[BioC] rtracklayer, ucscTableQuery -> wgEncodeSydhTfbs, stalling, WHY?

Chris Fenton [guest] guest at bioconductor.org
Wed Sep 19 14:50:38 CEST 2012

Does anyone have a clue why the following code stalls. 

#Just testing functionality of the package 
>session <- browserSession("UCSC")
>query   <- ucscTableQuery(session, "wgEncodeSydhTfbs", GRangesForUCSCGenome("hg19","chr1", IRanges(100, 101)))


"""Get track 'wgEncodeSydhTfbs' within hg19:chr1:100-101"""


44 min and still running. 
This can't be right ? 

Anyone have a work around? 

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: i686-pc-linux-gnu (32-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] rtracklayer_1.16.3   GenomicRanges_1.8.13 IRanges_1.14.4      
[4] BiocGenerics_0.2.0  

loaded via a namespace (and not attached):
[1] Biostrings_2.24.1 bitops_1.0-4.1    BSgenome_1.24.0   RCurl_1.91-1     
[5] Rsamtools_1.8.6   stats4_2.15.0     tools_2.15.0      XML_3.9-4        
[9] zlibbioc_1.2.0   

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