mtmorgan at fhcrc.org
Mon Aug 25 20:00:58 CEST 2008
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.
> On Mon, Aug 25, 2008 at 9:25 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
>> 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
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
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