This took some discussion, but it's finally resolved in devel and release.

Michael


On Thu, May 2, 2013 at 12:26 AM, Hahne, Florian
<florian.hahne@novartis.com>wrote:

> 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@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.
>
>

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