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After a fresh install of Ubuntu 12.04.1 (64bit), I get the following message when I want to install software via terminal:

The following packages were automatically installed and are no longer required:
linux-headers-3.2.0-29 linux-headers-3.2.0-29-generic

Is this normal? As it's related to the Linux core itself, I am confused that it might break my system.

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yes this message is normal it seems that you have updated your kernel before and these headers are no longer needed anyway before you make sudo apt-get autoremove you can test your kernel version by typing uname -r if the version is greater that 3.2.0-29 so you can do the autoremove and this wouldn't affect your system

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