Thanks a lot. Is it possible to install already executable R software in linux? If yes, how can I do it? Thanks for your help ________________________________ Da: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: "bioconductor@r-project.org" <bioconductor@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 > 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]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

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: Gioved? 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: Mercoled? 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]] >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>