Vincent, I tried changing nothing but the version (useDevel(devel=T)) and reinstalled Gviz and dependencies, and it worked. So, even if unintended symbol capture, the issue has been addressed in more recent version. Besides, I had tried it on a fresh R install to be sure it wasn't an unexpected interaction with my installation. So - it's a solved problem in devel version, which means it's a non- issue. Thanks for your help. W On Tue, Aug 21, 2012 at 5:35 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > In my opinion you are running into a method symbol collision owing to the > structure of your searchlist/loadlist. The run "succeeds" with the > following > > > > library(Gviz) > Loading required package: grid > Warning message: > No function found corresponding to methods exports from 'GenomicFeatures' > for: 'seqnameStyle' > > exfail=UcscTrack(track="CpG Islands", chromosome="chr6", genome="hg19", > + start="chromStart", end="chromEnd", name="CpG Islands", from=31731740, > + to=31736112) > > exfail > Annotation track 'CpG Islands' containing 0 items and mapping to > chromosome 6 of the hg19 genome: > > GRanges with 0 ranges and 0 elementMetadata cols: > seqnames ranges strand > <rle> <iranges> <rle> > --- > seqlengths: > > > R Under development (unstable) (2012-07-20 r59910) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] > en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII > > attached base packages: > [1] grid stats graphics grDevices datasets utils tools > [8] methods base > > other attached packages: > [1] Gviz_1.1.12 BiocInstaller_1.5.12 weaver_1.23.0 > [4] codetools_0.2-8 digest_0.5.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.19.28 Biobase_2.17.6 BiocGenerics_0.3.1 > [4] biomaRt_2.13.2 Biostrings_2.25.9 bitops_1.0-4.1 > [7] BSgenome_1.25.6 DBI_0.2-5 GenomicFeatures_1.9.29 > [10] GenomicRanges_1.9.47 IRanges_1.15.32 lattice_0.20-6 > [13] RColorBrewer_1.0-5 RCurl_1.91-1 Rsamtools_1.9.26 > [16] RSQLite_0.11.1 rtracklayer_1.17.16 stats4_2.16.0 > [19] XML_3.9-4 zlibbioc_1.3.0 > > of course i am using devel branch and the result is empty etc. etc. but > the stack trace you see looks to me to be a result of unintended symbol > capture. > > On Tue, Aug 21, 2012 at 4:08 PM, Winston Timp <wtimp1@jhmi.edu> wrote: > >> I seem to be having an issue with Ucsctrack in GViz: >> >> exfail=UcscTrack(track="CpG Islands", chromosome="chr6", genome="hg19", >> start="chromStart", end="chromEnd", name="CpG Islands", from=31731740, >> to=31736112) >> >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function ".buildRange", for >> signature "NULL", "logical", "logical", "NULL" >> >> This occurs when I try to get an area where there are no annotations(i.e. >> expected behavior is an empty object). Is this a known bug, or am I doing >> something horribly, horribly wrong? I'm using the release version of >> Gviz. >> >> traceback and sessionInfo included below. >> >> Thanks, >> >> Winston Timp >> >> > traceback() >> 6: stop("unable to find an inherited method for function \"", fdef@generic >> , >> "\", for signature ", cnames) >> 5: function (classes, fdef, mtable) >> { >> methods <- .findInheritedMethods(classes, fdef, mtable) >> if (length(methods) == 1L) >> return(methods[[1L]]) >> else if (length(methods) == 0L) { >> cnames <- paste0("\"", sapply(classes, as.character), >> "\"", collapse = ", ") >> stop("unable to find an inherited method for function \"", >> fdef@generic, "\", for signature ", cnames) >> } >> else stop("Internal error in finding inherited methods; didn't >> return a unique method") >> }(list("NULL", "logical", "logical", "NULL"), function (range, >> start, end, width, ...) >> standardGeneric(".buildRange"), <environment>) >> 4: .buildRange(range = range, start = start, end = end, width = width, >> args = list(feature = feature, group = group, id = id, strand = >> strand), >> defaults = list(feature = "unknown", group = group, id = id, >> strand = strand, density = 1), chromosome = chromosome) >> 3: AnnotationTrack(chromosome = "chr6", genome = "hg19", name = "CpG >> Islands", >> start = logical(0), end = logical(0)) >> 2: do.call(trackType, args = c(list(chromosome = chromosome, genome = >> genome, >> name = name), args)) >> 1: UcscTrack(track = "CpG Islands", chromosome = "chr6", genome = "hg19", >> start = "chromStart", end = "chromEnd", name = "CpG Islands", >> from = 31731740, to = 31736112) >> >> > sessionInfo() >> R version 2.15.1 Patched (2012-07-01 r59713) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] grid stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] Gviz_1.0.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.1 Biobase_2.16.0 BiocGenerics_0.2.0 >> [4] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 >> [7] BSgenome_1.24.0 DBI_0.2-5 GenomicRanges_1.8.12 >> [10] IRanges_1.14.4 lattice_0.20-6 RColorBrewer_1.0-5 >> [13] RCurl_1.91-1 Rsamtools_1.8.5 RSQLite_0.11.1 >> [16] rtracklayer_1.16.2 stats4_2.15.1 tools_2.15.1 >> [19] XML_3.9-4 zlibbioc_1.2.0 >> >> >> >> -- >> Winston Timp >> (410)-417-8467 >> Postdoctoral Fellow >> Johns Hopkins Medicine >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- Winston Timp (410)-417-8467 Postdoctoral Fellow Johns Hopkins Medicine [[alternative HTML version deleted]]