I was running low on disk space so I went and downloaded baobab a visual tool to show how muh space is being occupied by various directories on the file system. I saw that the /var/cache/apt/archives was using up a lot of space and since most of the directory contents were .deb files I decided to delete this files, the next day I tried running apt and got the error
"E:Archive directory /var/cache/apt/archives/partial is missing."
To fix this error make sure you recreate the archives folder as well as the partial folder. open a console window and type
1. cd /var/cache/apt
2. Type ls check to make sure archives folder is displayed in case you dont see the archives folder create the folder
sudo mkdir archives if you already have the archives folder then skip this step.
3. type cd archives , create the partial folder by typing sudo mkdir partial
4. type sudo apt-get autoclean to make sure apt is working properly.
Thats it you should now be able to get apt to work properly.