this is not a problem with R but a request for related advice.
i am trying to run a lengthy batch job from my home.
the OS is ...
Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST
2003 i686 athlon i386 GNU/Linux
i start the job and put it in the background. while i am connected, all is
well. eventually my ISP shuts down the connection if i do not do any
input. then:
Boxplots of G intensitiesError in X11(paste("png::", filename, sep =
""), width, height, pointsize, :
unable to start device PNG
Calls: doPlot -> qcBeadLevel -> png
In addition: Warning message:
In png(filename, width = 640, height = 480) :
unable to open connection to X11 display ''
Execution halted
is it possible to have X11() succeed when there is no real display to connect
to?
R version 2.6.0 Under development (unstable) (2007-06-29 r42093)
i686-pc-linux-gnu
locale:
LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] grid tools stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] beadarray_1.5.3 beadarraySNP_1.3.7 quantsmooth_1.3.0 lodplot_1.1
[5] quantreg_4.06 SparseM_0.73 affy_1.13.9 affyio_1.3.1
[9] geneplotter_1.13.4 lattice_0.15-11 annotate_1.13.3 Biobase_1.13.19
[13] limma_2.9.5
loaded via a namespace (and not attached):
[1] KernSmooth_2.22-20 RColorBrewer_0.2-3 rcompgen_0.1-13
---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu
I use a display on an Xvfb server: Xvfb :5 -screen 0 1280x1024x24 & setenv DISPLAY :5 You do most likely need a non-default depth (on my machine the default is 12 bits), and it is possible you may need to deal with authentication issues. On Sat, 21 Jul 2007, Vincent Carey 525-2265 wrote:> > this is not a problem with R but a request for related advice. > > i am trying to run a lengthy batch job from my home. > > the OS is ... > Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST > 2003 i686 athlon i386 GNU/Linux > > i start the job and put it in the background. while i am connected, all is > well. eventually my ISP shuts down the connection if i do not do any > input. then: > > > Boxplots of G intensitiesError in X11(paste("png::", filename, sep = ""), width, height, pointsize, : > unable to start device PNG > Calls: doPlot -> qcBeadLevel -> png > In addition: Warning message: > In png(filename, width = 640, height = 480) : > unable to open connection to X11 display '' > Execution halted > > is it possible to have X11() succeed when there is no real display to connect > to? > > R version 2.6.0 Under development (unstable) (2007-06-29 r42093) > i686-pc-linux-gnu > > locale: > LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > attached base packages: > [1] grid tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] beadarray_1.5.3 beadarraySNP_1.3.7 quantsmooth_1.3.0 lodplot_1.1 > [5] quantreg_4.06 SparseM_0.73 affy_1.13.9 affyio_1.3.1 > [9] geneplotter_1.13.4 lattice_0.15-11 annotate_1.13.3 Biobase_1.13.19 > [13] limma_2.9.5 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-20 RColorBrewer_0.2-3 rcompgen_0.1-13 > > > --- > Vince Carey, PhD > Assoc. Prof Med (Biostatistics) > Harvard Medical School > Channing Laboratory - ph 6175252265 fa 6177311541 > 181 Longwood Ave Boston MA 02115 USA > stvjc at channing.harvard.edu > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Vincent Carey 525-2265 <stvjc at channing.harvard.edu> writes:> this is not a problem with R but a request for related advice. > > i am trying to run a lengthy batch job from my home. > > the OS is ... > Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST > 2003 i686 athlon i386 GNU/Linux > > i start the job and put it in the background. while i am connected, all is > well. eventually my ISP shuts down the connection if i do not do any > input.One thing you might try is using screen. The screen program lets you multiplex terminals in a single window, but the feature you want here is that it allows you to detach and reattach to a session. So you could start a screen session at work or home, start something running, detach, and then come back later and attach to see how things are going. However, screen may further complicate your desire to use X11(), but perhaps with Xvfb run from the screen session things will work. Do all of the graphics devices require access to X11()? I thought you could use pdf() for example, without X11() but I'm not certain. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org