[Bioc-devel] Gviz AnnotationTrack fails when "["-operator is defined
Martin Morgan
mtmorgan at fhcrc.org
Tue May 6 01:09:48 CEST 2014
On 05/05/2014 10:56 AM, Sebastian Gibb wrote:
> Dear Florian,
>
> On 2014-05-05 16:17:41, florian.hahne at novartis.com wrote:
>> Hm, this looks odd indeed. I am wondering whether this is some sort of
>> name space problem. Does the same happen when you create your ³A² dummy
>> class and the ³[³ method in a little dummy package with its own name
>> space?
> Your guess was right! I created a small dummy package
> ( https://github.com/sgibb/dummyA ). And after loading it with `library`
> everything works like expected.
> But if I load it with devtools' `load_all` it crashes with the same error:
>
> Error in callNextMethod(x, i) :
> bad object found as method (class "function")
>
> Kind regards,
>
> Sebastian
>
> On 2014-05-05 16:17:41, florian.hahne at novartis.com wrote:
>> Something seems to be messing up the methods table when you define
>> the ³[³ method from the global environment.
>> Any advice from the name space gurus on the list?
I looked a little at this, and it seems like a methods bug in callNextMethod
when invoked inside a .local function. It can be worked around by revising Gviz
"[" method definitions as
setMethod("[", signature(x="StackedTrack"), function(x, i, j, ..., drop=TRUE) {
x <- callNextMethod(x,i)
x at stacks <- x at stacks[i]
return(x)})
A simple reproducible example is
.A = setClass("A", "numeric")
setMethod("[", "A", function(x, i) callNextMethod(x, i))
and then
> .A()[]
Error in callNextMethod(x, i) :
bad object found as method (class “function”)
Martin
>> Florian
>>
>> On 04/05/14 13:48, "Sebastian Gibb" <sgibb.debian at gmail.com> wrote:
>>
>>> Dear Florian, dear all,
>>>
>>> I want to use Gviz::AnnotationTrack to visualize my own class. This class
>>> overloads the "[" operator. It seems that just the definition of my own
>>> "["
>>> results in a method dispatching error:
>>>
>>> Error in callNextMethod(x, i) :
>>> bad object found as method (class ³function²)
>>>
>>> After defining "[" even AnnotationTrack instances that are not using my
>>> class
>>> throw this error.
>>>
>>> I do not understand the error. Did I something wrong? Can somebody
>>> enlighten me?
>>>
>>> Please find a minimal reproducible example below.
>>>
>>> Kind regards,
>>>
>>> Sebastian
>>>
>>> ###
>>> library("Gviz")
>>>
>>> ## create dummy class
>>> setClass("A",
>>> slots = list(start = "numeric", end = "numeric"),
>>> prototype = prototype(
>>> start = integer(),
>>> end = integer()))
>>>
>>> ## define a plotting function for A
>>> plotGVizA <- function(obj) {
>>> aTrack <- AnnotationTrack(start=obj at start, end=obj at end, name = "a",
>>> chromosome = "chr0", genome = "all")
>>> plotTracks(aTrack, from = min(obj at start), to = max(obj at end))
>>> }
>>>
>>> ## define a plotting function without any A
>>> plotGViz <- function() {
>>> aTrack <- AnnotationTrack(start=c(1, 5), end=c(3, 10), name = "a",
>>> chromosome = "chr0", genome = "all")
>>> plotTracks(aTrack, from = 1, to = 10)
>>> }
>>>
>>> ## create an object of class A
>>> a <- new("A", start=c(1, 5), end=c(3, 10))
>>>
>>> ## works
>>> plotGViz()
>>> plotGVizA(a)
>>>
>>> ## define the "[" operator for A
>>> setMethod("[", "A", function(x, i, j, ...) { return(c(x at start[i],
>>> x at end[i])) })
>>>
>>> ## crashes with the following error message:
>>> ## Error in callNextMethod(x, i) :
>>> ## bad object found as method (class ³function²)
>>> plotGVizA(a)
>>> plotGViz()
>>>
>>> traceback()
>>> #12: stop(gettextf("bad object found as method (class %s)",
>>> # dQuote(class(method))), domain = NA)
>>> #11: callNextMethod(x, i)
>>> #10: .local(x, i, ...)
