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

[Manlio Calvi]

> test_Cluster ... skipping. If you want to use Bio.Cluster, install NumPy first and then reinstall Biopython

And that's strange, Numpy IS installed in my case and usable by other
scripts... I tried to reinstall and rebuild, all seems the same as
before.

Apart from Numpy, seems the .pyd file is there but isn't importable by
python as module as it raise an "ImportError" kind of error.

This is the dump:
####################
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: cannot import name 'trie'
####################

Now, seems strange to me that File<string> thing

Manlio


On Mon, Apr 21, 2014 at 4:59 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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