[BioC] GetSeq function problems

Hervé Pagès hpages at fhcrc.org
Tue Aug 4 18:55:21 CEST 2009


Hi Arnaud,

Droit Arnaud wrote:
> Hello,
> 
> I am using getSeq function from Bsgenome to extract a set of sequence.
> When I try the example in the RD file :
> 
> library(BSgenome.Celegans.UCSC.ce2)
> myseqs <- data.frame(
>          chr=c("chrI", "chrX", "chrM", "chrM", "chrX", "chrI", "chrM", "chrI"),
>          start=c(NA, -40, 8510, 301, 30001, 9220500, -2804, -30),
>          end=c(50, NA, 8522, 324, 30011, 9220555, -2801, -11),
>          strand=c("+", "-", "+", "+", "-", "-", "+", "-")
>        )
>  getSeq(Celegans, myseqs$chr,
>               start=myseqs$start, end=myseqs$end)
> 
> a following message appear :
> 
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>   object '.normargSEW' not found
> 
> I am wondering if anyone knows this problems.

Please update your installation as explained here:

   http://bioconductor.org/docs/install/

and try again. Let us know if the problem persists.

Thanks,
H.


> 
> Thanks
> 
> Arnaud.
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin9.6.0
> 
> locale:
> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BSgenome.Celegans.UCSC.ce2_1.3.13  BSgenome.Hsapiens.UCSC.hg18_1.3.11
> [3] BSgenome_1.12.2                    Biostrings_2.12.1
> [5] GADEM_1.0.0                        IRanges_1.2.0
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.0 tools_2.9.0
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
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