Michael Lawrence wrote:
I might be wrong here, but it might be possible to run ShortRead on R 2.7.2
with all its dependencies (Biostrings, IRanges, ...) installed from
Bioconductor 2.3.
It won't, because ShortRead has C-level dependencies on two packages,
and this support was not working until relatively recently in R-devel
(r46267, Fri, 08 Aug 2008, I think).
In general I've found (though I'll admit to not being an ordinary R
user) that the cost to switching versions is minimal, and that R-devel
rarely has changes that fundamentally break what was previously working.
If the need is for a package that has seen recent heavy development
(ShortRead and Biostrings definitely fall into this category), then I'd
recommend switching to using R-devel.
Martin
On Mon, Aug 25, 2008 at 9:25 AM, Patrick Aboyoun <[EMAIL PROTECTED]> wrote:
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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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
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