Hi! There are *two* problems with the upgrade of hdf5 from Squeeze to Wheezy that are a consequence of the problem of the fix for #566541. One of then, reported in (#667599, #667526), can be solved easily as explained by marga at http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667599#62 and others have hinted before. The second problem is related with this one and more complicated to solve. I haved filed the bug report #699155 for this.
About this problem, in short, if you have installed the openmpi version, the upgrade will install you the serial implementation, and remove the openmpi implementation. E.g. minimal installation of squeeze where libhdf5-openmpi-1.8.4 and hdf5-tools are installed: ii hdf5-tools 1.8.4-patch1-2 Hierarchical Data Format 5 (HDF5) - Runtime tools ii libhdf5-openmpi-1.8.4 1.8.4-patch1-2 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version ii libhdf5-serial-1.8.4 1.8.4-patch1-2 Hierarchical Data Format 5 (HDF5) - runtime files - serial version ii r-cran-hdf5 1.6.9-2+b1 GNU R package interfacing the NCSA HDF5 library If we update this system to Wheezy, you'll get: # apt-get -u dist-upgrade Reading package lists... Done Building dependency tree Reading state information... Done Calculating upgrade... Done The following packages will be REMOVED: console-terminus defoma libept1 libhdf5-openmpi-1.8.4 libpango1.0-common libperl5.10 portmap x-ttcidfont-conf The following NEW packages will be installed: [...] libhdf5-7 [...] hdf5-tools [...] 368 upgraded, 174 newly installed, 8 to remove and 0 not upgraded. Need to get 252 MB of archives. After this operation, 302 MB of additional disk space will be used. Do you want to continue [Y/n]? The openmpi version is upgraded with the serial version instead of being replaced with libhdf5-openmpi-7. In the case of dolfin-dev (#667599) in Squeeze, the package has the following dependency chain to hdf5 (as somebody else has analyzed already in the bug report): dolfin-dev -> libdolfin1.0-dev -> libslepc3.0.0-dev -> libslepc3.0.0 -> libhdf5-openmpi-1.8.4 and when upgraded, we have the reported problem. In wheezy, libslepc3.2 depends explicitiy on the openmpi version only. This means if we install libslepc3.0.0 in wheezy we must switch all our system to use the openmpi library. For simgear-dev (#667526), the chain dependency in Squeeze is: simgear-dev -> simgear1.9.1 -> libopenscenegraph65 -> libgdal1-1.6.0 -> libhdf5-serial-1.8.4 | libhdf5-1.8.4 Where libhdf5-1.8.4 could be provided by libhdf5-openmpi-1.8.4 and we have the same problem that with dolfin-dev. Although in this case the dependency can be satisfied both by the serial and the openmpi packages in Wheezy. This is wrong because both libraries provided different ABIs as reported in bug #699155 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org