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Tasklist

FS#60536 - [netcdf] Rebuild with HDF5 1.10.4

Attached to Project: Community Packages
Opened by Rich Li (richli) - Monday, 22 October 2018, 19:16 GMT
Last edited by Bruno Pagani (ArchangeGabriel) - Tuesday, 23 October 2018, 18:13 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Bruno Pagani (ArchangeGabriel)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:

netcdf 4.6.1-3 was built against HDF5 1.10.3, but now that HDF5 1.10.4 is packaged, netCDF tools such as ncdump abort with an 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 1.10.3, library is 1.10.4

----------------------------

Additional info:
* netcdf 4.6.1-3
* hdf5 1.10.4-1

Steps to reproduce:

Run "ncdump" on a netCDF file.
This task depends upon

Closed by  Bruno Pagani (ArchangeGabriel)
Tuesday, 23 October 2018, 18:13 GMT
Reason for closing:  Fixed
Additional comments about closing:  Package has been rebuilt, opened  FS#60567  as a follow-up of the underlying issue.
Comment by Eli Schwartz (eschwartz) - Tuesday, 23 October 2018, 16:25 GMT
So, the reason we sometimes get these bug reports is because hdf5 includes macros which call an abort for every single public function the library provides. Ouch.

I guess there's no choice but to do strange patches to hdf5, or rebuild the entire hdf5 ecosystem on every single niggling patchlevel release.

(I'm secretly voting for the strange patch. They're already using sonames properly, but checking patchlevel versions here which don't actually map to that: https://github.com/live-clones/hdf5/blob/47f30b474bdc498c20bd6d2a0ba7e8947ab389f0/src/H5.c#L758 )
Comment by Rich Li (richli) - Tuesday, 23 October 2018, 16:56 GMT
For comparison, debian uses a patch as you describe: the version check is relaxed a little so it doesn't compare the release number.

https://salsa.debian.org/debian-gis-team/hdf5/blob/master/debian/patches/relax-version-check.patch

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