[Bioc-sig-seq] Shortreads

Terry Therneau therneau at mayo.edu
Fri Aug 22 17:40:57 CEST 2008

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 
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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