Comment 3 for bug 305080

The latest version of the bioinformatics template from http://www.oxfordjournals.org/our_journals/bioinformatics/for_authors/submission_online.html does not require mathtime anymore (the lines are commented out).
So, just use the latest version of "upstream" when writing your bioinformatics documents and everything's fine.

I guess the original bug is somewhat solved (at least the part dealing with mathtime), as the bioinformatics template does not require the template anymore.

I tested to compile the test document provided (as in "I tried to reproduce the bug with the latest version of the template and its test document) and it worked.

So it is working "out of the box" again, if you use the latest bioinformatics template. So this problem is solved.
Still other documents using mathtime.sty need to be updated, but if I get the Debian bug report right, there are licensing issues with it and therefore upstream (texlive) decided not to include it anymore (or has never included it, just a workaround, I'm not really sure. However, now it does not work anymore and they broke it by intend). So /this/ problem is a wontfix, just fix your documents (hints in /usr/share/doc/texlive-doc/fonts/belleek/ and the debian bug).