Ubuntu – How to fix apt error “W: Target Packages … is configured multiple times”

apt

I just installed Ubuntu Gnome 16.04. I told it to save my documents – which worked. Some software had to be reinstalled. Now when I run sudo apt-get update I see this:

W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (main/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (restricted/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (restricted/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (restricted/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (restricted/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (multiverse/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (multiverse/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (multiverse/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (multiverse/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: The repository 'http://extras.ubuntu.com/ubuntu xenial Release' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by key 4CCA1EAF950CEE4AB83976DCA040830F7FAC5991 uses weak digest algorithm (SHA1)
W: http://repo.sinew.in/dists/stable/InRelease: Signature by key B6DA722E2E65721AF54B93966F7565879798C2FC uses weak digest algorithm (SHA1)
E: Failed to fetch http://extras.ubuntu.com/ubuntu/dists/xenial/main/source/Sources  404  Not Found [IP: 91.189.92.152 80]
E: Failed to fetch http://extras.ubuntu.com/ubuntu/dists/xenial/main/binary-amd64/Packages  404  Not Found [IP: 91.189.92.152 80]
E: Failed to fetch http://extras.ubuntu.com/ubuntu/dists/xenial/main/binary-i386/Packages  404  Not Found [IP: 91.189.92.152 80]
E: Some index files failed to download. They have been ignored, or old ones used instead.
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (main/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (main/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (main/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (restricted/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (restricted/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (restricted/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (restricted/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (multiverse/i18n/Translation-en_GB) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target Translations (multiverse/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11 (multiverse/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87
W: Target DEP-11-icons (multiverse/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:33 and /etc/apt/sources.list:87

Is there an automated way to fix this?

Best Answer

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).