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

[Michael Lawrence]

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
>