[BioC] Error loading ShortRead

[Martin Morgan]

On 05/16/2011 06:50 AM, rcaloger wrote:
> Dear All,
> I am trying to load ShortRead package but I get the following error:
>
> library(Biostrings)
> library(ShortRead)
> Error : object ‘compact’ is not exported by 'namespace:Biostrings'
> Error: loading package/namespace failed for 'ShortRead'
>
> Any suggestions?

Biostrings and IRanges changed as a bug fix. You installed (maybe freom 
SVN?) an updated ShortRead but not the other packages. Try

   source("http://bioconductor.org/biocLite.R")
   update.packages(repos=biocinstallRepos())

perhaps with ask=FALSE.

Martin

> Cheers
> Raffaele
>
> ##########################################################
> sessionInfo()
>
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
> LC_MONETARY=Italian_Italy.1252
> [4] LC_NUMERIC=C LC_TIME=Italian_Italy.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Rsamtools_1.4.0 Biostrings_2.20.1 GenomicRanges_1.4.3 IRanges_1.10.3
> lattice_0.19-23
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.12.1 grid_2.13.0 tools_2.13.0
>
>


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