Malformed entry 63 in list file after upgrading to Gnome 16.04.01 [duplicate]

The lines of interest are:

63  deb http://star-www.st-andrews.ac.uk/cran/bin/linux/ubuntu xenial
64  # deb-src http://star-www.st-andrews.ac.uk/cran/bin/linux/ubuntu trusty/

As the error says, you're missing a component (the main, universe, etc. of other repos). However, the CRAN mirrors don't have components, and instead use a trivial repo, so you need to have a trailing / there like the trusty line:

deb http://star-www.st-andrews.ac.uk/cran/bin/linux/ubuntu xenial/

Correct the wrong entries in the /etc/apt/sources.list file.

Open a terminal and execute the following command :

sudo nano /etc/apt/sources.list  

Remove lines 63 and 64 in the /etc/apt/sources.list file.

Press Ctrl + X to close the file, confirm the change with Y.

Now re-add the repository to the software sources :

sudo nano /etc/apt/sources.list.d/star-st-andrews.list  

Add the following lines (entries) to the empty file :

deb http://www-star.st-and.ac.uk/cran/bin/linux/ubuntu/ xenial/
# deb-src http://www-star.st-and.ac.uk/cran/bin/linux/ubuntu/ xenial/

Press Ctrl + X to close the file, confirm the change with Y.

Reference: CRAN Repositories

If you are still getting an error message when updating the software sources, you should check the /etc/apt/sources.list file and the /etc/apt/sources.list.d folder for other wrong entries. Generally it is recommended to remove external sources before upgrading a system. After the upgrade re-add the sources, which leads to the correct entry in the correct place.

Note: In newer Ubuntu editions the /etc/apt/sources.list file is used for Ubuntu sources.
All external software sources reside as a .list file in the /etc/apt/sources.list.d folder.