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Last seen 10.2 years ago
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)))
>query
"""Get track 'wgEncodeSydhTfbs' within hg19:chr1:100-101"""
getTable(query)
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)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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