therneau at mayo.edu
Fri Aug 22 17:40:57 CEST 2008
I have tried to install the shortreads package, with no success.
R version 2.7.0 (2008-04-22)
Copyright (C) 2008 The R Foundation for Statistical Computing
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 =
argument 'lib' is missing: using
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
(working with Solexa data)
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