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

[Daniel McDonald]

Hi Steve,

Thanks for following up. As I understand it, this is an issue with either
h5py or libhdf5. We have not modified the behavior of these libraries, and
are using them in a very basic manner; endianness is outside of our control
here. It is possible the issue is related to (
https://github.com/h5py/h5py/issues/428) which appears to still be open.

Best,
Daniel

On Mon, Jul 11, 2016 at 11:42 AM, Steve Langasek <vorlon at debian.org> wrote:

> 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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