[Bio-Linux] Rapidir R-cran package
Pau Marc Muñoz Torres
paumarc at gmail.com
Tue Sep 15 04:24:06 EDT 2015
Hi Tim,
Thanks for your answer. I am trying to download the link but i can't
connect to it
http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova
pau
Pau Marc Muñoz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
2015-09-14 15:41 GMT+02:00 Tim Booth <tbooth at ceh.ac.uk>:
> 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
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
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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
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
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>
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