<div dir="ltr">Hello everybody<div><br></div><div> 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 <span style="color:rgb(0,0,0);font-family:'Lucida Console',monaco,monospace;line-height:14.56px;background-color:rgb(227,227,227)">GenomicAlignments</span> version <span style="color:rgb(0,0,0);font-family:Verdana,Arial,Helvetica,sans-serif;line-height:14.56px">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</span></div><div><span style="color:rgb(0,0,0);font-family:Verdana,Arial,Helvetica,sans-serif;line-height:14.56px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Verdana,Arial,Helvetica,sans-serif;line-height:14.56px">thanks</span></div><div><span style="color:rgb(0,0,0);font-family:Verdana,Arial,Helvetica,sans-serif;line-height:14.56px"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Verdana,Arial,Helvetica,sans-serif;line-height:14.56px">pau</span></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">2015-06-19 16:59 GMT+02:00 Pau Marc Muñoz Torres <span dir="ltr"><<a href="mailto:paumarc@gmail.com" target="_blank">paumarc@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Thanks</p><span class="HOEnZb"><font color="#888888">
<p dir="ltr">P</p></font></span><div class="HOEnZb"><div class="h5">
<div class="gmail_quote">El 19/06/2015 13:19, "Tim Booth" <<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>> escribió:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Pau Marc,<br>
<br>
On Bio-Linux 8 you can install all packages from the big auto-generated<br>
C2D4U repository via apt-get, so for example you can do:<br>
<br>
apt-get install r-bioc-genomicalignments<br>
<br>
However, RAPIDR is missing, so for now you have to install it via<br>
install.packages() and update it manually as Tony suggested.<br>
<br>
I'll look into adding a package for this myself. Its 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 system, nevertheless i<br>
> > do not find it at repositories neither in bioconductor<br>
> ><br>
> > i look at R-cram web page for Rapidir , and i have not found any linux<br>
> > binary.<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 it in biolinux?<br>
><br>
> Hi, Pau Marc.<br>
><br>
> The CRAN package "RAPIDR" requires a BioConductor package<br>
> "GenomicAlignments", which must be installed first. See:<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>
> > <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 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" target="_blank">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" target="_blank">+44 1491 69 2297</a><br>
<br>
<br>
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</blockquote></div>
</div></div></blockquote></div><br></div>