[R] rtracker dependencies installation problem?

[Martin Morgan]

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

> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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