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

[Ben Bolker]

   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 François,
> 
> 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, François 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,
>>    -- François
>>
>> 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
>>>
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel