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Today I checked for updates and got an error message telling me I must do a partial upgrade. I was shocked to see how many updates there were available. 900+ Updates!

By using synaptic I found out that it wanted to remove core packages from my system, such as compiz and python, but also update some as well.

I am very confused why package manager would want to do this all of a sudden, and why it wants to destroy my system. I really need an answer, because I now cannot update my system.

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From a Terminal, run:

sudo apt-get update

Once this command has finished, re-launch Update Manager, and see if it prompts you to do a normal upgrade.

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Or update from the terminal:

sudo apt-get update && sudo apt-get upgrade

That command will update all of your outdated packages.

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