[BioC] download packages VariantTools

[Dan Tenenbaum]

Hi Francesca,



On Fri, Aug 30, 2013 at 1:39 AM, francesca bergantino
<fbergantino at yahoo.it> wrote:
> Hi,
> my problem is that I tried to install executable R software in Linux UBUNTU
> 10.04 LTS - The lucid Lynx but it resulted:
> wrong architecture or impossible to install R-base
>
> So I decided to write a software but it is impossible to open the shell
> because a library miss:
> error while loading shared libraries: libRblas.so
>
> How can I solve this problem?
>

This is really a question for R-help but I'll try and answer.

I was able to install R on an Ubuntu 10.04 system as follows. This
should take care of all architecture-related issues.

First, edit etc/apt/sources.list and put this line at the end:

deb http://cran.fhcrc.org/bin/linux/ubuntu lucid/

If you don't want to mess around with editors, you can do this:

sudo echo "deb http://cran.fhcrc.org/bin/linux/ubuntu lucid/" >> \
/etc/apt/sources.list

You can replace cran.fhcrc.org with a mirror nearer to you, see the list at
http://cran.r-project.org/mirrors.html

Then run these commands:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install -y r-base r-base-dev libcurl4-openssl-dev libcurl-dev

Then I was able to start R and do the following:

source("http://bioconductor.org/biocLite.R")
biocLite("VariantTools")
library(VariantTools)

And it all worked.

Dan


> Thanks
> ________________________________
> Da: Dan Tenenbaum <dtenenba at fhcrc.org>
> A: francesca bergantino <fbergantino at yahoo.it>
> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Inviato: Giovedì 29 Agosto 2013 17:28
>
> Oggetto: Re: [BioC] download packages VariantTools
>
> Hi Francesca,
>
> On Thu, Aug 29, 2013 at 4:27 AM, francesca bergantino
> <fbergantino at yahoo.it> wrote:
>> Thanks a lot.
>> Is it possible to install already executable R software in linux? If yes,
>> how can I do it?
>>
>
> I don't understand the question, exactly.
> R and all Bioconductor packages are available for Linux.
> Binary versions of R are available for the various distributions:
>
> http://cran.r-project.org/bin/linux/
>
> And R can always be installed from source.
> Bioconductor packages can be installed as on any other OS:
>
> http://bioconductor.org/install/
>
> Dan
>
>
>> Thanks for your help
>>
>>
>>
>> ________________________________
>> Da: Dan Tenenbaum <dtenenba at fhcrc.org>
>> A: francesca bergantino <fbergantino at yahoo.it>
>> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
>> Inviato: Mercoledì 28 Agosto 2013 17:46
>> Oggetto: Re: [BioC] download packages VariantTools
>>
>> On Wed, Aug 28, 2013 at 7:27 AM, francesca bergantino
>> <fbergantino at yahoo.it> wrote:
>>> Dear Bioconductor list,I'm PhD student. I work in a Oncology research
>>> center.
>>> I have some question regard the VariantTools packages; I have already
>>> read
>>> the documentation: An Introduction to VariantTools and the Reference
>>> Manual.
>>>
>>> So I downloaded the Bioconductor version: Release (2.12) like suggestion,
>>> I installed this package and I started R and entered:
>>>
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>>
>>> biocLite("VariantTools")
>>>
>>> It results:
>>> Warning message: package ‘VariantTools’ is not available (for R version
>>> 3.0.1) If I downloaded the Bioconductor version like required why?
>>>
>>
>> What operating system are you on? At present, VariantTools is only
>> available on Linux.
>> Dan
>>
>>
>>> Thanks in advance
>>>
>>> Regards
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
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>>
>