This warning appears when a repository is listed multiple times in your apt sources configuration. While not an error that prevents apt from working, having duplicate repository entries causes apt to download the same packages redundantly. Fix this by identifying and removing duplicate sources from your /etc/apt/sources.list and /etc/apt/sources.list.d/ files.
APT uses configuration files to define which repositories to fetch packages from. When a repository is defined in multiple places—either in the same file with identical lines or in different source list files—apt detects this redundancy and issues a warning. This typically happens with entries like "main/binary-amd64/Packages" which indicates the main repository for 64-bit packages. The warning is not harmful to functionality; your system will still work and download packages correctly. However, duplicates waste bandwidth by checking the same repository multiple times and indicate leftover or conflicting configuration entries that should be cleaned up. APT expects each repository to be configured exactly once.
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:3Or 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:25Note 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.sourcesLook 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.sourcesNOTE: 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.listFind 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 mainAfter 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 updateIf 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... DoneWithout 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.pyzThe 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.
On modern Ubuntu systems (20.04+), repositories are increasingly managed through /etc/apt/sources.list.d/ with individual .sources files using DEB822 format instead of the traditional one-liner format in /etc/apt/sources.list. If you have both formats, ensure you do not duplicate entries across them. Cloud-init (used in cloud VMs and containers) automatically generates /etc/apt/sources.list.d/ubuntu.sources on first boot, which can conflict with manually configured entries in /etc/apt/sources.list. If you see this warning after provisioning, check whether cloud-init created duplicate entries. Proxmox and other systems may also auto-generate sources entries. For CI/CD pipelines or Docker containers, prevent this by either: (1) deleting /etc/apt/sources.list.d/ubuntu.sources after the base image setup, or (2) managing all sources through a single file and deleting others. The warning does not affect package installation, caching, or security; it is purely informational. However, having duplicates does slightly increase apt database size and causes apt to redundantly check the same repository, wasting minimal bandwidth during updates.
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