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budaria

Member

Registered: 2018-06-28

Posts: 11

[SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

Hello everyone,
I recently moved here from debian.

tl:dr; How to fix packages messed/mixed with pacman and sudo pip?

Story:
So before installing packages with pip, I searched google to find out if pip or sudo pip should be used.
From the answers that I found, It seemed that sudo just installed systemwide packages  and it seemed ok, nobody mentioned that it could conflict with python packages installed using package manager.

I was recently getting error:

Exception:
Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/pip/_internal/basecommand.py", line 228, in main
    status = self.run(options, args)
  File "/usr/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 291, in run
    resolver.resolve(requirement_set)
  File "/usr/lib/python3.6/site-packages/pip/_internal/resolve.py", line 103, in resolve
    self._resolve_one(requirement_set, req)
  File "/usr/lib/python3.6/site-packages/pip/_internal/resolve.py", line 257, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "/usr/lib/python3.6/site-packages/pip/_internal/resolve.py", line 200, in _get_abstract_dist_for
    skip_reason = self._check_skip_installed(req)
  File "/usr/lib/python3.6/site-packages/pip/_internal/resolve.py", line 171, in _check_skip_installed
    self.finder.find_requirement(req_to_install, upgrade=True)
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 484, in find_requirement
    all_candidates = self.find_all_candidates(req.name)
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 442, in find_all_candidates
    for page in self._get_pages(url_locations, project_name):
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 587, in _get_pages
    page = self._get_page(location)
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 705, in _get_page
    return HTMLPage.get_page(link, session=self.session)
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 833, in get_page
    inst = cls(resp.content, resp.url, resp.headers)
  File "/usr/lib/python3.6/site-packages/pip/_internal/index.py", line 753, in __init__
    namespaceHTMLElements=False,
TypeError: parse() got an unexpected keyword argument 'transport_encoding'

I got this error on every pip install/upgrade command.
The recommendation was to update htmllib. pip install --upgrade htm So it was either systemwide package or pip package version issue.

I started to uninstall python packages manually both using pacman and then reinstalling some, so it is really messed up right now.
tl:dr; How to fix packages messed/mixed with pacman and sudo pip?

next time I will use pip without sudo )
Thanks

Last edited by budaria (2018-06-28 17:02:43)

budaria

Member

Registered: 2018-06-28

Posts: 11

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

So, I uninstalled python and  pip with all its dependencies using pacman -Rsn ( I had to manually type in pacman -Rsn for  all those packages that depended on python itself).

I manually removed /usr/lib/python3.6  and python2.7

I think I should also remove any python packages installed in home directory if there are any.
But could not find one. I think they should be in ~/.local/bin but there is only directory "share" there.
Will try again.

After I'm done with all that I will reinstall python and packages that I need.
This time using pip without sudo.

That should work, right?

I think it's working, editing post as solved.

Last edited by budaria (2018-06-28 17:03:18)

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

BTW note that there will be nothing in ~/.local/bin if you never ran pip install --user.

Another fix, would be to:

1) use the "lostfiles" package to find files which are not owned by any package, and clean up things which were not supposed to be installed to /
2) use pacman -Qkk to check the integrity of installed packages. Any packages that contain non-backup files which are modified from the packaged versions, might be messed up (there are very few reasons for this to be happening).
3) add the following to ~/.config/pip/pip.conf:

[install]
user = yes

Last edited by eschwartz (2018-06-28 18:43:52)

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Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

budaria

Member

Registered: 2018-06-28

Posts: 11

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

BTW note that there will be nothing in ~/.local/bin if you never ran pip install --user.

Another fix, would be to:

1) use the "lostfiles" package to find files which are not owned by any package, and clean up things which were not supposed to be installed to /
2) use pacman -Qkk to check the integrity of installed packages. Any packages that contain non-backup files which are modified from the packaged versions, might be messed up (there are very few reasons for this to be happening).
3) add the following to ~/.config/pip/pip.conf:

[install]
user = yes

Hello, thank you.
Although pip became usable after what I did I ran pacman -Qkk as you suggested and there are missing files and directories:
https://i.imgur.com/7iO9YlQ.png
Should I just reinstall those?

and what does adding

[install]
user = yes

do? Does that mean --user option will be used automatically and I won't have to set it every time? I am sorry, I tried searching but could not find.
Thank you.

Mod Edit - Replaced oversized image with link.
Don't paste images of text, post the actual text.
CoC - Pasting pictures and code

Last edited by Slithery (2018-06-29 14:39:05)

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

Yes, you should reinstall them, and yes, adding that to pip.conf will set the default action for pip.

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Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

budaria

Member

Registered: 2018-06-28

Posts: 11

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

Thank you!

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: [SOLVED] Fixing dependency conflicts after mixing sudo pip and pacman

Well, specifically the pip configuration is documented here, but they don't spell out each key: https://pip.pypa.io/en/stable/user_guide/#config-file

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Managing AUR repos The Right Way -- aurpublish (now a standalone tool)