How can I fix apt error "W: Target Packages ... is configured multiple times"?

Recent, up-to-date solution

I wrote a Python script to automate this task. You can find the most recent version here.

Installation:

1. Install the prerequisites:

   sudo apt install python3-apt
   

2. Download the PYZ bundle (aptsources-cleanup.pyz) from the latest release.

3. Mark the PYZ bundle as executable:

   chmod a+x aptsources-cleanup.pyz
   

Usage:

1. From the download location of the PYZ bundle (see step 2 above) run:

   sudo ./aptsources-cleanup.pyz
   

2. Follow the instructions appearing on the screen.

If you wish to report an issue, leave a comment, or fork the source code, please do so on GitHub.

Historical, outdated solution

This is an older, shorter and simpler version more suitable to inline quotation:

#!/usr/bin/python3
"""
Detects and interactively deactivates duplicate Apt source entries.

Usage: sudo python3 apt-remove-duplicate-source-entries.py
"""

from __future__ import print_function
import aptsources.sourceslist

EMPTY_COMPONENT_LIST = (None,)

def get_duplicates(sourceslist):
    """
    Detects and returns duplicate Apt source entries.
    """

    sentry_map = dict()
    duplicates = list()
    for se in sourceslist.list:
        if not se.invalid and not se.disabled:
            for c in (se.comps or EMPTY_COMPONENT_LIST):
                key = (se.type, se.uri, se.dist, c)
                previous_se = sentry_map.setdefault(key, se)
                if previous_se is not se:
                    duplicates.append((se, previous_se))
                    break

    return duplicates


if __name__ == '__main__':
    try:
        input = raw_input
    except NameError:
        pass

    sourceslist = aptsources.sourceslist.SourcesList(False)
    duplicates = get_duplicates(sourceslist)

    if duplicates:
        for dupe, orig in duplicates:
            print(
                'Overlapping source entries:\n'
                '  1. {0}: {1}\n'
                '  2. {2}: {3}\n'
                'I disabled the latter entry.'.format(
                    orig.file, orig, dupe.file, dupe),
                end='\n\n')
            dupe.disabled = True

        print('\n{0} source entries were disabled:'.format(len(duplicates)),
            *[dupe for dupe, orig in duplicates], sep='\n  ', end='\n\n')
        if input('Do you want to save these changes? (y/N) ').upper() == 'Y':
            sourceslist.save()

    else:
        print('No duplicated entries were found.')

It takes no parameter and works on all /etc/apt/sources.list* with the help of the python3-apt package. Lines don't have to be exact duplicates (even after normalization) but its enough if type, URI, suite and at least one component overlap.

I'm not sure the equality test is correct in all corner cases (e. g. various “option” strings).

For me (16.04 LTS) going to

System settings >> Software and Updates >> Other Software and removing each duplicate entry from the list worked fine.

Reset your repositories like this:

1. IMPORTANT: First verify that you have software-properties-gtk installed (you can run software-properties-gtk -h to verify that you get a help-message)
2. sudo mv /etc/apt/sources.list /etc/apt/sources.list.bak
3. sudo software-properties-gtk
4. Pick your options
5. Save

Once everything is working, you can then delete your backup with sudo rm -rf /etc/apt/sources.list.bak.

Since the errors tell you where the problem is, and that all the problems are due to a single duplicated line, you can easily fix this manually with a text editor like vim, nano, etc. One benefit of this is that you can see exactly what the problem is and what you're doing to fix it.

In your case, with sudo or as root, open /etc/apt/sources.list in a text editor. Delete either line 33 or line 87. You can visually check that they're duplicates first.

If you like vim...

$ sudo vim /etc/apt/sources.list
33 [Shift]+g    # to goto line 33
87 [Shift]+g    # to goto line 87, don't need a duplicate of line 33
dd              # to delete the line you're on
:wq             # to write the file and quit

Or, to get out if you make a mistake...

:q!             # to quit without saving any changes