[Bio-Linux] Rapidir R-cran package

[Tim Booth]

Hi Pau Marc,

On Bio-Linux 8 you can install all packages from the big auto-generated
C2D4U repository via apt-get, so for example you can do:

apt-get install r-bioc-genomicalignments

However, RAPIDR is missing, so for now you have to install it via
install.packages() and update it manually as Tony suggested.

I'll look into adding a package for this myself.  Its normally very easy
to do.

Cheers,

TIM

On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
> On 19/06/15 11:04, Pau Marc Muñoz Torres wrote:
> > Hello9 everybody.
> > 
> >  I'm, interested to install R-cran package on my system, nevertheless i
> > do not find it at repositories neither in bioconductor
> > 
> > i look at R-cram web page for Rapidir , and i have not found any linux
> > binary.
> > 
> > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > 
> > Can some one told me if it is possible to install it in  biolinux?
> 
> Hi, Pau Marc.
> 
> The CRAN package "RAPIDR" requires a BioConductor package
> "GenomicAlignments", which must be installed first. See:
> 
> > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
> 
> This is how to install and load "RAPIDR" in Bio-Linux 8:
> 
>   R
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("GenomicAlignments")
>   install.packages("RAPIDR")
>   library(RAPIDR)
> 
> HTH,
> 
>   Tony.
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

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