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Re: Octave/HDF5 library/header mismatch

On 21/06/2016 06:20, Gavin King wrote:

My apologies if this is a bit verbose, or if the terminology is a bit
wrong; I know enough to get myself into trouble but not enough to
communicate problems well.

Hi Gavin,
nice to hear you.

After updating cygwin, a working script failed, causing octave to exit
(with an error code 6).

A minimal example is attached; it opens octave, creates a simple vector
of values, and tries to save the workspace to disc. The error message is
at the end.

It appears there is a mismatch between the compiled octave version and
the most recent version of the HDF5 headers.

The current version of the package octave is 4.0.1-1. Reverting it to
the previous version makes no difference.

Reverting the package libhdf5_10 from the current version 1.8.17-1 to
the previous version 1.8.16-1 means that octave 4.0.1-1 can save the

So: workaround: revert libhdf5_10 to 1.8.16-1. Presumably, the current
version of octave was compiled at an inopportune point; I don't think
this is something that I can remedy myself, is it?

the official workaround is mentioned on the warning message

"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"

so if you use, before running octave


you will still see the warning but the action will be completed


will suppress also the warning.

I think this is the correct place to report this to; it isn't a problem
per se with the individual programs, but with the way they're packed
together. I think. Do correct me if I am wrong; I'm a bit new to this
whole business.

It is the right place.
This problem is clearly a hdf5 upstream problem and a questionable
design choice.

I am following with them


Gavin King


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