[Bioc-sig-seq] Shortreads

[Martin Morgan]

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 <paboyoun at fhcrc.org> 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)
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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