[Biopython-dev] Compiling Biopython on 64 bit Windows, was: Volunteer buildslave machines?

[Manlio Calvi]

OK test on WinPython concluded. Analyzing it we have, the  expected
TogoWS problem,
a skipped test for a non-compiled C module, two tests really but
dependant from the same uncompiled module (
###################################
test_KDTree ... skipping. C module in Bio.KDTree not compiled
###################################

and this errors:

======================================================================
ERROR: test_unicode_exception (test_Phylo.IOTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File ".\test_Phylo.py", line 57, in test_unicode_exception
    tree = Phylo.read(EX_NEWICK_BOM, 'newick')
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Bio\Phylo\_io.py",
line 65, in read
    tree = next(tree_gen)
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Bio\Phylo\_io.py",
line 53, in parse
    for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Bio\Phylo\NewickIO.py",
line 107, in parse
    for line in self.handle:
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\encodings\cp1252.py",
line 23, in decode
    return codecs.charmap_decode(input,self.errors,decoding_table)[0]
UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position
15: character maps to <undefined>

======================================================================
ERROR: test_write_0 (test_Phylo_CDAO.WriterTests)
Write and re-parse the phylogenies in test.cdao.
----------------------------------------------------------------------
Traceback (most recent call last):
  File ".\test_Phylo_CDAO.py", line 62, in test_write
    CDAOIO.write([t1], outfile)
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Bio\Phylo\CDAOIO.py",
line 74, in write
    return Writer(trees).write(handle, plain=plain, **kwargs)
  File "C:\Users\CasuallyChaotic\Desktop\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Bio\Phylo\CDAOIO.py",
line 268, in write
    handle.write('@prefix %s: <%s> .\n' % (k, v))
TypeError: 'str' does not support the buffer interface

#################################################


The test output for CDAO reports a series of slightly messages (more
than an hundred) that looks like this:
file://C:\WinPython3.3\3.3 - Biopython
test\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\biopython\Tests\CDAO\test.cdao/tree0000001#node0000001
does not look like a valid URI, trying to serialize this will break.

Phylo.py related files was a recent commit, right?

Manlio



On Mon, Apr 21, 2014 at 7:02 PM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
> I'm running the tests against a WinPython x64 3.3.3.3 at the moment
> (so a non-Python.org distro) and will see if that happens there too,
> I'm planning to install a native one(if the time permits).
>
> Manlio
>
> On Mon, Apr 21, 2014 at 6:33 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Mon, Apr 21, 2014 at 5:25 PM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
>>> Works as expected because I have Numpy modules running in other
>>> scripts (dumps the path to __init__.py)
>>>
>>> In C:\Python34\Lib\site-packages\Bio the non-py files are two:
>>> cpairwise2.pyd
>>> trie.pyd
>>>
>>> The same are in the folder I used to build them, and by the extension
>>> should be callable/importable.
>>> I tried to import cpairwise2 but (don't) work the same way, same error
>>> raised as before.
>>>
>>
>> So, if you've done an install & can't import the C modules, that
>> tells me this isn't a simply problem in our test harness (run_tests.py
>> does some magic with the Python path to try to test using the just
>> built files rather than any installed files).
>>
>> This is a deeper problem with building/installing under Python 3.4
>> on your setup. I have for the moment run out of ideas :(
>>
>> (Other than trying Python 3.3 which may behave differently - and
>> will be useful anyway for checking the other test failures and if they
>> are in part due to the new Python version).
>>
>> Thanks,
>>
>> Peter