[Bioc-devel] Gviz AnnotationTrack fails when "["-operator is defined
Hahne, Florian
florian.hahne at novartis.com
Tue May 6 11:25:03 CEST 2014
Thanks Martin,
Btw, is there some sort of disconnect on BioC Devel right now with regards
to the latest package versions? Since the release there are some rather
strict requirements in my DESCRIPTION file, but some of the packages
versions are not available from BiocLite:
[s_itoxadm at chbslx1501:~/Rpacks/Gviz]$ svn blame DESCRIPTION
62472 m.carlson Package: Gviz
89967 fhahne Version: 1.9.3
62472 m.carlson Title: Plotting data and annotation information along
genomic coordinates
80543 fhahne Author: Florian Hahne, Steffen Durinck, Robert Ivanek,
Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09 at imperial.ac.uk>
62472 m.carlson Maintainer: Florian Hahne <florian.hahne at novartis.com>
89957 hpages at fhcrc.org Depends: R (>= 2.10.0), methods, grid,
BiocGenerics (>= 0.11.2), S4Vectors (>= 0.0.1), IRanges (>= 1.99.1),
GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.11)
89957 hpages at fhcrc.org Imports: XVector (>= 0.5.3), rtracklayer (>=
1.25.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>=
1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.5), BSgenome (>=
1.33.1), Biostrings (>= 2.33.3), biovizBase (>= 1.13.7), Rsamtools (>=
1.17.8), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14),
GenomicAlignments (>= 1.1.9)
85562 fhahne Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
62472 m.carlson biocViews: Visualization, Microarray
62472 m.carlson Description: Genomic data analyses requires integrated
visualization of known genomic information and new experimental data.
Gviz uses the biomaRt and the rtracklayer packages to perform live
annotation queries to Ensembl and UCSC and translates this to e.g.
gene/transcript structures in viewports of the grid graphics package. This
results in genomic information plotted together with your data.
62472 m.carlson Collate: Gviz.R AllGenerics.R AllClasses.R Gviz-methods.R
62472 m.carlson License: Artistic-2.0
62472 m.carlson LazyLoad: yes
62472 m.carlson
Available rtracklayer for example is only 1.25.4
http://www.bioconductor.org/packages/devel/bioc/html/rtracklayer.html
But the version in the svn is Version: 1.25.5
Any idea what went wrong there?
Florian
On 06/05/14 01:09, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
>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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>>
>
>
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