I am using bzip2 in my project and git as the version control system.
I found that git will do CR/LF line ending conversion automatically and this will fail sample3.ref test in Windows system (if git is not properly setup).
I suggest to add a .gitattributes file to the bzip2 source code, to treat .ref as binary files .
References:
Git - gitattributes Documentation
A collection of useful .gitattributes templates (github.com)