How to fix W: Target Packages (main/binary-amd64/Packages) is configured multiple times in APT

When you run apt update, the warning will tell you exactly which files have duplicate entries. For example:

W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:12 and /etc/apt/sources.list.d/ubuntu.sources:3

Or for duplicates within the same file:

W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:12 and /etc/apt/sources.list:25

Note the file paths and line numbers mentioned. This tells you exactly where to find and fix the duplicates.

List the contents of your source files to identify duplicates:

# View main sources file
cat /etc/apt/sources.list

# View all source files in sources.list.d
ls -la /etc/apt/sources.list.d/

# View contents of individual .list or .sources files
cat /etc/apt/sources.list.d/ubuntu.sources

Look for identical repository entries. For example, if you see:
- /etc/apt/sources.list contains: deb http://archive.ubuntu.com/ubuntu jammy main
- /etc/apt/sources.list.d/ubuntu.sources contains: deb http://archive.ubuntu.com/ubuntu jammy main

Then you have a duplicate that needs to be removed.

If duplicates exist in separate files under /etc/apt/sources.list.d/, the easiest solution is to delete the unnecessary .list file:

# First, backup the file in case you need it
sudo cp /etc/apt/sources.list.d/ubuntu.sources /etc/apt/sources.list.d/ubuntu.sources.bak

# Delete the duplicate file
sudo rm /etc/apt/sources.list.d/ubuntu.sources

NOTE: Do not delete files in /etc/apt/sources.list.d/ unless you are certain they are truly duplicates of entries elsewhere. Ubuntu systems typically prefer to keep repository definitions in /etc/apt/sources.list (the main file) and not in separate .list files in the directory.

For multiple .list files with the same repository, keep the one you recognize or the one most recently created, and delete the others.

If the warning shows duplicates on different lines of the same /etc/apt/sources.list file:

# First, backup the file
sudo cp /etc/apt/sources.list /etc/apt/sources.list.bak

# Edit the file
sudo nano /etc/apt/sources.list

Find the duplicate lines mentioned in the warning and:
- Delete one of the duplicate lines completely, OR
- Comment out the duplicate by adding # at the beginning

For example, if lines 12 and 25 are identical:

# Line 12 (keep this one)
deb http://archive.ubuntu.com/ubuntu jammy main

# ... other lines ...

# Line 25 (comment this out or delete)
# deb http://archive.ubuntu.com/ubuntu jammy main

After editing, save the file (Ctrl+O, Enter, Ctrl+X in nano).

After removing or commenting out duplicates, run apt update to check if the warnings are gone:

sudo apt update

If the warnings about target packages being configured multiple times no longer appear, you have successfully removed the duplicates. You should see output like:

Get:1 http://archive.ubuntu.com/ubuntu jammy InRelease []
Get:2 http://archive.ubuntu.com/ubuntu jammy-updates InRelease []
...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done

Without any "W: Target Packages is configured multiple times" warnings.

If you have many duplicate entries and prefer automated removal, you can use the aptsources-cleanup tool:

# Install required dependencies
sudo apt install python3-apt python3-regex

# Download and run the cleanup script
wget https://git.launchpad.net/~foersteri/+junk/apt-remove-duplicate-source-entries/+archive/branch/master/+files/apt-remove-duplicate-source-entries.pyz
python3 apt-remove-duplicate-source-entries.pyz

The script will:
1. Detect duplicate entries in your sources configuration
2. Show you which duplicates were found
3. Ask for confirmation before removing them
4. Deactivate duplicate entries (by commenting them out)

This approach is safer as it backs up your configuration before making changes. However, manual removal as described above is often faster for most systems.