R SIG Debian - May 2016 - Problem with Install R on Linux Ubuntu 16.04 Xenial Xerus

Hi,

I am running a dual-booted Ubuntu 16.04 from a USB stick and having problems
installing R.
I have been following the steps at this site:
https://www.datascienceriot.com/how-to-install-r-in-linux-ubuntu-16-04-xenial-xerus/kris/
Below is the the output and the commands from the terminal:

sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" |
sudo tee -a /etc/apt/sources.list
[sudo] password for atakan: 
deb http://cran.rstudio.com/bin/linux/ubuntu xenial/

gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
gpg: key E084DAB9: "Michael Rutter <marutter at gmail.com>" not
changed
gpg: Total number processed: 1
gpg:              unchanged: 1

gpg -a --export E084DAB9 | sudo apt-key add -
OK

sudo apt-get update
Hit:1 http://tr.archive.ubuntu.com/ubuntu xenial InRelease
Hit:2 http://security.ubuntu.com/ubuntu xenial-security InRelease
Hit:3 http://tr.archive.ubuntu.com/ubuntu xenial-updates InRelease
Hit:4 http://tr.archive.ubuntu.com/ubuntu xenial-backports InRelease
Hit:5 http://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease             
Reading package lists... Done
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:57
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:58
W: Target Packages (Packages) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59
W: Target Translations (en_US) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59
W: Target Translations (en) is configured multiple times in
/etc/apt/sources.list:54 and /etc/apt/sources.list:59

sudo apt-get install r-base r-base-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base : Depends: r-base-core (>= 3.3.0-1xenial0) but it is not going to be
installed
          Depends: r-recommended (= 3.3.0-1xenial0) but it is not going to be
installed
          Recommends: r-base-html but it is not going to be installed
 r-base-dev : Depends: r-base-core (>= 3.3.0-1xenial0) but it is not going to
be installed
              Depends: gfortran but it is not going to be installed
              Depends: libblas-dev but it is not going to be installed or
                       libatlas-base-dev but it is not going to be installed
              Depends: liblapack-dev but it is not going to be installed or
                       libatlas-base-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.


Any help is appreciated, thanks.

Atakan Okan

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 at bud:~$ cat /etc/apt/sources.list.d/cran.list
      deb https://cran.rstudio.com/bin/linux/ubuntu xenial/ # disabled on
upgrade to xenial
      edd at 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 | edd at debian.org

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: atakanokan at outlook.com
> CC: r-sig-debian at r-project.org
> Subject: Re: [R-sig-Debian] Problem with Install R on Linux Ubuntu 16.04
Xenial Xerus
> From: edd at 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 at bud:~$ cat /etc/apt/sources.list.d/cran.list
> deb https://cran.rstudio.com/bin/linux/ubuntu xenial/ # disabled on upgrade
to xenial
> edd at 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 | edd at debian.org