I tried to compile afni using cygwin and got this output.
Steps
1) downloaded afni_src.tgz
2) followed the commands in website
make totality_exe
( cd niml/ ; make all 'CC=gcc -O2 -ffast-math -DCYGWIN -DNO_GAMMA -DHAVE_XDBE -UUSE_TRACING -DDONT_USE_MCW_MALLOC' ; /bin/mv -f *.o .. ; )
make[1]: Entering directory `/home/Surya/afni/afni_src/niml'
gcc -O2 -ffast-math -DCYGWIN -DNO_GAMMA -DHAVE_XDBE -UUSE_TRACING -DDONT_USE_MCW_MALLOC -c niml_b64.c
make[1]: *** [niml_b64.o] Error 255
make[1]: Leaving directory `/home/Surya/afni/afni_src/niml'
/bin/mv: cannot stat `*.o': No such file or directory
make: *** [niml_b64.o] Error
If it makes any sense let me know what I can do next. I do recognize that AFNI is not compiled for cygwin anymore. However, help in this case is appreicated.
Partha