[SOLVED] Different output for rpy2.ipython library and default R

Different output for rpy2.ipython library and default R

Alternative question: RStudio and Jupyter Notebook produces different output

_{This may look like too trivial QA, but if debug is not easily available within R binary package, it's not a prior knowledge that library actually used stderr instead of expected stdout.}

Under raw R (and RStudio) library function prints just progress bar:

....

While under rpy2.ipython (which can be used from Jupyter Notebook) same function outputs extra message and newlines:

R[write to console]: .
R[write to console]: .
R[write to console]: .
R[write to console]: .

What is the reason and how to fix?

Solution

It appears to be rpy2.ipython adds extra message when stderr is used under R.
Redirecting to stdout is one of possible fixes:

sink(stdout(), type = "message")
# call library function here

And just in case - for complicated debug cases, mocking output may be handy. There must be a better way to keep base::cat than simply copying it's code, but this worked well for diagnostics too:

original_cat <- function(..., file = "", sep = " ", fill = FALSE, labels = NULL, 
                     append = FALSE){
    if (is.character(file)) 
        if (file == "") 
            file <- stdout()
    else if (startsWith(file, "|")) {
        file <- pipe(substring(file, 2L), "w")
        on.exit(close(file))
    }
    else {
        file <- file(file, ifelse(append, "a", "w"))
        on.exit(close(file))
    }
    .Internal(cat(list(...), file, sep, fill, labels, append))
}


cat_ex <- function(...){
    # original_cat(...)
    args <- list(...)
    if (!is.null(args[["file"]]))
        args[["file"]] <- NULL
    do.call(original_cat, args)
}


library(testthat)
with_mock(
    cat = cat_ex,
    # call library function here
)