* package dev-python/sphinx-1.1.3-r5 NOT merged
* Detected file collision(s):
* Searching all installed packages for file collisions...
* Press Ctrl-C to Stop
* None of the installed packages claim the file(s).
* Package 'dev-python/sphinx-1.1.3-r5' NOT merged due to file
* collisions. If necessary, refer to your elog messages for the whole
* content of the above message.
Presumably these files belong to sphinx but aren't known to portage; maybe in previous versions they were autogenerated after installation but now they are generated by the make file?
Yes, that's the case. It is a leftover junk from previous maintainer and there's basically no way we can avoid this. Even if we wanted to remove the files in pkg_preinst(), collision check is done earlier.
There's two things you can do:
1) remove the files by hand, then install sphinx.
If you didn't remove the files from PORTAGE_TEMPDIR, you can use 'ebuild /usr/portage/dev-python/sphinx/sphinx-1.1.3-r5.ebuild merge' to resume the install.
2) disable 'collision-protect' in favor of 'protect-owned'. The latter will only complain if files are owned by some package.
Yes, in the end I just removed the files. I just thought it was worth reporting this in case it could be fixed in the ebuild.