[BioC] GenomeGraphs 1.4.0 fails to plot empty GeneRegion

Tim Rayner tfrayner at gmail.com
Wed May 6 12:41:29 CEST 2009


I don't know if this is by accident or design, but some code I had
working with GenomeGraphs 1.2.3 is now failing under version 1.4.0.
I've reduced the problem to the following test case:

> require('biomaRt')
> require('GenomeGraphs')
> mart <- useDataset('hsapiens_gene_ensembl', useMart('ensembl'))
> genesminus <- makeGeneRegion(start = 10662805, end = 10718158, strand = "-",  chromosome=12, biomart=mart)
> genesplus  <- makeGeneRegion(start = 10662805, end = 10718158, strand = "+",  chromosome=12, biomart=mart)
> gdPlot(list('minus strand'=genesminus, 'plus strand'=genesplus))

This draws the minus strand just fine, but the plus strand (which, I
think crucially, retrieves no genes) fails with the following message:

"Error in if (ens[1, 6] == 1) { : missing value where TRUE/FALSE needed"

I know that the same code running under R 2.8.1/BioC 2.3/GenomeGraphs
1.2.3 draws both strands without complaining. Is this change to
GenomeGraphs behaviour intentional, or can this be considered a bug?

Many thanks,


> sessionInfo()
R version 2.9.0 (2009-04-17)


attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomeGraphs_1.4.0 biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_2.3-0

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