I've removed all finalizers on these classes for this version and are still seeing it. I'll try with gctorture on and see if I can track it down. Any finalizers on GenomicRanges? GNCList or GRanges?
On Fri, Apr 29, 2016 at 3:42 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > I don't think there are any reference classes in GenomeInfoDb. This > must be something weird happening to one of the epivizr reference > classes. It just shows up in that stack trace under GenomeInfoDb > because of the GC. I haven't managed to reproduce it yet though. > > Michael > > On Fri, Apr 29, 2016 at 12:15 PM, Michael Lawrence <micha...@gene.com> > wrote: > > I can look into it. I guess it fails sporadically because of the > > garbage collector. Activating GC torture might make this easier to > > reproduce. > > > > On Fri, Apr 29, 2016 at 12:06 PM, Hector Corrada Bravo > > <hcorr...@gmail.com> wrote: > >> I've seen this type of error for a while and have really struggled to > track > >> it down. I have a package with unit tests that sporadically fail on R > CMD > >> check with errors of this type: > >> > >> --- > >>> test_check("epivizrData") > >> 1. Error: new creates a proper object (@test-creation.R#17) > >> -------------------- > >> attempt to apply non-function > >> 1: expect_equal(mgr$.seqinfo, GenomeInfoDb::Seqinfo()) at > >> testthat/test-creation.R:17 > >> 2: compare(object, expected, ...) > >> 3: compare.default(object, expected, ...) > >> 4: all.equal(x, y, ...) > >> 5: all.equal.default(x, y, ...) > >> 6: GenomeInfoDb::Seqinfo() > >> 7: .normargGenome(genome, seqnames) > >> 8: rep.int(ugenome, length(seqnames)) > >> 9: (function (classes, fdef, mtable) > >> { > >> methods <- .findInheritedMethods(classes, fdef, mtable) > >> if (length(methods) == 1L) > >> return(methods[[1L]]) > >> else if (length(methods) == 0L) { > >> cnames <- paste0("\"", vapply(classes, as.character, ""), > "\"", > >> collapse = ", ") > >> stop(gettextf("unable to find an inherited method for > function > >> %s for signature %s", > >> sQuote(fdef@generic), sQuote(cnames)), domain = NA) > >> } > >> else stop("Internal error in finding inherited methods; didn't > >> return a unique method", > >> domain = NA) > >> })(list("character"), structure(function (x, times) > >> standardGeneric("rep.int"), generic = structure("rep.int", package = > >> "base"), package = "base", group = list(), valueClass = character(0), > >> signature = c("x", > >> "times"), default = structure(function (x, times) > >> .Internal(rep.int(x, times)), target = structure("ANY", class = > >> structure("signature", package = "methods"), .Names = "x", package = > >> "methods"), defined = structure("ANY", class = structure("signature", > >> package = "methods"), .Names = "x", package = "methods"), generic = > >> structure("rep.int", package = "base"), class = > >> structure("derivedDefaultMethod", package = "methods")), skeleton = > >> (structure(function (x, > >> times) > >> .Internal(rep.int(x, times)), target = structure("ANY", class = > >> structure("signature", package = "methods"), .Names = "x", package = > >> "methods"), defined = structure("ANY", class = structure("signature", > >> package = "methods"), .Names = "x", package = "methods"), generic = > >> structure("rep.int", package = "base"), class = > >> structure("derivedDefaultMethod", package = "methods")))(x, > >> times), class = structure("standardGeneric", package = > "methods")), > >> <environment>) > >> 10: .findInheritedMethods(classes, fdef, mtable) > >> 11: .inheritedArgsExpression(m@target, m@defined, body(m)) > >> 12: extends(target[[i]], defined[[i]], fullInfo = TRUE) > >> 13: target[[i]] > >> 14: (function (x) > >> x$.self$finalize())(<environment>) > >> --- > >> > >> I do not define any finalize method on classes defined on my package. > This > >> stems from a finalizer on a class defined in a package imported by my > >> package (GenomeInfoDb), which I'm guessing is detached from the > environment > >> before this finalize function is called. > >> > >> Any ideas on how to avoid this error? > >> > >> Package source here: > >> https://github.com/bioconductor-mirror/epivizrData > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel