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@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.ta...@imperial.ac.uk> 62472 m.carlson Maintainer: Florian Hahne <florian.ha...@novartis.com> 89957 hpa...@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 hpa...@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" <mtmor...@fhcrc.org> wrote: >On 05/05/2014 10:56 AM, Sebastian Gibb wrote: >> Dear Florian, >> >> On 2014-05-05 16:17:41, florian.ha...@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.ha...@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@stacks <- x@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.deb...@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@start, end=obj@end, name = "a", >>>> chromosome = "chr0", genome = "all") >>>> plotTracks(aTrack, from = min(obj@start), to = max(obj@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@start[i], >>>> x@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 >>> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > >-- >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M1 B861 >Phone: (206) 667-2793 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
