The error message seems to be clear.
Where do you expect the executable "libsvm-2.88\windows\svm-train.exe" to be? Relative to the current folder in the subfolder "libsvm-2.88\windows\"? Then prefer the absolute path name:
svmOutFile = fullfile(prefix, 'svmOut.dat');
exe = fullfile(cd, 'libsvm-2.88\windows\svm-train.exe');
command = [exe, ' -t 0 -c ', num2str(c), ' -v ', num2str(n), ' ', trainFile, ' > ', svmOutFile];
system(command)
I do not like eval.
Instead of relying on the current folder by using cd, better use absolute path names even to define the base folder.
