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

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri, 13 Jun 2008 07:37:29 +0100 (BST)

?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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> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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

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Received on Fri 13 Jun 2008 - 06:40:22 GMT

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