[BioC] DNAString: Error for long sequences

Ann Hess hess at stat.colostate.edu
Tue Aug 26 17:31:43 CEST 2008

I am having trouble creating long (~1000+ characters) DNAStrings. 
Specifically, I seem to get an error when R has to go to a new line in the 
command window when copy/pasting the sequence from an R script (with no 
breaks).  I recently upgraded R and BioConductor, but previously I did not have this problem.

Code and error is below.  Any suggestions?



> library(Biostrings)

# "Short" example with no error
> Temp1<-DNAString(
> Temp1
   969-letter "DNAString" instance

# "Long" example, such that R needs a new line to complete the sequence
> Temp2<-DNAString(
Error in charToXRaw(x, start = start, end = end, width = width, lkup = 
lkup,  :
   key 10 not in lookup table

> sessionInfo()
R version 2.7.1 (2008-06-23)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biostrings_2.8.17

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