Output Error/Warning Log (Txt File) When Running R Script Under Command Line

Output error/warning log (txt file) when running R script under command line

You can use sink() to divert messages as well as warnings to a file. The trick is to set the argument type="message":

Here is an example adapted from the help for ?sink:

setwd(tempdir())

## capture messages and errors to a file.
zz <- file("all.Rout", open="wt")
sink(zz, type="message")

try(log("a"))

## reset message sink and close the file connection
sink(type="message")
close(zz)

## Display the log file
readLines("all.Rout")
[1] "Error in log(\"a\") : Non-numeric argument to mathematical function"

Create warning log file when running R script

Try options(warn=1)

From ?options:

'warn': sets the handling of warning messages.  If 'warn' is
      negative all warnings are ignored.  If 'warn' is zero (the
      default) warnings are stored until the top-level function
      returns.  If 10 or fewer warnings were signalled they will be
      printed otherwise a message saying how many were signalled.
      An object called 'last.warning' is created and can be printed
      through the function 'warnings'.  If 'warn' is one, warnings
      are printed as they occur.  If 'warn' is two or larger all
      warnings are turned into errors.

How to write errors and warnings to a log file?

I'm sure of all of the pitfalls, I've read some people having trouble with sink not releasing file access to a log file, and you could potentially forget to reset sink to output back to console instead of the log file, which could potentially corrupt your log file. But you should be able to generate an error log by running your code to download the files through a try-catch block and writing out the error messages similar to below.

log.path <- # Path to log file

tryCatch({
  # Code to attempt
  log(q)

}, error = function(err.msg){
             # Add error message to the error log file
             write(toString(err.msg), log.path, append=TRUE)
          }
)

How to make a log-file of an R-session which combines commands, results and warnings/messages/errors from the R-console

If you are running R from a Unix/Linux/Mac/etc. terminal, you can do:

R | tee mydir/mylog.txt

On windows, you can run the script in

R CMD BATCH yourscript.R

and your result will appear in the same folder as yourscript.out

Error Handling and logging in R

use sink() to divert messages as well as warnings to a file. The trick is to set the argument type="message"

refer http://www.statmethods.net/interface/io.html
and Output error/warning log (txt file) when running R script under command line
https://stat.ethz.ch/R-manual/R-devel/library/base/html/sink.html

The sink( ) function defines the direction of the output.

Description

sink diverts R output to a connection (and stops such diversions).

sink.number()

reports how many diversions are in use.

sink.number(type = "message") reports the number of the connection currently being used for error messages.
Usage

sink(file = NULL, append = FALSE, type = c("output", "message"),
     split = FALSE)

sink.number(type = c("output", "message"))

direct output to a file

sink("myfile", append=FALSE, split=FALSE)

return output to the terminal

sink()

The append option controls whether output overwrites or adds to a file. The split option determines if output is also sent to the screen as well as the output file.

Here are some examples of the sink() function.

output directed to output.txt in c:\projects directory.
output overwrites existing file. no output to terminal.

sink("c:/projects/output.txt")

output directed to myfile.txt in cwd. output is appended
to existing file. output also send to terminal.

sink("myfile.txt", append=TRUE, split=TRUE)

When redirecting output, use the cat( ) function to annotate the output.

Unix Run Command is not generating the log for R Script

as it turned out, i had a script to cleanup the output folder and was deleting these .txt files in the process.
Appreciate your inputs guys, thanks.

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