send R diagnostic messages to stdout instead stderr

Question

Looking for an options which let me to redirect R diagnostic messages (produces by message()) to stdout, not stderr as it is by defaul

Answer 1

The OP showed the execution happening via the Rscript command and using some I/O redirection. If you want to use redirection to log everything and only show to console on error, the best method I've found is to use || to check if the script had non-zero exit status before printing to screen:

Rscript myrscript.R > temp.log 2>&1 || cat temp.log

This method relies strictly on the exit code for printing, which only partly gets around message() going to stderr, but I thought this example helpful to mention since messages won't necessarily trigger a non-zero exit status and you can continue to log quietly with this method.

If you'd like to go one step further and keep appending to a single log file, then this will work:

Rscript myrscript.R > temp.log 2>&1 || cat temp.log && cat temp.log >> persistent.log && rm temp.log

The pseudocode for this command is:

1. Redirect stderr and stdout into temp.log
2. If command had non-zero exit status then write to screen
3. Then redirect the contents of temp.log into your persistent.log
4. Then remove temp.log