How to fix E: Cannot mark package as manually installed in APT

First, check if the package is truly installed on your system:

dpkg -l | grep package-name

or more specifically:

dpkg -l | grep '^ii' | grep package-name

The output should show lines starting with ii (installed). If you see nothing, the package is not installed. You cannot mark a non-installed package as manually installed.

If the package is not installed, install it first:

sudo apt install package-name

Then try marking it:

sudo apt-mark manual package-name

Virtual packages are references to other packages and cannot be directly marked. Check if your package is virtual:

apt-cache show package-name | grep -E '^(Package|Virtual):'

If the output shows "Virtual: yes" or "Provides:", the package is virtual. Virtual packages are typically metapackages like:
- java-runtime (virtual, provided by openjdk-11-jre, openjdk-17-jre, etc.)
- python (virtual, provided by specific Python versions)
- mailserver (virtual, provided by postfix, sendmail, etc.)

Solution for virtual packages: Mark the real package that provides it instead:

# Find what provides the virtual package
apt-cache depends --recurse package-name

# Then mark the concrete package:
sudo apt-mark manual openjdk-11-jre

Or use apt-cache rdepends to see reverse dependencies:

apt-cache rdepends package-name

A corrupted or out-of-sync APT cache can cause marking issues. Refresh it:

sudo apt update

Then try marking the package again:

sudo apt-mark manual package-name

If that still fails, you can clean the cache and rebuild it:

sudo apt clean
sudo apt update

The apt clean command removes cached package files (you can safely delete these), while apt update refreshes the package list from repositories.

Get detailed information about the package's installation state:

apt-cache policy package-name

This shows:
- Candidate version (what would be installed)
- Installed version (what's actually on your system)
- Available versions from repositories

Also check if it's marked as on-hold:

apt-mark showhold

If your package is in the hold list, it might prevent marking:

sudo apt-mark unhold package-name
sudo apt-mark manual package-name

If the package has unmet dependencies, apt may refuse to mark it. Check for issues:

sudo apt --fix-broken install

This command tries to fix dependency issues without making changes:

sudo apt check

If there are broken dependencies, fix them first before marking:

# Show what depends on this package
apt-cache rdepends package-name

# Show what this package depends on
apt-cache depends package-name

# Try to fix dependency issues
sudo apt --fix-broken install

After resolving dependencies, try marking again:

sudo apt-mark manual package-name

Package names are case-sensitive and may differ from what you expect. Find the exact name:

apt search pattern

For example:

# Wrong: trying to mark 'Java'
sudo apt-mark manual Java
# Error: Package not found

# Correct: use the actual package name
apt search java-runtime
sudo apt-mark manual default-jre

Common package name confusions:
- node vs nodejs (Node.js)
- python vs python3 vs python3.10 (specific Python version)
- java vs default-jre vs openjdk-11-jre (Java runtime)
- docker vs docker.io (Docker)

Always use:

apt-cache show package-name

to confirm the package exists before trying to mark it.

Sometimes resetting the marking state helps resolve conflicts. Try this sequence:

# Check current state
apt-mark showmanual | grep package-name

# Try marking as auto first
sudo apt-mark auto package-name

# Then mark as manual
sudo apt-mark manual package-name

If the package is already in the manual list, this refresh can clear any state issues.

You can also view all manually and automatically installed packages:

# Show all manually installed packages
apt-mark showmanual

# Show all automatically installed packages
apt-mark showauto

# Count them
apt-mark showmanual | wc -l
apt-mark showauto | wc -l