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

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 ?A? dummy
class and the ?[? 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 ?[? 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 ?function?)

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 ?function?)
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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