[Bioc-sig-seq] Shortreads

[Sean Davis]

On Fri, Aug 22, 2008 at 11:40 AM, Terry Therneau <therneau at mayo.edu> 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

I think ShortRead is available for the R-devel only, at this point.
You can certainly install your own R-devel in your home directory for
the purposes of using ShortRead.  Martin Morgan might be able to
comment better on compatibility of the current version with older
versions of R.

As for bioconductor being designed NOT to work with standard R install
tools, that isn't quite true.  The problem is that for all of the
packages of bioconductor to work well together and to work with the
correct version of R, the Bioconductor team decided to use their own
versioning system that necessitates using functions for installation
that are aware of the versioning--hence, biocLite().

Hope that helps,
Sean