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

[Peter Cock]

On Fri, Apr 18, 2014 at 7:40 PM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
> And at last of this forward I'm posting the build and tests logs (more a
> dump than a log)  for those who want peek into it.
> As you'll see the only consistent error was the TogoWS' XHTML error.
>
> Cheers,
> Manlio

Thanks Manlio,

Following the discussion here, I've looked at your Python 3.4 test
log in more detail - and sadly it looks like none of the C code
extensions are also not working (but they are for Python 2.7):

running test
test_Ace ... ok
...
test_Cluster ... skipping. If you want to use Bio.Cluster, install
NumPy first and then reinstall Biopython
...
test_KDTree ... skipping. C module in Bio.KDTree not compiled
...
test_PDB_KDTree ... skipping. C module in Bio.KDTree not compiled
...
test_pairwise2 ... ok
...
test_trie ... skipping. Could not import Bio.trie, check C code was compiled.


Note that test_pairwise2 is probably testing the pure Python
fallback here (assuming its C code also didn't get used).

My hunch in the absence of compilation errors, is something is
amiss with Python 3.4 finding the compiled modules when we
run the tests.

Can you try installing Biopython under Python 3.4, and trying
to import any of the C code modules? e.g.

[Mac] $ python3.4 -c "from Bio import trie; print(trie.__file__)"
/Users/pjcock/lib/python3.4/site-packages/Bio/trie.so

[Linux] $ python3.4 -c "from Bio import trie; print(trie.__file__)"
/home_local/buildslave/lib/python3.4/site-packages/Bio/trie.cpython-34m.so

[32 bit Windows] > c:\python34\python -c "from Bio import trie;
print(trie.__file__)"
c:\python34\lib\site-packages\Bio\trie.pyd

Thanks,

Peter

[*] available on the archive here,
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011265.html