[Bioc-devel] Gviz AnnotationTrack fails when "["-operator is defined

[Hahne, Florian]

Hi Sebastian,
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? 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?
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