Displaying warnings generated by R script as they happen

Question

I have a script that contains multiple blocks with lines that look like this...

#Read data for X
DataX = read.delim(file = 'XRecords.txt',
                   col.names = XFields[,'FieldName'])
print('Data X read')
#Convert fields that should be numeric into numeric so they can summed
DataX[,NumFieldNames] = as.numeric(as.character(XData[,NumFieldNames]))
print('Data X scrubbed')

When I source the script I get an output like this...

[1] "Data X read"
[1] "Data X scrubbed"
[1] "Data Y read"
[1] "Data Y scrubbed"
Warning message:
In eval(expr, envir, enclos) : NAs introduced by coercion

Based on that output, I reload data Y and began looking for records where the string to numeric conversion failed. After a couple hours of frustration, I realized that data X was actually the one that had type conversion errors.

It looks like what's happening is that an warning is raised, but it does not display on the console until the script finishes. Is there a way to make warnings output to the console as soon as they are raised? I tried flush.console(), but it doesn't seem to work for warnings.

I'd prefer not to have load any additional packages onto my system if it can be avoided. I'm using this for work, and I had to jump through a few hoops just to get the CRAN distribution installed on my computer.

Thank you. I appreciate the help.

You'll have to pardon my (probably) loose vocabulary around R. I'm very new to the software. — Adam Hoelscher, Mar 15 '13 at 18:10

score 26 · Accepted Answer · answered Mar 15 '13 at 18:45

Let's make an example that shows the problem

foo <- function() {
  X <- c("1", "2", "three")
  print("Data X read")
  X <- as.numeric(X)
  print("Data X scrubbed")
  Y <- c("1", "2", "3")
  print("Data Y read")
  Y <- as.numeric(Y)
  print("Data Y scrubbed")
}

If run (even interactively), the behavior you see appears

> foo()
[1] "Data X read"
[1] "Data X scrubbed"
[1] "Data Y read"
[1] "Data Y scrubbed"
Warning message:
In foo() : NAs introduced by coercion

Behavior of warnings is handled with the warn option (see help("options")). That gives the choices including

If warn is one, warnings are printed as they occur.

Changing the option to 1 then gives

> options(warn=1)
> foo()
[1] "Data X read"
Warning in foo() : NAs introduced by coercion
[1] "Data X scrubbed"
[1] "Data Y read"
[1] "Data Y scrubbed"

score -1 · Answer 2 · answered Mar 15 '13 at 18:23

-1

The problem is that warnings in R are printed to stderr instead of stdout. Flushing both stderr and out should solve the problem.

flush(stderr())

answered Mar 15 '13 at 18:23

kith

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Is this really right? - - Can you have a more complete example? – Léo Léopold Hertz 준영 Nov 10 '16 at 17:23
The combo `flush(stderr())` and `flush(stdout())` did not work. Neither did `flush.console()`. – Earlien Nov 15 '22 at 20:10

Displaying warnings generated by R script as they happen

2 Answers2

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