> On Oct 13, 2016, at 11:32 AM, Ryan Schmidt <[email protected]> wrote: > >> >> On Oct 13, 2016, at 10:14 AM, Adam Dershowitz <[email protected]> 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 >> continues. >> 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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