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

Michael Lawrence lawrence.michael at gene.com
Fri Apr 29 21:42:23 CEST 2016


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]]
>>
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>>



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