From edd at debian.org  Tue May  3 13:32:08 2011
From: edd at debian.org (Dirk Eddelbuettel)
Date: Tue, 3 May 2011 06:32:08 -0500
Subject: [Rd] [R] Sweave stops when opening X11 device fails
In-Reply-To: <63D70846-DC0E-44B7-83E9-6EC494E0BCEE@gmail.com>
References: <4DBFDA8A.3020901@unimedizin-mainz.de>
	<63D70846-DC0E-44B7-83E9-6EC494E0BCEE@gmail.com>
Message-ID: <19903.59320.416101.414134@max.nulle.part>


On 3 May 2011 at 13:19, peter dalgaard wrote:
| 
| On May 3, 2011, at 12:35 , Andreas Borg wrote:
| 
| > Hi all,
| > 
| > I am posting this again because I got no reply on r-help. Maybe the devel-list is the right place for this kind of question.
| 
| Actually, not an R problem at all, but try one of these...
| 
| 1) get rid of the DISPLAY environment variable before starting R 
| 
| 2) replace the su command with ssh -Y localhost to get the X server tunneled properly.
| 
| 3) xhost +localhost  (may be a security liability)

4) If available, use the 'xvfb-run' frontend to simulate X11 in a virtual
   framebuffer. That is how the Debian packages build when a given package
   requires X11 at init or load time (here's looking at you, tcltk).

   This can be as simple as

       xvfb-run R CMD Sweave someFile.Rnw

   Debian / Ubuntu have xvfb-run available in a package 'xvfb', I suspect
   other distros do to.

Dirk 

| -pd 
| 
| > 
| > I've run into the following problem with Sweave: I frequently run Sweave
| > from a xterm console within an X session owned by a different user, i.e.
| > my colleague is logged in on this computer and I do "su" with my
| > username and start R and Sweave afterwards. Now, when Sweave comes to a
| > figure chunk, it sees that there is an X server running and tries to
| > show whatever I plot in that chunk on the screen, additionally to
| > writing a pdf file. The problem is that I am not logged into the X
| > session myself, and the script fails with a message saying someting like
| > "could not open device X11" (I have German messages, so I do not know
| > what the exact phrase would be in English). When I log in with putty,
| > where there is no X11 at all, everything works fine. Is there a way to
| > prevent Sweave from failing in the former case? Would this even account
| > as a bug? I think it would be nice if the script just kept on running
| > without plotting on the screen if opening X11 fails, just like it does
| > when no X11 is available at all.
| > 
| > Best regards,
| > 
| > Andreas
| > 
| > p.s.: I would be willing to dig in the code and look for a fix myself, but it would be great if anyone could give a hint where to look. I suspect "RweaveDriverRuncode" is the right place, but in what namespace is it?
| > 
| > -- 
| > Andreas Borg
| > Medizinische Informatik
| > 
| > UNIVERSIT?TSMEDIZIN
| > der Johannes Gutenberg-Universit?t
| > Institut f?r Medizinische Biometrie, Epidemiologie und Informatik
| > Obere Zahlbacher Stra?e 69, 55131 Mainz
| > www.imbei.uni-mainz.de
| > 
| > Telefon +49 (0) 6131 175062
| > E-Mail: borg at imbei.uni-mainz.de
| > 
| > Diese E-Mail enth?lt vertrauliche und/oder rechtlich gesch?tzte Informationen. Wenn Sie nicht der
| > richtige Adressat sind oder diese E-Mail irrt?mlich erhalten haben, informieren Sie bitte sofort den
| > Absender und l?schen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe
| > dieser Mail und der darin enthaltenen Informationen ist nicht gestattet.
| > 
| > ______________________________________________
| > R-help at r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-help
| > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| > and provide commented, minimal, self-contained, reproducible code.
| > 
| > ______________________________________________
| > R-devel at r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-devel
| 
| -- 
| Peter Dalgaard
| Center for Statistics, Copenhagen Business School
| Solbjerg Plads 3, 2000 Frederiksberg, Denmark
| Phone: (+45)38153501
| Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
| 
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com



[Rd] [R] Sweave stops when opening X11 device fails
Dirk Eddelbuettel