[R-pkg-devel] Warning that are Unintentionally OS-Specific (Maybe Bug in warning?)

    Digging into the code (specifically by setting
options(warn=2,error=recover), I see that the warning is happening
during this call:

     tmp.results <- parallel::mclapply(X = conc.dose, FUN =
pk.nca.intervals,
     intervals = data$intervals, options = data$options)

Since mclapply "relies on forking and hence is not available on Windows
unless ?mc.cores = 1?" (from ?mclapply), I can imagine that it's *not*
actually being run in parallel on Windows.  It also wouldn't surprise me
at all if it took a little bit of care to make sure that warnings were
correctly passed back from code chunks run in parallel.

   This StackOverflow post seems to ask the same question as yours:

http://stackoverflow.com/questions/21486658/warnings-suppressed-with-mclapply-in-r

   based on the discussion there, it seems as though it might be worth
bringing this up on r-devel/submitting a bug report ...

    Ben Bolker




On 16-07-20 03:13 PM, Bill Denney wrote:

Hi Fran?ois,

I thought that was the issue, too, but I confirmed it wasn't that by
adding a print statement right above the warning in my code. The print
statement displays the message even when the warning (one line below
with no conditionals between) doesn't show anything.

Also, why would it behave differently when options(warn=1) is set rather
than the default of options(warn=0)?

Thanks,

Bill


On 7/20/2016 3:06 PM, Fran?ois Michonneau wrote:

Hi Bill,

    The problem is not with the warning() function but with your if()
test that triggers the warning. It probably has something to do with
slight differences in rounding. I suggest you use debug() or browser()
on each platform to see why your condition is TRUE or FALSE.

    Cheers,
    -- Fran?ois

On Wed, Jul 20, 2016 at 2:42 PM, Bill Denney <bill at denney.ws> wrote:

Hi,

I'm developing the PKNCA package, and I've got an odd difference between
warning behavior on different operating systems that I can't figure out.

When I run the following code on Windows 10 (with R 3.3.0), I get the
following warning:

library(PKNCA)
source("https://raw.githubusercontent.com/billdenney/pknca/master/tests/testthat/generate.data.R")

tmpconc <- generate.conc(2, 1, 0:24)
tmpconc$conc <- 0
tmpdose <- generate.dose(tmpconc)
myconc <- PKNCAconc(tmpconc, conc~time|treatment+ID)
mydose <- PKNCAdose(tmpdose, dose~time|treatment+ID)
mydata <- PKNCAdata(myconc, mydose)
myresult <- pk.nca(mydata)

Warning messages:
1: In pk.calc.half.life(conc = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,  :
    Too few points for half-life calculation (min.hl.points=3 with only 0
points)
2: In pk.calc.half.life(conc = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,  :
    Too few points for half-life calculation (min.hl.points=3 with only 0
points)

When I run the code on Linux (Ubuntu 16.04 with R 3.3.1), I do not get a
warning.  When I run the code on Linux after "options(warn=1)", I get
the
warning.  I have confirmed that the same code path is taken in both
Windows
and Linux by simply inserting a print statement next to the warning.
The
actual warning code is:

      warning(sprintf(
        "Too few points for half-life calculation (min.hl.points=%g
with only
%g points)",
        min.hl.points, nrow(dfK)))

This platform inconsistency is causing issues with my package because
the
package expects the warnings, and the user should know about the
warnings.
I've got test cases expecting the warnings, and they fail everywhere but
Windows
(https://cran.r-project.org/web/checks/check_results_PKNCA.html).

Does anyone have an idea why warnings may behave differently on Windows
compared to non-Windows platforms?  Is this a bug in R somewhere?
(I've not
been able to make a simpler example that triggers the issue,
unfortunately.)

Thanks,

Bill