sci-biology/ncbi-tools++ automatically links against gnutls if present on the build host. This is expected to cause trouble if the software is subsequently used on machines lacking gnutls. From the package's configure script, it would seem this affects a whole lot of other functionality as well, e.g. boost.
Steps to Reproduce:
1. emerge ncbi-tools++
In the special case of building ncbi-tools++ on a Fedora 11 host, the build actually dies.
ncbi-tools++ merged and not linked against gnutls.
Adding something like $(use_with gnutls) to the configure invocation in the ebuild fixes the problem. I imagine the same strategy will work for the other dependencies as well.
ncbi-tools++ was removed from the tree it seems, so these bugs aren't relevant anymore.