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

[Steve Lianoglou]

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