It is not recommended to operate package management tools such as pip installed on other packages as root. For example, pip on Gentoo. The Gentoo Wiki also says:
https://wiki.gentoo.org/wiki/Pip
Warning Running pip as root is not advised. It can render important system tools like emerge useless.
"It is not recommended to work with pip as root. It can render important system tools like emerge useless."
This is the result of forgetting it and inadvertently pip install --upgrade pip!
# 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 is a good civilization. Let's rebuild while biting.
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