[R] Getting Batch mode to continue running a script after running into errors

[Prof Brian Ripley]

?stop explains why this happens and how to change it.

You can also set options(error=expression(NULL)) to ignore all errors, and
use tryCatch() (or its wrapper try()) skip particular expressions if tjhey 
fail.

But surely in your example your script should check for existence of the 
file by file.exists() or file.access()?


On Thu, 12 Jun 2008, Josh wrote:

> I'm invoking R in batch mode from a bash script as follows:
>
> R --no-restore --no-save --vanilla
> <$TARGET/$directory/o2sat-$VERSION.R>
> $TARGET/$directory/o2sat-$VERSION.Routput
>
> When R comes across some error in the script however it seems to halt
> instead of running subsequent lines in the script:
>
> Error in file(file, "r") : cannot open the connection
> Calls: read.table -> file
> In addition: Warning message:
> In file(file, "r") :
>  cannot open file '/datapool/experiments/ois/080502/petri': No such
> file or directory
> Execution halted
>
>
> How can I get R to continue running the script even if it comes across
> errors? Thanks in advance
>
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-- 
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)
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