i tried updata.packages("Biostings") but it is still 2.13.1 the new one is 2.14.1, so i tried source("http://www.bioconductor.org/biocLite.R") biocLite("Biostrings") Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "Biostrings" Please wait... Installing package(s) into ‘C:/Users/shangao/Documents/R/win- library/2.13’ (as ‘lib’ is unspecified) Warning: package 'Biostrings' is in use and will not be installed [[alternative HTML version deleted]]

There is a different version of Bioconductor for each (major) version of R. To get the newest Bioconductor, you need to use the newest version of R, which in this case is the 2.14 (<- refering to the R version) release candidate. This has been discussed an infinite number of times on the email list. Considering the amount of help emails you have been sending in the least weeks, I strongly suggest spending a bit more time familiarizing yourself with the stuff you are doing. Well-thought out questions are much more likely to be answered. As a first step, please read the posting guide AND FOLLOW IT. Kasper On Thu, Oct 6, 2011 at 11:31 AM, wang peter <wng.peter at="" gmail.com=""> wrote: > i tried > updata.packages("Biostings") > but it is still 2.13.1 > the new one is 2.14.1, > > so i tried > > source("http://www.bioconductor.org/biocLite.R") > biocLite("Biostrings") > > Using R version 2.13.1, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "Biostrings" > Please wait... > Installing package(s) into ?C:/Users/shangao/Documents/R/win- library/2.13? > (as ?lib? is unspecified) > Warning: package 'Biostrings' is in use and will not be installed > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

On Thu, Oct 6, 2011 at 11:31 AM, wang peter <wng.peter at="" gmail.com=""> wrote: > i tried > updata.packages("Biostings") > but it is still 2.13.1 > the new one is 2.14.1, > > so i tried > > source("http://www.bioconductor.org/biocLite.R") > biocLite("Biostrings") > > Using R version 2.13.1, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "Biostrings" > Please wait... > Installing package(s) into ?C:/Users/shangao/Documents/R/win- library/2.13? > (as ?lib? is unspecified) > Warning: package 'Biostrings' is in use and will not be installed Yes. Just restart R and before loading any packages use: source("http://www.bioconductor.org/biocLite.R") biocLite("Biostrings") If this doesn't work for you, be sure to include the output of sessionInfo() when you write back to the list. Sean

On Thu, Oct 6, 2011 at 11:48 AM, wang peter <wng.peter at="" gmail.com=""> wrote: > thank you sean, thank you very much > they already fix the bug in the new version of Biostring > > this is the bug > > serSEW(width(x), start = start, end = end, width = width) : > ? solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (0) is > < 1 Yes. We are working on that problem on another email, are we not? Let's deal with the problem one step at a time, OK? Sean

oops, seems like you missed the "Reply All" button... again ;-) On 11-10-07 11:22 AM, wang peter wrote: > dear Herv? > i tried the newest version > that bug doesnot exist > another bug also disppeared > Error in solveUserSEW(width(x), start = start, end = end, width = width) : > solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (2) > is > refwidth + 1 > thank u very much No problem. Thanks! H. > shan gao -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319