Dear R-Help,
On a new server (Ubuntu 10.04.1/Lucid), with R2.14.0, I am trying to create
a heatmap using a script that works fine elsewhere (R2.12 on a different
Ubuntu server). The script halts when calling png, "Error in X11...unable
to start device PNG" (full error message and session info at the bottom of
this e-mail).
I checked the system requirements within R using:
> test = c("X11", "png", "libxml", "tcltk")
> capabilities(test)
X11 png libxml tcltk
FALSE FALSE TRUE FALSE
I suspect something is missing with X11, and that is probably preventing
png from working (and probably tcltk). But, when I check the installed
packages on the server, everything I can think to check seems to be
present/installed:
libpng12-0 1.2.42-1ubuntu2.2 PNG library - runtime
libpng12-dev 1.2.42-1ubuntu2.2 PNG library - development
libx11-6 2:1.3.2-1ubuntu3 X11 client-side library
libx11-data 2:1.3.2-1ubuntu3 X11 client-side library
libx11-dev 2:1.3.2-1ubuntu3 X11 client-side library (development
headers)
tcl8.5 8.5.8-2 Tcl (the Tool Command Language)
v8.5 - run-time files
tk8.5 8.5.8-1 Tk toolkit for Tcl and X11, v8.5 -
run-time files
x11-common 1:7.5+5ubuntu1 X Window System (X.Org) infrastructure
x11-utils 7.5+3 X11 utilities
x11-xserver-utils 7.5+1ubuntu2.1 X server utilities
x11proto-bigreqs-de 1:1.1.0-1 X11 Big Requests extension wire
protocol
x11proto-composite- 1:0.4.1-1 X11 Composite extension wire
protocol
<truncated for brevity, but everything else is an x11proto- item>
Does anyone have any suggestions for what this server might be missing?
Are there any other steps/sources/test I might look into?
Thank you very much for your time!
-Emily
>From script: (if I substitute in, say, outFilePath="~/test.png", I can get
the same error from the command line)
> #### PNG Config section #########
> png(outFilePath, width=1200, height=1200)
Error in X11(paste("png::", filename, sep = ""), g$width, g$height,
pointsize, :
unable to start device PNG
Calls: png
In addition: Warning message:
In png(outFilePath, width = 1200, height = 1200) :
unable to open connection to X11 display ''
Execution halted
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 bitops_1.0-4.1
[5] gdata_2.8.2 gtools_2.6.2
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