[Bioc-devel] graph package conflict with rtracklayer

Cook, Malcolm MEC at stowers.org
Fri Jun 10 21:56:41 CEST 2011

Michael & Robert,

If I load the graph package prior to rtracklayer, import.bed generates an error and fails.  It otherwise succeeds if I don't load the graph package.

It happens both with rtracklayer from svn and production.


In a fresh session:

> library(graph)
> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops
> b <- import.bed('my.bed')
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "import.ucsc", for signature "file"
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] C

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

other attached packages:
[1] rtracklayer_1.13.3 RCurl_1.5-0        bitops_1.0-4.1     graph_1.30.0      

loaded via a namespace (and not attached):
[1] BSgenome_1.20.0     Biostrings_2.20.1   GenomicRanges_1.4.6
[4] IRanges_1.10.4      XML_3.4-0           tools_2.13.0       

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