Right now, Portage can't handle overwriting a symlink with a directory, even if it knows that the package installed said symlink (no risk of overwriting something from the user then). PMS says: 1) "Ebuilds must not attempt to merge a directory on top of any existing file that is not either a directory or a symlink to a directory." [0] 2) "Ebuilds must not attempt to merge a regular file on top of any existing file that is not either a regular file or a symlink to a regular file." [1] The first bug I remember hitting this is android-studio (bug 815118) but I'm sure there's been some before that. I don't think there were any substantial objections to this idea in that bug, other than it not being an immediate solution for that package given it needed to be implemented & propagate to users (and the same is true for Squid now). [0] https://dev.gentoo.org/~ulm/pms/head/pms.html#x1-14000013.2 [1] https://dev.gentoo.org/~ulm/pms/head/pms.html#x1-14300013.3
To be clear: Portage currently will reject replacing a symlink to a directory with a directory and vice-versa, but it looks like it'd be valid for it to introspect whether the package owns both and do the replacement itself if so.
I also have hit this some times, I see also some ebuilds in the tree workarounding the problem by removing the directory at pkg_preinst phase :/
This also affects coreutils, which is probably more of a worry for everyone.
(In reply to Richard Gray from comment #3) > This also affects coreutils, which is probably more of a worry for everyone. I'm not sure how it does. We're not doing any replacements between symlinks and directories there.
I'm rather confused myself. I'll post more detail when I'm (more-or-less) up and running. I'm in the middle of a rebuild right now. Since everything seems to be converging on /usr/bin/ these days, I'll probably try removing the symlinks temporarily just to appease portage and have in intact installation tree.
I suggest filing a bug (or perhaps better, going on IRC to #gentoo) and showing full output. Sounds like possibly botched merge-usr conversion.