Hi Andreas,
I managed to reproduce conditions when that strange message with pdb2pqr appears and when not:
It appears if I download, build, and call tests.
It doesn't appear if I download, *call quilt push -a*, build, call tests.
It also appears if I build project at first time, then *call quilt push -a*, and then build again.
This happens because of rules defined in debian/rules, and pMC_mult_wrap.cpp and *.saved files in pdb2pka folder.
How can be solved manually?
after call quilt push -a, cd to pdb2pka, when remove *.saved files and run command
swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i
The same command as in `override_dh_auto_configure` in debian/rules. When I noticed that, I run build in verbose mode.
Scons also builds all .cpp files, so, when it is run after swig regenerates pMC_mult_wrap.cpp, it uses version of that file which correspond to unpatched sources, Because in any previous run of `override_dh_auto_clean` it is reset to version which is stored in .saved. That's why I think there should be different order of commands, and this should fix that problem. At least I tried to reproduce, it doesn't appear any more. Please check my recent commit, and tell me if the error still appears.
There is also 1 problem with this package - in last test it can't load apbs package, even if it is installed. pdb2pqr doesn't fail, still some functionality which involves apbs call, is not available. For the moment I worked on that package I decided to postpone it and to fix later. Now I'll try to install apbs from sources and check where the problem is - if you don't mind.