>>> #9: GdObject[seqnames(GdObject) == chromosome(GdObject)]
>>> #8: .computeGroupRange(GdObject, hasAxis = hasAxis, hasTitle = hasTitle,
>>> # title.width = title.width)
>>> #7: .local(GdObject, ...)
>>> #6: FUN(X[[1L]], ...)
>>> #5: FUN(X[[1L]], ...)
>>> #4: lapply(trackList, consolidateTrack, chromosome = chromosome,
>>> # any(.needsAxis(trackList)), any(.needsTitle(trackList)),
>>> # title.width, alpha = hasAlpha, ...)
>>> #3: lapply(trackList, consolidateTrack, chromosome = chromosome,
>>> # any(.needsAxis(trackList)), any(.needsTitle(trackList)),
>>> # title.width, alpha = hasAlpha, ...)
>>> #2: plotTracks(aTrack, from = 1, to = 10) at #4
>>> #1: plotGViz()
>>>
>>> sessionInfo()
>>> #R version 3.1.0 (2014-04-10)
>>> #Platform: x86_64-pc-linux-gnu (64-bit)
>>> #
>>> #locale:
>>> # [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> # [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> # [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>> # [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>> # [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> #[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>> #
>>> #attached base packages:
>>> #[1] parallel grid stats graphics grDevices utils datasets
>>> #[8] methods base
>>> #
>>> #other attached packages:
>>> #[1] XVector_0.4.0 IRanges_1.22.6 Gviz_1.8.0
>>> #[4] BiocGenerics_0.10.0 devtools_1.5 vimcom.plus_0.9-93
>>> #[7] setwidth_1.0-3 colorout_1.0-2
>>> #
>>> #loaded via a namespace (and not attached):
>>> # [1] AnnotationDbi_1.26.0 BatchJobs_1.2
>>> # [3] BBmisc_1.6 Biobase_2.24.0
>>> # [5] BiocParallel_0.6.0 biomaRt_2.20.0
>>> # [7] Biostrings_2.32.0 biovizBase_1.12.1
>>> # [9] bitops_1.0-6 brew_1.0-6
>>> #[11] BSgenome_1.32.0 cluster_1.15.2
>>> #[13] codetools_0.2-8 colorspace_1.2-4
>>> #[15] DBI_0.2-7 dichromat_2.0-0
>>> #[17] digest_0.6.4 evaluate_0.5.5
>>> #[19] fail_1.2 foreach_1.4.2
>>> #[21] Formula_1.1-1 GenomeInfoDb_1.0.2
>>> #[23] GenomicAlignments_1.0.1 GenomicFeatures_1.16.0
>>> #[25] GenomicRanges_1.16.3 Hmisc_3.14-4
>>> #[27] httr_0.3 iterators_1.0.7
>>> #[29] lattice_0.20-29 latticeExtra_0.6-26
>>> #[31] matrixStats_0.8.14 memoise_0.2.1
>>> #[33] munsell_0.4.2 plyr_1.8.1
>>> #[35] RColorBrewer_1.0-5 Rcpp_0.11.1
>>> #[37] RCurl_1.95-4.1 R.methodsS3_1.6.1
>>> #[39] Rsamtools_1.16.0 RSQLite_0.11.4
>>> #[41] rtracklayer_1.24.0 scales_0.2.4
>>> #[43] sendmailR_1.1-2 splines_3.1.0
>>> #[45] stats4_3.1.0 stringr_0.6.2
>>> #[47] survival_2.37-7 tools_3.1.0
>>> #[49] VariantAnnotation_1.10.1 whisker_0.3-2
>>> #[51] XML_3.98-1.1 zlibbioc_1.10.0
>>
>
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