[BioC] readAligned input failed?

[Martin Morgan]

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]]
> 
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