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 <b...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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