On Sun, Sep 6, 2009 at 8:48 PM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

> Dear Bioc-sig-sequencing,
>
> I would like to learn about the rtracklayer package by working thru its
> vignette using code in rtracklayer.R
>
> I have tried using both the stable and developer versions of R.  There
> appears to be an error when using the stable version.  The developer version
> comes to a point where I don't know how to proceed.  A short description for
> each attempt follows.
>
> P.Terry
> pterry@huskers.unl.edu
>
> ##########################################################################
>
> 1. Stable version.
>
> Chunk 19 produces error message:
>
> > subTargetTrack <- targetTrack[1,] # get first feature
> > view <- browserView(session, range(subTargetTrack) * -10,
> +                     pack = "targets")
> Error in resolveTrackIndex(x, i) : Unknown tracks:targets
> >
>
> If skip forward to chunk 22 (2.2.4 A shortcut)
>
> > browseGenome(subTargetTrack)
> A genome browser session of class 'UCSCSession' with 1 views and 206 tracks
> >
>
> Produces new Foxfire browser page at ucsc browser, but with a window (box)
> near top of the page with the error message:
>
>                                  Error(s):
>
>    * Sorry, couldn't locate chrchr1 in genome database
>
> My sessionInfo() is:
>
> > sessionInfo()
> R version 2.9.2 (2009-08-24)
> x86_64-pc-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] rtracklayer_1.4.1     RCurl_0.98-1          bitops_1.0-4.1
>  [4] org.Hs.eg.db_2.2.11   microRNA_1.2.0        Rlibstree_0.3-2
>  [7] Biostrings_2.12.8     IRanges_1.2.3         limma_2.18.3
> [10] genefilter_1.24.2     humanStemCell_0.2.2   hgu133plus2.db_2.2.11
> [13] RSQLite_0.7-2         DBI_0.2-4             AnnotationDbi_1.6.1
> [16] Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] annotate_1.22.0 BSgenome_1.12.3 splines_2.9.2   survival_2.35-5
> [5] tools_2.9.2     XML_2.5-1       xtable_1.5-5
> >
>
>
> 2. Developer version (R-49517)
>
> At chunk 14:
>
> > track(session, "targets") <- targetTrack
> Called from: FUN(X[[1L]], ...)
> Browse[1]>
>
> My question is what to do at this point?
>
>
Sorry, just checked in change (version 1.5.13) to remove a stray browser()
command. Should be fixed in devel.

Michael


> Ctl^C won't return to R prompt ?
>
> My sessionInfo() is
>
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-01 r49517)
> x86_64-unknown-linux-gnu
>
> 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=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] rtracklayer_1.5.12   RCurl_1.2-0          bitops_1.0-4.1
>  [4] microRNA_1.3.1       Rlibstree_0.3-2      Biostrings_2.13.36
>  [7] IRanges_1.3.66       limma_2.19.4         genefilter_1.25.7
> [10] humanStemCell_0.2.3  hgu133plus2.db_2.3.4 org.Hs.eg.db_2.3.4
> [13] RSQLite_0.7-2        DBI_0.2-4            AnnotationDbi_1.7.11
> [16] Biobase_2.5.6
>
> loaded via a namespace (and not attached):
> [1] annotate_1.23.1  BSgenome_1.13.11 splines_2.10.0   survival_2.35-5
> [5] tools_2.10.0     XML_2.6-0        xtable_1.5-5
>
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>

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