– I would suggest abandon attempts on compiling 3.2 – its have PyRosetta 1.1 and it very outdated.
– Regarding 3.3: from the output it looks like it missing header. Try to include core/io/silent/SilentFileData.hh in to protocols/jobdist/Jobs.hh
Also, it might be easier to use our binaries, just re-compile Python2.6 on your system and try to use run PyRosetta with it.