他パッケージ上で導入されたpip等のパッケージ管理ツールをrootで操作するのはあまりオススメされない。
例えばGentoo上でのpip。
Gentoo Wiki上でも次のように書かれている。
Warning
Running pip as root is not advised. It can render important system tools like emerge useless.
「rootでpipを操作するのは推奨されない。emergeのような重要なシステムツールを役に立たなくする可能性がある」
それを忘れてうっかり pip install --upgrade pip した結果がこれだよ！
# emerge -uDNp @world
<snip>
* This package will overwrite one or more files that may belong to other
* packages (see list below). You can use a command such as `portageq
* owners / <filename>` to identify the installed package that owns a
* file. If portageq reports that only one package owns a file then do
* NOT file a bug report. A bug report is only useful if it identifies at
* least two or more packages that are known to install the same file(s).
* If a collision occurs and you can not explain where the file came from
* then you should simply ignore the collision since there is not enough
* information to determine if a real problem exists. Please do NOT file
* a bug report at https://bugs.gentoo.org/ unless you report exactly
* which two packages install the same file(s). See
* https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how
* to solve the problem. And once again, please do NOT file a bug report
* unless you have completely understood the above message.
virtualenvは良い文明。噛み締めつつ再構築しよう。