[Bioc-devel] reverseComplement broken in development version of R and Biostrings

[Martin Morgan]

Hi Matt --

'devel' packages have odd-numbered y in version string x.y.z, so you've 
got a mix of devel and release packages. So update packages as at

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

See also the build report

  http://bioconductor.org/checkResults/2.6/bioc-LATEST/

which shows Biostrings passing build and check (which implies that the 
examples run without error).

Martin

Matt Settles wrote:
> the function reverseComplement in Biostrings appears to be broken in 
> the development version of R and Biostrings
> Matt Settles
>
> > library(Biostrings)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
>
>    The following object(s) are masked from package:base :
>
>     cbind,
>     Map,
>     mapply,
>     order,
>     pmax,
>     pmax.int,
>     pmin,
>     pmin.int,
>     rbind,
>     rep.int,
>     table
>
> > example(reverseComplement)
>
> rvrsCm>   ## 
> ---------------------------------------------------------------------
> rvrsCm>   ## A. SOME SIMPLE EXAMPLES
> rvrsCm>   ## 
> ---------------------------------------------------------------------
> rvrsCm>
> rvrsCm>   x <- DNAString("ACGT-YN-")
>
> rvrsCm>   reverseComplement(x)
> Error in reverseComplement(x) : could not find function "xvcopy"
> > sessionInfo()
> R version 2.11.0 Under development (unstable) (2009-12-14 r50724)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     
> LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8    
> LC_PAPER=en_US.UTF-8     [8] LC_NAME=C                  
> LC_ADDRESS=C               LC_TELEPHONE=C             
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C     
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base   
> other attached packages:
> [1] Biostrings_2.14.8 IRanges_1.5.2  
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.1 tools_2.11.0
> >
>


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793