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So it seems that the problem is that library is in PYTHONPATH. You can remove it just doing
$ unset PYTHONPATH
$ source /path/to/venv/bin/activate
Now regarding how it got there: probably you installed something (QGIS) that add it there. You can try to find it where it is defined and remove it
$ grep -r "PYTHONPATH" /etc
Also you should check in your .bashrc
and .profile
files in your home folder. Of course if you remove that entry from python path, the software that needs it may stop working…
Source:stackexchange.com