Re: [Rd] [R] Sweave stops when opening X11 device fails
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 | > | > UNIVERSITÄTSMEDIZIN | > der Johannes Gutenberg-Universität | > Institut für Medizinische Biometrie, Epidemiologie und Informatik | > Obere Zahlbacher Straße 69, 55131 Mainz | > www.imbei.uni-mainz.de | > | > Telefon +49 (0) 6131 175062 | > E-Mail: b...@imbei.uni-mainz.de | > | > Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der | > richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den | > Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe | > dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. | > | > __ | > r-h...@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@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@cbs.dk Priv: pda...@gmail.com | | __ | R-devel@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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] Sweave stops when opening X11 device fails
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) -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 > > UNIVERSITÄTSMEDIZIN > der Johannes Gutenberg-Universität > Institut für Medizinische Biometrie, Epidemiologie und Informatik > Obere Zahlbacher Straße 69, 55131 Mainz > www.imbei.uni-mainz.de > > Telefon +49 (0) 6131 175062 > E-Mail: b...@imbei.uni-mainz.de > > Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte > Informationen. Wenn Sie nicht der > richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, > informieren Sie bitte sofort den > Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die > unbefugte Weitergabe > dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. > > __ > r-h...@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@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@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] [R] Sweave stops when opening X11 device fails
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. 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 UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Medizinische Biometrie, Epidemiologie und Informatik Obere Zahlbacher Straße 69, 55131 Mainz www.imbei.uni-mainz.de Telefon +49 (0) 6131 175062 E-Mail: b...@imbei.uni-mainz.de Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und löschen Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail und der darin enthaltenen Informationen ist nicht gestattet. __ r-h...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
