paboyoun at fhcrc.org
Mon Aug 25 18:25:40 CEST 2008
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.
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
> 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)
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
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