In general, see the patchfile(s) in this directory

CDFFIleData.cpp.pacth
  Issue: long CDF reference string
  Fix: change the number 65000 to 400000 in lines 723, 724

There may be issues in that GCC 4.3.1+ has stricter include
statements: our old notes tells us to #include <stdlib.h> but
Affy seems to use <cstdlib>, we'll see if it works.


- use of atoi()
 in fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp
 requires #include <stdlib.h>

- use of wcstombs and mbstowcs
 in fusion_sdk/calvin_files/utils/src/StringUtils.cpp
 requires #include <stdlib.h>

- use of EXIT_FAILURE and EXIT_SUCCESS
 in fusion_sdk/file/BPMAPFileData.cpp
 requires #include <stdlib.h>

gcc/g++ 4.7:
More specific about includes. See gcc-4.7.cpp-patch.