> On Oct 13, 2016, at 11:32 AM, Ryan Schmidt <ryandes...@macports.org> wrote:
>> On Oct 13, 2016, at 10:14 AM, Adam Dershowitz <de...@alum.mit.edu> wrote:
>> I just updated hdf5 and hdf5-18:
>> hdf5 1.10.0_1 < 1.10.0-patch1_0
>> hdf5-18 1.8.16_6 < 1.8.17_0
>> Now when I try to use pandas to open an HDF5 file I get this error:
>> Warning! ***HDF5 library version mismatched error***
>> The HDF5 header files used to compile this application do not match
>> the version used by the HDF5 library to which this application is linked.
>> Data corruption or segmentation faults may occur if the application
>> This can happen when an application was compiled by one version of HDF5 but
>> linked with a different version of static or shared HDF5 library.
>> You should recompile the application or check your shared library related
>> settings such as 'LD_LIBRARY_PATH'.
>> You can, at your own risk, disable this warning by setting the environment
>> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
>> Setting it to 2 or higher will suppress the warning messages totally.
>> Headers are 1.8.16, library is 1.8.17
> Sounds like whatever library generated that error (you mentioned py27-pandas
> and py27-tables but I don't know) is being possibly overzealous in its hdf5
> version checking. Sounds like we should increase the revision of whichever
> port is triggering this error, and add a comment to the hdf5 port to remind
> us to do that every time the version of hdf5 is increased.
> It looks to me like py27-tables is the one that depends on hdf5-18, so that's
> the one that probably needs to be rebuilt. py27-pandas only depends on
> py27-tables and other python modules.
>> I tried uninstalling and reinstalling pandas and py27-tables, but that
>> didn’t help.
> If you received a binary from our server, it would be a binary built with the
> old version of hdf5. We need to increase that port's revision to cause it to
> rebuild with the new version of hdf5.
> You can try rebuilding from source on your system to identify the problem.
> sudo port -ns upgrade --force py27-tables
> If that works, let us know so we can increase its revision.
Yes, forcing the rebuild of py27-tables seems to fix the problem.
Although, it was slightly more complicated because that rebuild complained that
py27-tables can’t be built with hdf5 active, so i had to force deactivate that,
then it built fine, and reactivated hdf5 after.
> Looking a little further, I see that the "HDF5 library version mismatched
> error" actually comes from the hdf5-18 (and hdf5) source code. This makes me
> think that *any* port that uses hdf5-18 (or hdf5) will encounter this
> problem, and they should all be revbumped any time the version of hdf5-18 (or
> hdf5) is increased. This is a pain and the developers of hdf5 should be
> contacted to explain this to them, so that they can weigh in on why they are
> inflicting this pain on us and what they can do to mitigate it in subsequent
> versions of their software.
>> So, I’m not sure where the bug actually is, what to do about it, or what
>> port to file a bug report against.
>> Any suggestions?
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