[Bioc-sig-seq] Shortreads

[Patrick Aboyoun]

Terry,
The ShortRead package is only available for the BioC 2.3 / R-devel code 
line. It depends on the development version of Biostrings. A number of C 
interfaces to Biostrings were opened up in the development version of 
Biostrings to allow packages like ShortRead to have a tight integration 
for fast string manipulation. Using biocLite("ShortRead") when running 
R-devel will get you up and running.


Cheers,
Patrick


Terry Therneau wrote:
> I have tried to install the shortreads package, with no success.
>
> tmt36% R
>
> R version 2.7.0 (2008-04-22)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
>   
>> biocLite('ShortRead')
>>     
> Running biocinstall version 2.1.11 with R version 2.7.0 
> Your version of R requires version 2.1 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = 
> dependencies,  :
>   argument 'lib' is missing: using 
> '/home/therneau/R/x86_64-unknown-linux-gnu-library/2.7'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   package âShortReadâ is not available
>
> ----
>  The bottom line says it all.
>  
>  So then I tried downloading the source, and using the standard R 
> install.packages call.  That fails because it expects "_Biostrings_stubs.c" to 
> be in the standard R include directory, which is clearly false.
>  
>   I'd like to install the new material in my own library -- but it rather looks 
> like bioconductor as a whole is designed to NOT work with the usual R install 
> tools.  Is this correct?  (Bioconductor as a whole is installed on the system by 
> our administrator).
>   
>     Terry Therneau
>     (working with Solexa data)
>     
>
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