[Bioc-devel] BUG? rtracklayer import.bed on a connection hangs

Cook, Malcolm MEC at stowers.org
Thu Jan 19 19:53:52 CET 2012

I find that 

	x<-import (pipe("head my.bed"),'bed')

succeeds, thank you very much ;)

whereas both of the following

	x<-import.bed(pipe("head my.bed"))

	x<-import.bed(pipe("head my.bed"),'base',TRUE)

hang, never returning and using CPU ;(

Is there a difference I am not appreciating, or is this a BUG?


Malcolm Cook
Stowers Institute for Medical Research

> sessionInfo()
R version 2.14.0 (2011-10-31)
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_1.14.4 RCurl_1.9-4        bitops_1.0-4.1    

loaded via a namespace (and not attached):
[1] BSgenome_1.22.0     Biostrings_2.22.0   GenomicRanges_1.6.4
[4] IRanges_1.12.5      XML_3.6-2           tools_2.14.0       
[7] zlibbioc_1.0.0     

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