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

[Matt Settles]

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
 >

-- 
------------------------------------
Matt Settles
Bioinformatics Scientist
IBEST DNA Sequencing Analysis Core
Department of Biological Sciences
University of Idaho
Moscow, Idaho 83844