<div dir="ltr">Hi Tim,<div><br></div><div> Thanks for your answer. I am trying to download the link but i can't connect to it</div><div><br></div><div><a href="http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova">http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova</a><br></div><div><br></div><div>pau</div><div> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div>Pau Marc Muñoz Torres<br></div>skype: pau_marc<br><div><div><a href="http://www.linkedin.com/in/paumarc" target="_blank">http://www.linkedin.com/in/paumarc</a><br><a href="http://www.researchgate.net/profile/Pau_Marc_Torres3/info/" target="_blank">http://www.researchgate.net/profile/Pau_Marc_Torres3/info/</a><br><br></div></div></div></div></div>
<br><div class="gmail_quote">2015-09-14 15:41 GMT+02:00 Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I honestly don't know if RapidR will install cleanly on BL7. However, I<br>
would direct you to<br>
<a href="http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova" rel="noreferrer" target="_blank">http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova</a> which is a BL7<br>
image you can import in VirtualBox, which will be much quicker than<br>
installing it on bare metal. Note the admin account is manager,<br>
password also manager.<br>
<br>
I'll have another look at the package. I'd assumed before that you<br>
could install it easily via install.packages() but if it's problematic<br>
then it's more worth my time to fix it for everyone.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<div class="HOEnZb"><div class="h5"><br>
On Mon, 2015-09-14 at 14:01 +0200, Pau Marc Muñoz Torres wrote:<br>
> Hello everybody<br>
><br>
><br>
> I still trying to work with Rapidr package from R. As someone pointed<br>
> in a mail, I think it was Dr Tony Travis, it uses some packages that<br>
> have changed recently. I thought I could deal with this installing the<br>
> R package GenomicAlignments version 1.14.4 locally. Unfortunately, the<br>
> compilation of the package failed. I have been thinking on install<br>
> biolinux 7 in another computer, but I not sure if it would work. Could<br>
> you tell me which version of the package is in biolinux 7? I amb not<br>
> worried about biolinux actualizacions as long as it only will be used<br>
> to run this programs<br>
><br>
><br>
> thanks<br>
><br>
><br>
> pau<br>
><br>
> Pau Marc Muñoz Torres<br>
><br>
> skype: pau_marc<br>
> <a href="http://www.linkedin.com/in/paumarc" rel="noreferrer" target="_blank">http://www.linkedin.com/in/paumarc</a><br>
> <a href="http://www.researchgate.net/profile/Pau_Marc_Torres3/info/" rel="noreferrer" target="_blank">http://www.researchgate.net/profile/Pau_Marc_Torres3/info/</a><br>
><br>
><br>
><br>
> 2015-06-19 16:59 GMT+02:00 Pau Marc Muñoz Torres <<a href="mailto:paumarc@gmail.com">paumarc@gmail.com</a>>:<br>
> Thanks<br>
><br>
> P<br>
><br>
> El 19/06/2015 13:19, "Tim Booth" <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> escribió:<br>
> Hi Pau Marc,<br>
><br>
> On Bio-Linux 8 you can install all packages from the<br>
> big auto-generated<br>
> C2D4U repository via apt-get, so for example you can<br>
> do:<br>
><br>
> apt-get install r-bioc-genomicalignments<br>
><br>
> However, RAPIDR is missing, so for now you have to<br>
> install it via<br>
> install.packages() and update it manually as Tony<br>
> suggested.<br>
><br>
> I'll look into adding a package for this myself. Its<br>
> normally very easy<br>
> to do.<br>
><br>
> Cheers,<br>
><br>
> TIM<br>
><br>
> On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:<br>
> > On 19/06/15 11:04, Pau Marc Muñoz Torres wrote:<br>
> > > Hello9 everybody.<br>
> > ><br>
> > > I'm, interested to install R-cran package on my<br>
> system, nevertheless i<br>
> > > do not find it at repositories neither in<br>
> bioconductor<br>
> > ><br>
> > > i look at R-cram web page for Rapidir , and i have<br>
> not found any linux<br>
> > > binary.<br>
> > ><br>
> > ><br>
> <a href="http://cran.r-project.org/web/packages/RAPIDR/index.html" rel="noreferrer" target="_blank">http://cran.r-project.org/web/packages/RAPIDR/index.html</a><br>
> > ><br>
> > > Can some one told me if it is possible to install<br>
> it in biolinux?<br>
> ><br>
> > Hi, Pau Marc.<br>
> ><br>
> > The CRAN package "RAPIDR" requires a BioConductor<br>
> package<br>
> > "GenomicAlignments", which must be installed first.<br>
> See:<br>
> ><br>
> > ><br>
> <a href="http://cran.r-project.org/web/packages/RAPIDR/index.html" rel="noreferrer" target="_blank">http://cran.r-project.org/web/packages/RAPIDR/index.html</a><br>
> > ><br>
> <a href="http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf" rel="noreferrer" target="_blank">http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf</a><br>
> ><br>
> > This is how to install and load "RAPIDR" in<br>
> Bio-Linux 8:<br>
> ><br>
> > R<br>
> > source("<a href="http://bioconductor.org/biocLite.R" rel="noreferrer" target="_blank">http://bioconductor.org/biocLite.R</a>")<br>
> > biocLite("GenomicAlignments")<br>
> > install.packages("RAPIDR")<br>
> > library(RAPIDR)<br>
> ><br>
> > HTH,<br>
> ><br>
> > Tony.<br>
> ><br>
><br>
> --<br>
> Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
><br>
> Centre for Ecology and Hydrology<br>
> Maclean Bldg, Benson Lane<br>
> Crowmarsh Gifford<br>
> Wallingford, England<br>
> OX10 8BB<br>
><br>
> <a href="http://environmentalomics.org/bio-linux" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux</a><br>
> <a href="tel:%2B44%201491%2069%202297" value="+441491692297">+44 1491 69 2297</a><br>
><br>
><br>
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<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://environmentalomics.org/bio-linux" rel="noreferrer" target="_blank">http://environmentalomics.org/bio-linux</a><br>
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</div></div></blockquote></div><br></div>