get_adaptor('dna')
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> -> > > adaptor.py", line 460, in get_adaptor
> -> > > tbAdaptor = adaptorClass(name, itemClass=rowClass,
> -> > > serverInfo=self.conn)
> -> > > File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/
> -> > > adaptor.py", line 214, in __init__
> -> > > sqlgraph.SQLTable.__init__(self, name,
> -> > > itemSliceClass=seqdb.SeqDBSlice, attrAlias=dict(seq='sequence'),
> -> > > **kwargs)
> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> -> > > sqlgraph.py", line 269, in __init__
> -> > > self.objclass(itemClass) # NEED TO SUBCLASS OUR ITEM CLASS
> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> -> > > sqlgraph.py", line 352, in objclass
> -> > > subclassArgs=dict(db=self)) # bind itemClass
> -> > > File "/Library/Frameworks/Python.framework/Versions/2.5/lib/
> -> > > python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/
> -> > > classutil.py", line 217, in get_bound_subclass
> -> > > subclass_init(**subclassArgs)
> -> > > TypeError: unbound method _init_subclass() must be called with
> -> > > shadowClass instance as first argument (got nothing instead)
> -> >
> -> > This error message seems to say that the itemClass has an
> -> > _init_subclass() attribute that is callable, but which has not been
> -> > "decorated" as a classmethod as it must be. For correct examples of
> -> > how to do this, see seqdb.FileDBSequence or sqlgraph.TupleO. I guess
> -> > I would need to scrutinize Jenny's rowClass code to verify if I'm
> -> > interpreting this right.
> -> >
> -> > I don't see how this error could pass a test suite; it will die
> -> > whenever it tries to construct an instance of this table class. Is
> -> > this only happening on your computer, or does Jenny get the same
> error?
> -> >
> -> > -- Chris
> -> >
> -> > >
> -> >
> ->
> -> ->
>
> --
> C. Titus Brown, [EMAIL PROTECTED]
>
> >
>
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