[BioC] Gviz: UcscTrack function error

[Hahne, Florian]

Hi Michael(s),
this looks like a problem in the rtracklayer package. I can reproduce it
independently of any of the code in Gviz:

session <- browserSession()
genome(session) <- "mm9"
gr <- GRanges(seqnames="chr12", ranges=IRanges(start=57589600,
end=57639895))
ucscTableQuery(session, "cons30way", gr)
Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) :
  when 'new2old' is NULL, the first elements in the
  supplied 'seqlevels' must be identical to 'seqlevels(x)'

Would be great if you could take a look, Michael (Lawrence)

Florian





-- 






On 5/1/13 6:13 PM, "Michael Morley [guest]" <guest at bioconductor.org> wrote:

>
>I recently upgraded to R 3.0 and BioC 2.12. I upgraded all my BioC
>packages and having an error with Gviz
>
>If I try:
>
>chr="chr12" 
>start=57591600
>end=57637895
>conservation <- UcscTrack(genome = 'mm9', chromosome = chr,
>                          track = "Conservation", table =
>"phyloP30wayPlacental",
>                          from = start-2000, to = end+2000, trackType =
>"DataTrack",
>                          start = "start", end = "end", data = "score",
>                          type = "hist", window = "auto", col.histogram =
>"darkblue",
>                          fill.histogram = "darkblue", ylim = c(-.5, 4),
>                          name = "Conservation")
>
>
>I receive the following error:
>
>Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) :
>  when 'new2old' is NULL, the first elements in the
>  supplied 'seqlevels' must be identical to 'seqlevels(x)'
>
>> traceback()
>9: stop("when 'new2old' is NULL, the first elements in the\n", "
>supplied 'seqlevels' must be identical to 'seqlevels(x)'")
>8: makeNewSeqnames(x, new2old = new2old, seqlevels(value))
>7: `seqinfo<-`(`*tmp*`, value = <S4 object of class "Seqinfo">)
>6: `seqinfo<-`(`*tmp*`, value = <S4 object of class "Seqinfo">)
>5: normGenomeRange(range, x, single = FALSE)
>4: .local(x, ...)
>3: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr)
>2: ucscTableQuery(sessionInfo$session, sessionInfo$track, gr)
>1: UcscTrack(genome = "mm9", chromosome = chr, track = "Conservation",
>       table = "phyloP30wayPlacental", from = start - 2000, to = end +
>           2000, trackType = "DataTrack", start = "start", end = "end",
>       data = "score", type = "hist", window = "auto", col.histogram =
>"darkblue", 
>       fill.histogram = "darkblue", ylim = c(-0.5, 4), name =
>"Conservation")
>
>
>Any suggestions?
>
>Thank you,
>
>Mike
>
>
>
> -- output of sessionInfo():
>
>R version 3.0.0 (2013-04-03)
>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=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>attached base packages:
>[1] grid      stats     graphics  grDevices utils     datasets  methods
>[8] base     
>
>other attached packages:
>[1] Gviz_1.4.1
>
>loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.22.3   Biobase_2.20.0         BiocGenerics_0.6.0
> [4] biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.0
> [7] bitops_1.0-5           BSgenome_1.28.0        cluster_1.14.4
>[10] colorspace_1.2-2       DBI_0.2-6              dichromat_2.0-0
>[13] GenomicFeatures_1.12.1 GenomicRanges_1.12.2   Hmisc_3.10-1
>[16] IRanges_1.18.0         labeling_0.1           lattice_0.20-15
>[19] munsell_0.4            parallel_3.0.0         plyr_1.8
>[22] RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.12.2
>[25] RSQLite_0.11.3         rtracklayer_1.20.1     scales_0.2.3
>[28] stats4_3.0.0           stringr_0.6.2          tools_3.0.0
>[31] XML_3.96-1.1           zlibbioc_1.6.0
>
>
>--
>Sent via the guest posting facility at bioconductor.org.