[Bug 1034210] New: Application:Geo qgis compiled with HDF5 1.8.18
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 Bug ID: 1034210 Summary: Application:Geo qgis compiled with HDF5 1.8.18 Classification: openSUSE Product: openSUSE.org Version: unspecified Hardware: Other OS: Other Status: NEW Severity: Normal Priority: P5 - None Component: 3rd party software Assignee: opensuse-communityscreening@forge.provo.novell.com Reporter: dmitri.chubarov@gmail.com QA Contact: opensuse-communityscreening@forge.provo.novell.com Found By: --- Blocker: --- After upgrading QGIS to qgis-2.18.6-1.1 I get an error message when starting QGIS that says: 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'. 'HDF5_DISABLE_VERSION_CHECK' environment variable is set to 1, application will continue at your own risk. Headers are 1.8.18, library is 1.8.15 OpenSUSE Leap 42.1 provides HDF5 version 1.8.15. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 Dmitri Chubarov <dmitri.chubarov@gmail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |dmitri.chubarov@gmail.com -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c1 Martin Pluskal <mpluskal@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |bruno@ioda-net.ch, | |mpluskal@suse.com, | |nrochard@gmail.com --- Comment #1 from Martin Pluskal <mpluskal@suse.com> --- Works fine for me on 42.2 (well almost fine, qgis mentions missing python-pygments on start). I am not sure how this could happen as qgis for Leap 42.1 is build using same hdf5 as Leap contains, in fact I am not aware of any version of openSUSE/SLE which would contain 1.8.18 -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c2 --- Comment #2 from Bruno Friedmann <bruno@ioda-net.ch> --- Dimitri, it could be possible that you have HDF5 coming from another repository than oss or Application:Geo ? zypper se -si hdf5 should show from which repo it come. Try to use the one coming from Application:Geo and report here what's happening. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c3 --- Comment #3 from Bruno Friedmann <bruno@ioda-net.ch> --- @Martin is there any python2-pygment existing now under Leap 42.2 ? It can be cause by the singlespec introduction. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c4 --- Comment #4 from Dmitri Chubarov <dmitri.chubarov@gmail.com> --- I do not see anything suspicious zypper se -si hdf5 Loading repository data... Reading installed packages... S | Name | Type | Version | Arch | Repository --+-----------------+---------+--------------+--------+------------------- i | hdf5 | package | 1.8.15-3.9 | x86_64 | repo-leap/42.1-oss i | hdf5-devel | package | 1.8.15-3.9 | x86_64 | repo-leap/42.1-oss i | hdf5-devel-data | package | 1.8.15-3.9 | x86_64 | repo-leap/42.1-oss i | libhdf5-10 | package | 1.8.15-3.9 | x86_64 | repo-leap/42.1-oss i | libhdf5-100 | package | 1.10.0-43.2 | x86_64 | science-leap/42.1 i | libhdf5-8 | package | 1.8.13-2.1.9 | x86_64 | (System Packages) i | libhdf5-9 | package | 1.8.14-61.6 | x86_64 | (System Packages) i | libhdf5_hl10 | package | 1.8.15-3.9 | x86_64 | repo-leap/42.1-oss i | libhdf5_hl100 | package | 1.10.0-43.2 | x86_64 | science-leap/42.1 -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c5 Bruno Friedmann <bruno@ioda-net.ch> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution|--- |WORKSFORME --- Comment #5 from Bruno Friedmann <bruno@ioda-net.ch> ---
From build log available here https://build.opensuse.org/build/Application:Geo/openSUSE_Leap_42.1/x86_64/q... There's no 1.8.18 used only pure oss libhdf5-10-1.8.15-3.9
Not sure about the version you have installed from science repo. i | libhdf5-100 | package | 1.10.0-43.2 | x86_64 | science-leap/42.1 i | libhdf5_hl100 | package | 1.10.0-43.2 | x86_64 | science-leap/42.1 Which I suspect to provide the 1.8.18 And you can remove the 2 orphans i | libhdf5-8 | package | 1.8.13-2.1.9 | x86_64 | (System Packages) i | libhdf5-9 | package | 1.8.14-61.6 | x86_64 | (System Packages) I've been able to restest on 42.1 and 42.2, and tumbleweed and everything works. You should check you system especially the LD_LIBRARY_PATH to have 1.8.15 only available for all, and make the other optionnal. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=1034210 http://bugzilla.opensuse.org/show_bug.cgi?id=1034210#c6 --- Comment #6 from Dmitri Chubarov <dmitri.chubarov@gmail.com> --- The issue was caused by h5py. It was recently upgraded via pip. After h5py was uninstalled with pip uninstall h5py And the HDF5 libraries from science repo were uninstalled also zypper rm libhdf5_hl100 libhdf5-100 QGIS was able to start without an error. -- You are receiving this mail because: You are on the CC list for the bug.
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