Thanks, the warning/error has already been suggested and I've been meaning
to commit it. It will be in the next release.
On Wed, Sep 4, 2013 at 7:00 PM, Dario Strbenac
<dstr7...@uni.sydney.edu.au>wrote:
> Hello,
>
> I get an error :
>
> > session <- browserSession("UCSC")
> > consQuery <- ucscTableQuery(session, "Conservation",
> GRangesForUCSCGenome("hg9", "chr1", IRanges(100000000, 101000000)),
> "phyloP46wayPlacental")
> > consQuery
> Get table 'phyloP46wayPlacental' from track 'Conservation' within
> hg19:chr1:100000000-101000000
> > conservation <- track(consQuery)
> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
> :
> solving row 100001: range cannot be determined from the supplied
> arguments (too many NAs)
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] rtracklayer_1.20.4 GenomicRanges_1.12.5 IRanges_1.18.3
> [4] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 RCurl_1.95-4.1
> [5] Rsamtools_1.12.4 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1
> [9] zlibbioc_1.6.0
>
> This could be because of a limit on the size of the results from the UCSC
> server. It works with a smaller width query 1000 bases wide. It could fail
> with a more informative error, and provide a warning about this in the help
> file of ucscTableQuery. I wish we could convince UCSC to remove these
> restrictions from a time when computing power was much less.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
