[Bio-Linux] Rapidir R-cran package

Pau Marc Muñoz Torres paumarc at gmail.com
Mon Sep 14 08:01:12 EDT 2015


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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