[Bioc-devel] Spurious errors unit testing on R CMD check

[Hector Corrada Bravo]

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.michael at 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 <michafla at 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
> > <hcorrada at 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 at 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 at target, m at 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 at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>

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