[Bioc-sig-seq] Running rtracklayer vignette

[pterry at huskers.unl.edu]

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 at 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?

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