[BioC] download packages VariantTools

[Dan Tenenbaum]

Two small corrections:

On Fri, Aug 30, 2013 at 3:01 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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:
>

That should be /etc/apt/sources.list

> 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

This should be:

sudo apt-get install -y r-base r-base-dev libcurl4-openssl-dev libxml2-dev

Dan


>
> 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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>>>
>>