[Bio-Linux] Rapidir R-cran package
Tim Booth
tbooth at ceh.ac.uk
Tue Sep 15 14:09:26 EDT 2015
Hi Pau,
I did a bunch of Bioconductor package updates and tried making a RAPIDR
package for Bio-Linux 8. I checked that it loads into R, but can you
try it and see if it actually works?
$ sudo apt-get install r-cran-rapidr
...
$ R
...
> library(RAPIDR)
Creating a generic function for ‘nchar’ from package ‘base’ in package
‘S4Vectors’
>
So there is a warning message. Hopefully not a problem.
If it doesn't work, what errors do you get?
For the download link, that link is good but you could also try the
mirror site:
http://ftp.yzu.edu.tw/Linux/bio-linux-iso/bio-linux-7-20131211.ova
Cheers,
TIM
On Tue, 2015-09-15 at 10:24 +0200, Pau Marc Muñoz Torres wrote:
> 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
> >
> >
> >
> _______________________________________________
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> >
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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
>
>
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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
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