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]]
>>
>> _______________________________________________
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>>
>
>


-- 
Winston Timp
(410)-417-8467
Postdoctoral Fellow
Johns Hopkins Medicine

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