Sorry! Somehow I've installed conflicting versions of IRanges and Biostrings, reinstalling IRanges version 1.6.6 solves my issue. It seems all is well and sorry for the spam. -steve On Thu, Jun 17, 2010 at 12:18 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > 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 > -- 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