This was a bug in rtracklayer itself, not the vignette. It's fixed in
1.5.16.

Thanks,
Michael

On Thu, Sep 24, 2009 at 8:53 PM, LiGang <luzifer.li@gmail.com> wrote:

>
>
> Following code were taken from the 'rtracklayer' vignette, and will lead to
> an
> error message:
>
> #====================================================
> library(rtracklayer)
> session <- browserSession()
> data(cpneTrack)
>
> track(session, "cpne2", autoScale = FALSE, yLineOnOff = TRUE,
> yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack
>
> ##Error in .local(object, con, variant, color, ...) :
> ##unused argument(s) (autoScale = FALSE, yLineOnOff = TRUE, yLineMark =
>
> view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2")
>
> #Error in resolveTrackIndex(x, i) : Unknown tracks:cpne2
> #In addition: Warning message:
> #closing unused connection 3 ()
> #====================================================
>
>
>
> and the following code does work, i.e. you must specify the 'format' as
> 'wig':
>
>
> track(session, "cpne2", format="wig",autoScale = FALSE, yLineOnOff = TRUE,
> yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack
>
> view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2")
>
>
>
> #=============================================================
> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-14 r49685)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.5.15 RCurl_1.2-0        bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.7      Biostrings_2.13.43 BSgenome_1.13.14
> IRanges_1.3.79     Rcompression_0.6-0 tools_2.10.0
> [7] XML_2.6-0
>
>
> ---
> LiGang
>
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