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Subject: Re: Octave/HDF5 library/header mismatch
To: cygwin AT cygwin DOT com
References: <93d9b19e-d234-b2db-65be-e65f828a9df6 AT photonicinnovations DOT com>
From: Marco Atzeri <marco DOT atzeri AT gmail DOT com>
Message-ID: <6d5164b3-75e6-e7c0-1095-3e61363bd9fa@gmail.com>
Date: Tue, 21 Jun 2016 11:03:56 +0200
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On 21/06/2016 06:20, Gavin King wrote:
> Hello
>
> 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
> workspace.
>
> 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

   export HDF5_DISABLE_VERSION_CHECK=1

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

   export HDF5_DISABLE_VERSION_CHECK=2

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

https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2016-June/009564.html


> yours
>
> Gavin King

Regards
Marco


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