[BioC] rtracklayer bug? cannot coerce type 'externalptr' to vector of type 'double' in browseGenome call

[Paul Shannon]

Hi Michael,

Updating XML (and rJava, since I was at it) removed the problem  
nicely.  Thank you.

rtracklayer is a very impressive piece of software.  Nice work.

- Paul


On Jan 26, 2009, at 7:26 AM, Michael Lawrence wrote:

>
>
> On Mon, Jan 26, 2009 at 5:06 AM, Paul Shannon <pshannon at systemsbiology.org 
> > wrote:
> I am following the vignette provided by the 1.2.2 rtracklayer  
> package -- and delighted to find such capabilities in bioc!
>
> When I call, browseGenome(subTargetTrack)
>
> I get this error (with traceback and sessionInfo to follow).  Can  
> anyone help?
>
> Not sure what happened here, as it's specified in DESCRIPTION, but  
> somehow your XML version (1.95) does not match the requirements of  
> rtracklayer (1.98). Please upgrade your XML package and see if that  
> works.
>
> Thanks,
> Michael
>
>
> - Paul
>
> Error in as.numeric(hgsid) :
> cannot coerce type 'externalptr' to vector of type 'double'
> > traceback ()
> 5: browserView(<S4 object of class "ucscSession">, <S4 object of  
> class "genomeSegment">)
> 4: browserView(<S4 object of class "ucscSession">, <S4 object of  
> class "genomeSegment">)
> 3: do.call("browserView", viewParams)
> 2: browseGenome(subTargetTrack)
> 1: browseGenome(subTargetTrack)
> > sessionInfo ()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.2.2    RCurl_0.94-0         org.Hs.eg.db_2.2.6    
> microRNA_1.0.0       Rlibstree_0.3-1      matchprobes_1.14.1    
> affy_1.20.2
> [8] limma_2.16.4         genefilter_1.22.0    survival_2.34-1       
> humanStemCell_0.2.0  hgu133plus2.db_2.2.5 RSQLite_0.6-9         
> DBI_0.2-4
> [15] AnnotationDbi_1.4.2  Biobase_2.2.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.10.15   IRanges_1.0.9        Matrix_0.999375-18    
> XML_1.95-2           affyio_1.8.0         annotate_1.20.1       
> grid_2.8.1
> [8] lattice_0.17-17      preprocessCore_1.4.0 rJava_0.5-1
>
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