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

[Bill Denney]

Max and Ben got the right answer.  It is a bug with mclapply dropping 
warnings.  I confirmed by a quick change to the code to just use lapply, 
and the warnings appeared as expected.

I've submitted the bug at 
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17122

Thanks for the help!

Bill


On 7/20/2016 3:40 PM, Ben Bolker wrote:
>     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