On Wed, Sep 19, 2012 at 8:54 AM, Fenton Christopher Graham <
christopher.fenton@uit.no> wrote:

> 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?
>
>
This is an interesting little debugging problem.  If you run with something
like options(error=recover) and interrupt after a little while you'll see a
complicated traceback and you can poke around in the stack.

Basically, the query you have issued involves 781 tables.  A checking
operation is applied to each of them.  If you really want this computation,
you may have to wait.


a little more detail

Browse[3]> object
Get track 'wgEncodeSydhTfbs' within hg19:chr1:100-101


Browse[3]> tableName(object)
NULL

this sends us into

4: tableNames(object)
 5: tableNames(object)
 6: .local(object, ...)
 7: sapply(tables, checkOutput)
 8: sapply(tables, checkOutput)
 9: lapply(X = X, FUN = FUN, ...)
10: FUN(c("wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk",
"wgEncodeSydhTfbsGm12878Bh

with a vector of 781 tables to be checked.  perhaps you can focus your
query, or retrieve the specific data you want for local import to R


> Chris
>
> 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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