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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