[Biopython-dev] test_Entrez.py fails on Linux?

Michiel de Hoon mjldehoon at yahoo.com
Fri Jun 20 12:14:30 UTC 2008

Hi Peter,

Thanks for letting me know.

It turned out that there were two problems with older Python versions (2.3 and 2.4).
One issue was not in Bio.Entrez but in the test script itself, using a feature that is only available in Python 2.5. This is now fixed in CVS.
The second issue is with Python 2.3: It does not copy data files to the build directory. Then, when you run "python run_tests.py test_Entrez.py" you will get many error messages about missing DTD files. If you run "python test_entrez.py" instead, the tests are done from the installed Biopython instead of the one in the build directory, and then no errors occur.
I guess the only way to solve this is to modify run_tests.py to skip test_Entrez if Python is version 2.3. Unless somebody else has a better suggestion, I will do that.


Peter <biopython at maubp.freeserve.co.uk> wrote: > Hi Michiel,
> I've just tried the unit tests on a clean checkout on Linux, and there
> is a problem with test_Entrez.py (shown below).  I'm pretty sure it
> was working for me on Mac OS X this afternoon, so this may be platform
> specific.  I haven't using Biopython on Windows recently so I don't
> know if that is working or not.

I've just checked, and on a clean CVS checkout under Mac OS 10.5
Leopard with python 2.5.2, test_Entrez.py passes.

A clean check out last night on 64bit Ubuntu Dapper Drake with python
2.4.3 failed.

So whatever is going wrong is probably OS specific or perhaps python
version specific.

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