[R] Runing R in a bash script

[Henrik Bengtsson]

Or see png2() in R.utils, which imitates png() but uses bitmap(),
which in turn uses postscript-to-png via ghostscript.  BTW, personally
I think PNGs generated via bitmap() look way better than the ones
generated via png().

/Henrik

On 4/17/07, Jeffrey Horner <jeff.horner at vanderbilt.edu> wrote:
> Ulrik Stervbo wrote:
>  > Hello!
>  >
>  > I am having issues trying to plot to a ong (or jpg)  when the R-code in a
>  > bash script is executed from cron.
>  >
>  > I can generate a pdf file, but when I try to write to a png, the file is
>  > created, but nothing is written. If I execute the bash script from my
>  > console, everything works file. Any ideas?
>  >
>  > In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and the
>  > folowing enery, so example is executed every minute
>  > * * * * * [path]/example.sh
>  >
>  > I am running
>  > R version 2.4.1 (2006-12-18)
>  >
>  > Here's a minimal example - two files one R-script ('example.r') and one
>  > bash-script ('example.sh')
>  >
>  > example.r
>  > # Example R-script
>  > x <- c(1:10)
>  > y <- x^2
>  > png(file="example2.png")
>  > #pdf(file="example2.pdf")
>  > plot(x,y)
>  > graphics.off()
>  >
>  > example.sh
>  > #/bin/bash
>  > #
>  > # Hello world is written to exhotext every time cron executes this script
>  > echo "Hello world" > echotext
>  > # This works, but not when executed from cron
>  > n=`R --save < example.r`
>  > # using exec as in `exec R --save < example.r` dosent work with cron
> either
>  > # This also works, but nothing is written to the png when executed
> from cron
>  > R --save <<RSCRIPT
>  > x <- c(1:10)
>  > y <- x^2
>  > png(file="example2.png")
>  > #pdf(file="example2.pdf")
>  > plot(x,y)
>  > graphics.off()
>  > #dev.off() dosent work at all when executed from cron
>  > RSCRIPT
>
> The png() device requires an X server for the image rendering. You might
> be able to get away with exporting the DISPLAY environment variable
>
> export DISPLAY=:0.0 # try and connect to X server on display 0.0
>
> within your script, but it will only work if the script is executed by
> the same user as is running the X server, *and* the X server is running
> at the time the script is executed.
>
> There are a handful of packages that will create a png without the
> presence of an X server, and I'm partial to Cairo (since I've done some
> work on it). You can install the latest version like this:
>
> install.packages("Cairo",,'http://rforge.net/',type='source')
>
> Cairo can also outputs nice pdf's with embedded fonts... useful if you
> want to embed high-quality OpenType or TrueType fonts.
>
> Best,
>
> Jeff
> --
> http://biostat.mc.vanderbilt.edu/JeffreyHorner
>
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