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Issues starting RStudio Server and release file expiration under Debian (Jessie)

2 messages · Kelly Rensing, Charles Plessy

Original
Kelly Rensing
# 
Hi! I am a new user of Debian and am having an issue loading RStudio Server, which may or may not be related to a previous 'Release file expiration error' when trying to perform apt-get update prior to installing r-base into my remote Debian system.

E: Release file for http://mirror.optus.net/debian/dists/jessie-updates/InRelease is expired (invalid since 13d 17h 49min 2s). Updates for this repository will not be applied.

To work around the release file error I executed the following command which then allowed R to be installed:

$ sudo apt-get -o Acquire::Check-Valid-Until=false update

I then added this line to etc/apt/sources.list:

deb http://cran.csiro.au/bin/linux/debian jessie-cran3/

Next I added the appropriate key, and performed the above command to update the system again so R could be reinstalled:

$ sudo apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480
$ sudo apt-get -o Acquire::Check-Valid-Until=false update
$ sudo apt-get install r-base

This gave me the newest version of R. I then installed RStudio, but when I attempted to access the server from my browser it fails to load.

$ wget https://download2.rstudio.org/rstudio-server-0.99.489-amd64.deb
$ sudo gdebi rstudio-server-0.99.489-amd64.deb

I have attempted to troubleshoot, but from my terminal everything seems to be okay:

debian at r-docs-debian2:~$ sudo rstudio-server verify-installation
debian at r-docs-debian2:~$ sudo rstudio-server restart
debian at r-docs-debian2:~$ sudo rstudio status
sudo: rstudio: command not found
debian at r-docs-debian2:~$ sudo rstudio-server status
? rstudio-server.service - RStudio Server
  Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled)
  Active: active (running) since Thu 2015-11-26 15:03:39 AEDT; 58s ago
 Process: 19464 ExecStop=/usr/bin/killall -TERM rserver (code=exited, status=0/SUCCESS)
 Process: 19465 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS)
Main PID: 19467 (rserver)
  CGroup: /system.slice/rstudio-server.service
          ??19467 /usr/lib/rstudio-server/bin/rserver

Nov 26 15:03:39 r-docs-debian2 systemd[1]: Starting RStudio Server...
Nov 26 15:03:39 r-docs-debian2 systemd[1]: Started RStudio Server.
debian at r-docs-debian2:~$ which R
/usr/bin/R

I followed the instructions on RStudio support (https://support.rstudio.com/hc/en-us/articles/200717193), but I believe this might be a Debian specific problem as I was able to get RStudio working on my remote instance using Ubuntu vivid using the same/similar commands. I would like to get RStudio working on a Debian system as I am using the information for some internal documentation for how to use R and RStudio in the cloud.

Many thanks!
Charles Plessy
# 
Le Thu, Nov 26, 2015 at 02:05:10PM +0800, Kelly Rensing a ?crit :
Dear Kelly,

indeed, mirror.optus.net seems to be outdated.  Compare for instance with Debian's
primary australian mirror:

$ links -dump http://mirror.optus.net/debian/dists/jessie-updates
                     Index of /debian/dists/jessie-updates

   [ICO]      Name                  Last modified                 Size      
     --------------------------------------------------------------------
   [DIR]      Parent Directory                                            -   
   [DIR]      contrib/                          19-Nov-2015 14:21         -   
   [DIR]      main/                             19-Nov-2015 14:21         -   
   [DIR]      non-free/                         19-Nov-2015 14:21         -   
   [   ]      InRelease                         05-Nov-2015 19:49      132K   
   [   ]      Release                           05-Nov-2015 19:49      130K   
   [   ]      Release.gpg                       05-Nov-2015 19:49      1.5K   
     --------------------------------------------------------------------


$ links -dump http://ftp.au.debian.org/debian/dists/jessie-updates
   Welcome to the WAIX Mirror..

 Icon Name                    Last modified      Size 

     ----------------------------------------------------------------------

 [DIR] Parent Directory                             -  
 [DIR] contrib/                26-Nov-2015 11:23    -  
 [DIR] main/                   26-Nov-2015 11:23    -  
 [DIR] non-free/               26-Nov-2015 11:23    -  
 [   ] InRelease               26-Nov-2015 04:53  132K 
 [   ] Release                 26-Nov-2015 04:53  130K 
 [   ] Release.gpg             26-Nov-2015 04:53  1.5K 

     ----------------------------------------------------------------------

   Thursday, 26-Nov-2015 14:14:22 AWST

Therefore, it is a good thing that apt refuses to use the outdated mirror,
because if no action is taken and if the mirror does not recover, you will
eventually to miss updates for important bugs, etc.

By setting Acquire::Check-Valid-Until=false, you have allowed apt to use an
outdated mirror.  However, it would be better to switch to an equally fast one,
that is up to date.

Anyway, the problems you encounter later are not caused by the outdated mirrror.
rstudio.org provides Debian packages for RStudio server and for RStudio desktop.
You installed the rstudio-server package, and it does not provide the rstudio
command, which is in the rstudio package.

$ dpkg -L rstudio-server | grep bin/rstudio$
(no output)

$ dpkg -L rstudio | grep bin/rstudio$
/usr/lib/rstudio/bin/rstudio

Have a nice day,