Is it easier to understand the problem now, Grant?
Much! Thank you, Spider, I really appreciate it.
On a related note, that's not the only way that our handling of binary tbz2 packages is broken. Many of our ebuilds check to see exactly which version of a dependency is installed, and that invariably leads to binary packages being broken. For example, most python packages install stuff into /usr/lib/pythonX.Y/site-packages, with the ebuild detecting what X and Y should be. The binary, however, uses whichever values of X and Y were detected when the package was built, which may well be different than the values on the target machine. Of course, this problem is far wider than just python packages. Every ebuild that uses the has_version or a related function is probably broken in this sense.
My guess is that the problem I just raised could be solved by adding a portage function that runs at install-time and can either relocate files or just cause the emerge to fail with a warning, whereas the general linking issue is going to require a great deal more thought.
Best, g2boojum
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