Fix/fix werror

It seems like turning on `-Werror` caused some havoc on cdash: no other compilation than gcc 4.6 actually ran through. This patch fixes most warnings, I am not sure about this one though:

- `/.../HEAD/src/topp/PeptideIndexer.cpp:240:18: error: narrowing conversion of ‘-1’ from ‘int’ to ‘const unsigned int’ inside { } is ill-formed in C++11 [-Werror=narrowing]`

I hope that @cbielow could give some insight into that, specifically whether the -1 is really needed there and whether the compiler might be happy if we use a static_cast<unsigned>(-1). It seems from http://stackoverflow.com/questions/8578791/what-are-the-consequences-of-ignoring-narrowing-conversions-in-c0x that these conversions are illegal in C++11 so we need to do something about them anyways.