Hi, Martin It is working after updated packages following your suggestion. Thanks. Best, Anyou On Mon, Dec 13, 2010 at 9:37 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 12/13/2010 09:24 AM, ANYOU WANG wrote: > > Hello, everyone > > > > A question about readAligned. I tried to input the .map > > aligned sequence data using readAligned, but it failed (detail > > below), even using the testing data downloaded from the ShortRead > website. > > Could anyone give some suggestions? Thanks. > > > > Anyou > > > > expdir<-"/disk2/lab/tmp1/" > > Test.me3 <- sapply( list.files( expdir, "*.map" ),function(filename) > > readAligned(expdir, filename, type="MAQMapShort" )) > > > > Error: Input/Output > > > > 'readAligned' failed to parse files > > > > dirPath: '/disk2/lab/tmp1/' > > > > pattern: 'run4_lane8.map' > > > > type: 'MAQMapShort' > > > > error: function '_new_RoSeqs_from_CharAEAE' not provided by > > package 'Biostrings' > > Hi > > This suggests an incorrect version of Biostrings. Follow the directions > here > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > to update packages, and please let us know how it goes -- use > sessionInfo() to report your session information > > Best, > > Martin > > > > > > ***my system info below > > > > Mandriva Linux 2010, 64bit, 8 CPU,12G RAM. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]