[Debian-med-packaging] Bug#820060: Re: Debian Bug#820060: python-biom-format: broken on big-endian architectures

[Steve Langasek]

Hi folks,

Please keep me on Cc:, the Debian BTS does not automatically cc: bug
submitters :)

> Andreas, my read of the bug report suggests that the issue across
> architectures is h5py or hdf5.  The access being made is to an attribute
> of an h5py object which happens within python and is a valid API
> operation; testing locally I'd expect a different KeyError to be thrown
> under normal operation.

> Looking closer at one of the failing tests (offending call linked below),
> you can see that this is on read of a hdf5 table that ships with the
> biom-format project.

> https://github.com/biocore/biom-format/blob/master/tests/test_table.py#L527-528

> The implication is that this is happening when reading a table that ships
> as part of the test code, suggesting that h5py or hdf5 are unable to
> interact with the file as expected.  My take is that the failure we're
> observing is a manifestation of a bug at a lower level.

So it sounds like your test data is written in a little-endian format, but
hdf5 on big-endian architectures is trying to read it in a big-endian
format.  Is it defined somewhere that hdf5 data should be in an
architecture-independent format (always little-endian)?

-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                    http://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
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