Apologies for the long post. This is an issue I have been struggling with and I have tried to be as complete, to the point, and reproducible as possible.
In documenting a package with roxygen2, I have come across an error that does not occur in R 3.2.4 revised, but does occur in R 3.3.0 and 3.3.1. Using traceback() and debug(), I've traced the error to a call made to as.vector(x, "character") that seems to get stuck in a loop which culminates in this error: Error: C stack usage 7970892 is too close to the limit The object that causes this error is of a signature type for a method. With some playing around, I've been able to work out that the error is actually associated with the method that roxygen2 creates when doing its magic. Something happens when this method definition with its associated environment is in the workspace that causes the error. At this point, I should stress again that the error does NOT occur in R 3.2.4 revised or earlier, but does occur in R 3.3.0 and 3.3.1. I have also tested this with several versions of roxygen2 and that does not make a difference. Thus, my ultimate question is what has changed in R 3.3.0 that would lead to this so that the roxygen2 maintainers can correct it? As a test, I created a signature identical to the one that causes the error and tried the as.vector() command that would generate the loop. I don't get the error in my command line generated object, nor with the object that is extracted from the method definition. However, when I load the method definition into the workspace, the error will happen on either my command line generated object, or the one extracted from the method definition and will not stop happening until I restart R. I have reported this error as an issue on the roxygen2 GitHub repository and it has been crossposted by another user who had a similar experience with a different package on the devtools repository. Those posts, which contain more information are here: https://github.com/klutometis/roxygen/issues/475 https://github.com/hadley/devtools/issues/1234 Below is the result of sessionInfo() and the output of a session demonstrating the effect. The files used are in a zip file here: https://github.com/klutometis/roxygen/files/335417/error.test.rdata.files.zip > sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.3.0 > rm(list = ls()) > > # Create test class and method > setClass(Class = "gtypes", slots = c(loci = "data.frame", ploidy = "numeric"), package = "roxygen_devtest") > setGeneric("nInd", function(x, ...) standardGeneric("nInd"), package = "adegenet") [1] "nInd" > setMethod("nInd", "gtypes", function(x, ...) nrow(x@loci) / x@ploidy) [1] "nInd" > > test.method <- getMethod("nInd", "gtypes") > str(test.method) Formal class 'MethodDefinition' [package "methods"] with 4 slots ..@ .Data :function (x, ...) ..@ target :Formal class 'signature' [package "methods"] with 3 slots .. .. ..@ .Data : chr "gtypes" .. .. ..@ names : chr "x" .. .. ..@ package: chr "roxygen_devtest" ..@ defined:Formal class 'signature' [package "methods"] with 3 slots .. .. ..@ .Data : chr "gtypes" .. .. ..@ names : chr "x" .. .. ..@ package: chr "roxygen_devtest" ..@ generic: atomic [1:1] nInd .. ..- attr(*, "package")= chr "adegenet" > > # No error: > as.vector(test.method@defined, "character") [1] "gtypes" > > # This is the method that generates the error > load("problem.method.rdata") > > # Notice the difference in the environments of the two functions: > test.method@.Data function (x, ...) nrow(x@loci)/x@ploidy > problem.method@.Data function (x, ...) nrow(x@loci)/x@ploidy <environment: 0x101f85040> > > # Swap the problem function for the one I created: > problem.method@.Data <- test.method@.Data > save(problem.method, file = "fixed.method.rdata") > > # Here's the error (both with my method and the original): > as.vector(test.method@defined, "character") Error: C stack usage 7970892 is too close to the limit > as.vector(problem.method@defined, "character") Error: C stack usage 7970892 is too close to the limit Restarting R session... > # *** Restart R for this to work *** > rm(list = ls()) > > load("fixed.method.rdata") > as.vector(problem.method@defined, "character") [1] "gtypes" ---- *Eric Archer, Ph.D.* Southwest Fisheries Science Center NMFS, NOAA 8901 La Jolla Shores Drive La Jolla, CA 92037 USA 858-546-7121 (work) 858-546-7003 (FAX) Marine Mammal Genetics Group: swfsc.noaa.gov/mmtd-mmgenetics ETP Cetacean Assessment Program: swfsc.noaa.gov/mmtd-etp https://github/ericarcher " *The universe doesn't care what you believe. The wonderful thing about science is that it doesn't ask for your faith, it just asks for your eyes.*" - Randall Munroe "*Lighthouses are more helpful than churches.*" - Benjamin Franklin "*...but I'll take a GPS over either one.*" - John C. "Craig" George [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
