Thanks for the reply Mr. Eddelbuettel. However I somehow couldn't manage to 
solve the problem completely.

So I cleaned the sources.list file so taht the output is this:
sudo apt-get update
Hit:1 http://tr.archive.ubuntu.com/ubuntu xenial InRelease
Hit:2 http://tr.archive.ubuntu.com/ubuntu xenial-updates InRelease              
                                                       
Hit:3 http://tr.archive.ubuntu.com/ubuntu xenial-backports InRelease            
                                                       
Hit:4 http://security.ubuntu.com/ubuntu xenial-security InRelease               
                                                 
Hit:5 http://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease                
                                                 
Reading package lists... Done

So after that:
sudo gedit /etc/apt/sources.list
[sudo] password for atakan: 


(gedit:7094): Gtk-WARNING **: Calling Inhibit failed: 
GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name 
org.gnome.SessionManager was not provided by any .service files

** (gedit:7094): WARNING **: Set document metadata failed: Setting attribute 
metadata::gedit-spell-enabled not supported

** (gedit:7094): WARNING **: Set document metadata failed: Setting attribute 
metadata::gedit-encoding not supported

** (gedit:7094): WARNING **: Set document metadata failed: Setting attribute 
metadata::gedit-position not supported

And then I check the /etc/apt/sources.list.d/ directory and it was empty, so I 
tried to create a cran.list file wth gedit and when I tried to save it, it 
raised an error "Could not save the file, you do not have the permissions 
necessary....". I am logged in as the administrator, I am not sure how to fix 
this.

cat /etc/apt/sources.list.d/cran.list
cat: /etc/apt/sources.list.d/cran.list: No such file or directory


----------------------------------------
> Date: Thu, 12 May 2016 07:11:39 -0500
> To: atakano...@outlook.com
> CC: r-sig-debian@r-project.org
> Subject: Re: [R-sig-Debian] Problem with Install R on Linux Ubuntu 16.04 
> Xenial Xerus
> From: e...@debian.org
>
>
> On 12 May 2016 at 15:00, Atakan Okan wrote:
> | Any help is appreciated, thanks.
>
> 1) Clean up sources.list as suggested in the error messages you quoted.
>
> 2) Do that until 'sudo apt-get update' no longer complains.
>
> 3) Then re-read the README at https://cloud.r-project.org/bin/linux/ubuntu/
> and add one line. I have this __one line__ in the directory meant for this:
>
> edd@bud:~$ cat /etc/apt/sources.list.d/cran.list
> deb https://cran.rstudio.com/bin/linux/ubuntu xenial/ # disabled on upgrade 
> to xenial
> edd@bud:~$
>
> and I have been using the CRAN repos maintained by Michael for years on
> multiple machines. It. Just. Works.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
                                          
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