That patch is out of date and will corrupt any binary files you have. It's better to use the program dos2unix, as it will skip binary files automatically:
find -type f -exec dos2unix {} \;
if for some reason you don't have dos2unix available, you can try this slower method:
find -type f -exec file {} \; | grep CRLF | awk 'BEGIN{FS=":"}{print $1}' | xargs perl -pi -e 's/\r\n?/\n/g'
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Re: MAME 0.149 Compile Error on OS X 10.8.4
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