Just a note: this is a long-standing bug. I'll try to look into it soon.

Michael

On Mon, Oct 22, 2012 at 12:29 PM, J.T. Poirier <poirier@jhmi.edu> wrote:

> I recently updated my R packages and some code that I used to run with
> rtracklayer started failing. In particular, laying a new track was failing
> silently. I found that the same bug is reproducible in the vignette, but
> eval=FALSE for the code chunk in question and thus the vignette compiles to
> PDF as normal. Can anyone else reproduce this bug? Code and session info
> below.
>
> # This code chunk fails without an error.
>
> ###################################################
> ### code chunk number 15: layTrack (eval = FALSE)
> ###################################################
> ## track(session, "targets") <- targetTrack
>
> # We know the code is failing due to the below code and output
> table(trackNames(session)=="targets")
>
> FALSE
>   223
>
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
>
> locale:
> [1] C/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII
>
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
>
> other attached packages:
>  [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19
>  [2] BSgenome_1.26.0
>  [3] Biostrings_2.26.0
>  [4] rtracklayer_1.18.0
>  [5] GenomicRanges_1.10.0
>
>
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>
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