Bug#1140677: med-fichier: FTBFS against HDF5 2.1.0

[Tobias Frost]

Control: tags -1 patch

Hi Gilles,

I was looking into this yesterday/today
I've tracked down the failures and prepared three
patches:

  * fix the Python bindings for current SWIG/Python versions to avoid an
    early FTBFS
  * relax the HDF5 version compatibility check, this will fix some
  * explicitly close the MED file in Test_MEDnStructElement, avoiding the
    HDF5 library shutdown error with HDF5 2.1.0 (manifesting as the
    infinite loop you've described below. (a quick $searchengine check
    seems that this might be a bug in HDF5.)

With these patches applied, the test suite completes successfully.

I've uploaded the packages for a testbuild to
https://debusine.debian.net/debian/developers/work-request/1090706
(ignore the FreeCAD autopkgtest failure, that's a bad newly added test)

I've also locally updated the package to upstream version 4.1.1, which is
available and can be provided as part of the update.

As the package is currently under RFA, how would you like me to proceed?
I can certainly add my name to Uploaders to share the load, but I have
no experience with HDF5 ecosystem...

I'm attaching the (three) patches as a diff to the current pacakge in
the archives.

-- 
Cheers,
tobi

On Wed, 24 Jun 2026 15:02:55 +0200 Gilles Filippini <pini at debian.org>
wrote:
> Source: med-fichier
> Version: 4.1.0+repack-10
> Severity: important
> Tags: ftbfs
> X-Debbugs-Cc: tobi at debian.org
> 
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
> 
> Hi,
> 
> During a test rebuild of HDF5's reverse dependcies against HDF5 2.1.0
> currently in experimental, med-fichier FTBFS with 2 failing tests.
> 
> Patching src/ci/MEDfileCompatibility.c to relax the HDF5 version
check
> works, but then another test fails more badly in tests/unittests/c:
> 
> FAIL: Test_MEDnStructElement_Rd.sh
> 
> The output from this failing test is:
> 
> ../../../../tests/unittests/c/Test_MEDnStructElement.c [48] :
_nstructelement = 2
> HDF5: infinite loop closing library
>      
L,T_top,F,P,P,FD,VL,VL,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,F
L,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,
FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,F
L,FL,FL,FL,FL,FL,FL,FL
> Aborted
> 
> Best,
> _g.
> 
> - -- System Information:
> Debian Release: 12.0
> Architecture: amd64 (x86_64)
> 
> Kernel: Linux 6.1.0-44-amd64 (SMP w/12 CPU threads; PREEMPT)
> Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
> Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8),
LANGUAGE not set
> Shell: /bin/sh linked to /usr/bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
> 
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> 
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> 
> 
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