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.
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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>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
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