[Bio-Linux] Rapidir R-cran package

[Tim Booth]

Hi,

I honestly don't know if RapidR will install cleanly on BL7.  However, I
would direct you to
http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova which is a BL7
image you can import in VirtualBox, which will be much quicker than
installing it on bare metal.  Note the admin account is manager,
password also manager.

I'll have another look at the package.  I'd assumed before that you
could install it easily via install.packages() but if it's problematic
then it's more worth my time to fix it for everyone.

Cheers,

TIM

On Mon, 2015-09-14 at 14:01 +0200, Pau Marc Muñoz Torres wrote:
> Hello everybody
> 
> 
>  I still trying to work with Rapidr package from R. As someone pointed
> in a mail, I think it was Dr Tony Travis, it uses some packages that
> have changed recently. I thought I could deal with this installing the
> R package GenomicAlignments version 1.14.4 locally. Unfortunately, the
> compilation of the package failed. I have been thinking on install
> biolinux 7 in another computer, but I not sure if it would work. Could
> you tell me which version of the package is in biolinux 7? I amb not
> worried about biolinux actualizacions as long as it only will be used
> to run this programs
> 
> 
> thanks
> 
> 
> pau
> 
> Pau Marc Muñoz Torres
> 
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> 
> 
> 
> 2015-06-19 16:59 GMT+02:00 Pau Marc Muñoz Torres <paumarc at gmail.com>:
>         Thanks
>         
>         P
>         
>         El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk> escribió:
>                 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>
>                 
>                 Centre for Ecology and Hydrology
>                 Maclean Bldg, Benson Lane
>                 Crowmarsh Gifford
>                 Wallingford, England
>                 OX10 8BB
>                 
>                 http://environmentalomics.org/bio-linux
>                 +44 1491 69 2297
>                 
>                 
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> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297