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I initially had a problem with apt-get update. It stopped on 99%, "waiting for headers". This problem came when attempting to install GeoGebra following instructions at this page.

Trying to solve this problem I deleted the apt folder from /var/cache. Now apt-get doesn't work at all. I have no idea of how to solve this problem. Ubuntu works fine but I'm unable to install new software. Please help!

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As per this answer on ServerFault you need to do:

sudo mkdir -p /var/cache/apt/archives/partial
sudo touch /var/cache/apt/archives/lock
sudo chmod 640 /var/cache/apt/archives/lock
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It worked! Thank you very much. However, apt-get update still does not work. I'm still stuck at 99% [Waiting for headers]. – Eivhje Jan 12 '12 at 12:29
Have a look at this. – SimonJGreen Jan 12 '12 at 12:35

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