On 05/09/2010 07:11 PM, Sigal Blay wrote:
> Why do I get this error message?
>
>> library("rtracklayer")
>> session <- browserSession()
>> x<-ucscTableQuery(session, "knownGene" , GenomicRanges(0,12000,"chr1"))
>
> Error in solveUserSEW0(start = start, end = end, width = width) :
> solving row 1: range cannot be determined from the supplied arguments (too
> many NAs)
> In addition: Warning message:
> In range(c("mammal", "hg19", "Human", "chr21:33,031,597-33,041,570" :
> NAs introduced by coercion
>
>> traceback()
>
> 10: .Call("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
> 9: solveUserSEW0(start = start, end = end, width = width)
> 8: IRanges(start, end)
> 7: GenomicRanges(range[1], range[2], posSplit[1], x[["db"]])
> 6: range(c("mammal", "hg19", "Human", "chr21:33,031,597-33,041,570"), na.rm =
> FALSE)
> 5: range(<S4 object of class "UCSCSession">, na.rm = FALSE)
> 4: mergeRange(range(x), range)
> 3: .local(x, ...)
> 2: ucscTableQuery(session, "knownGene", GenomicRanges(0, 1e+05, "chr1"))
> 1: ucscTableQuery(session, "knownGene", GenomicRanges(0, 1e+05, "chr1"))
Hi Sigal --
ask questions about Bioconductor packages on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Provide the output of sessionInfo(), and ensure that your packages are
up-to-date, e.g., following instructions at the bottom of
http://bioconductor.org/docs/install/
Your traceback() looks suspicious -- why 1e+05, and not 12000 ? Have you
copy / pasted correctly?
Post a new message when starting a new topic, rather than replying to an
unrelated article with a new title.
And FWIW
> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops
> session=browserSession()
> x = ucscTableQuery(session, "knownGene", GenomicRanges(0, 12000, "chr1"))
> sessionInfo()
R version 2.11.0 Patched (2010-05-01 r51886)
x86_64-unknown-linux-gnu
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=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 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_1.8.1 RCurl_1.4-1 bitops_1.0-4.1
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 Biostrings_2.16.0 BSgenome_1.16.1
[4] GenomicRanges_1.0.1 IRanges_1.6.0 XML_2.8-1
Martin
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
