It isn't ram space. I downloaded and installed the two libraries, messed with them to get them to compile with V1.0.1, and then ran your test which fails as expected.
I fiddled with the charlieplexing library until I found that it is failing when it calls SetBrightness(). This requires that Timer2 cause an interrupt before the function can proceed and so it appears that Timer2 isn't interrupting.
It also crashes even if the Wire.begin() is removed so it isn't a conflict with the DS3231 library which as far as I can tell doesn't use anything other than the I2C Wire library.
If I have time I'll try to dig deeper into this but I'm not familiar with the bit-banging of hardware registers that is used in the charlieplexing library.
Pete