R help - Jun 2008 - Getting Batch mode to continue running a script after running into errors

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

There is a "try" function that you can wrap around functions.

Hope this helps!

Sincerely,
Erin


On 6/12/08, Josh <jcchang at mednet.ucla.edu>
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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com

?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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> 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