Control: found -1 2.4.0+dfsg-5 Nope, that didn't work. Wrong version. Use
-Breaks: libbamtools-dev (<< 2.4.0-4) -Replaces: libbamtools-dev (<< 2.4.0-4) +Breaks: libbamtools-dev (<< 2.4.0+dfsg-4) +Replaces: libbamtools-dev (<< 2.4.0+dfsg-4) Andreas PS: the git repository doesn't have -5, yet.