[BioC] Biostrings_2.16.5 / IRanges_1.7.1 :: Broken(?)

[Steve Lianoglou]

Hi,

I just updated all my bioc packages and am experiencing some funky errors:

R> library(Biostrings)
R> example(pairwiseAlignment)
## ...
prwsAl>   globalAlign <-
prwsAl+     pairwiseAlignment(s1, s2, substitutionMatrix = mat,
prwsAl+                       gapOpening = -5, gapExtension = -2)
Error in solveUserSEW(length(ans_xvector), start = start, end = end,
width = width,  :
  unused argument(s) (rep.refwidths = TRUE)

See also:

R> PhredQuality(1:10)
Error in solveUserSEW(length(ans_xvector), start = start, end = end,
width = width,  :
  unused argument(s) (rep.refwidths = TRUE)

R> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Biostrings_2.16.5 IRanges_1.7.1

loaded via a namespace (and not attached):
[1] Biobase_2.8.0


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact