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