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I run the command (for i in $(grep -IURl --color --exclude={".pdf",".png",".jpg",".zip",".ppt",".DS_Store",".mat",".pyc"} --exclude-dir=".git" "^M" .); do echo $i; dos2unix -o $i; done) from the top of the repository to get rid of the "check for CRLF line endings" error. If the error persists then I am not sure what else to do.