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How I install a R package?

Dear R users: as you have probably experienced, many of the times that we think a new R package is going to save our life, it ends up just frustrating us. In the meanwhile, we have asked Angel or Edu to install such a promising package, wasting their time (and ours) in vain and waiting for what would be useless. A way to improve the work flow and accelerate the test of new packages is to install first the package locally. And then, if worthwhile, ask for the system installation.

To easily do the local installation of a CRAN package:

e.g. to install the package clv: http://cran.r-project.org/src/contrib/Descriptions/clv.html

  1. Within R:

>install.packages("clv",dependencies = TRUE) Warning in install.packages("vlc") : 'lib = "/usr/local/lib64/R/library"' is not writable Would you like to create a personal library '~/R/x86_64-unknown-linux-gnu-library/2.6' to install packages into? (y/n)

  1. say "y"

--- Please select a CRAN mirror for use in this session ---

  1. set the option to your nearest CRAN mirror on the new window displayed, push 'OK' and that's all

You can find more details in : http://cran.r-project.org/doc/manuals/R-admin.pdf. Hope this helps,


BIOCONDUCTOR packages: If you want to install a local Bioconductor library you can use biocLite():

First connect to Bioconductor (within R):

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

Then request instalation of the package you wish:

> biocLite("VanillaICE") Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R requires version 2.2 of BioConductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  : 'lib = "/Library/Frameworks/R.framework/Resources/library"' is not writable Would you like to create a personal library '~/R/powerpc-apple-darwin8.10.1-library/2.7' to install packages into? (y/n)

  1. say "y"


LOCAL FILES (tar.gz)

If the package you like is not in CRAN or BioConductor, you can still install it locally like this:

> install.packages("FASeg", pkgs="/home/drico/Desktop/DOWNLOADS/FASeg_2.0.tar.gz",repos=NULL)

Warning in install.packages("FASeg", pkgs = "/home/drico/Desktop/DOWNLOADS/FASeg_2.0.tar.gz",  :'lib = "FASeg"' is not writable Would you like to create a personal library '~/R/x86_64-unknown-linux-gnu-library/2.6' to install packages into? (y/n)

  1. say "y"

How can I connect to a CNIO machine from outside?

Since is not possible to access CNIO resources using bare ssh/telnet, it is needed to establish a connection between your computer and the CNIO network. This is done using a VPN connection. Once you have the VPN software running, your computer will work as if you would be inside the CNIO network (wherever the computer is: your home, a hotel...)

You will need a special software in your computer to stablish the  VPN connection. We use Cisco's VPN client, which you can download here after choosing your computer's Operating System:

Please be aware that the download links will work only if you are inside the CNIO network

Once you have the software installed, you will need some configuration files to connect to CNIO's VPN (submit an issue to Bioinformatics Unit to get these files).

Finally, to get connected to CNIO you can use your favorite ssh client. Here you have some: putty, ssh.