[R] cron job install/update problems: tcltk can't find display (installing e.g., pbatR)

Peter Dalgaard p.dalgaard at biostat.ku.dk
Fri Jan 20 19:09:11 CET 2006

Paul Johnson <pauljohn32 at gmail.com> writes:

> On Fedora Core Linux 4, I have a cron job that causes R to update all
> packages and install new ones.  Lately, I notice in the log that some
> packages fail to install.  These are ones that assume X is running. 
> For example, the pbatR install requires tcltk to be loaded, and then
> the install fails because in a cron job, there is no DISPLAY
> environment.  I suppose the same happens if you try to install R
> packages in the console, without X running?
> Error output is pasted here.  I wonder if you can advise me whether
> this is the kind of thing that can be fixed in the cron job or not. 
> I've verified that pbatR does install interactively (because tcltk
> does start).  If you think this is a pbatR-specific problem, i will
> contact the author directly.  When I have the repos option set, the
> interactive install does not cause any tcltk widgets to pop up, so I
> wonder if it is really necessary.

The procedure used by CRAN (e.g.) for the automated testing involves
running a virtual X server (Xvfb).

On FC4 you'll need to install the RPM xorg-x11-Xvfb-6.8.2-37.FC4.49.2,
start it as part of the cron job and point your DISPLAY variable at

   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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