Hello everyone .

I am new to R ,want to install bioconductor package in ubuntu(14.04) . The following message was displayed when i tried the installation :

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
A newer version of Bioconductor is available after installing a new version of
  R, ?BiocUpgrade for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Warning message:
installed directory not writable, cannot update packages 'boot', 'class',
  'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'mgcv',
  'nlme', 'nnet', 'rpart', 'spatial', 'survival'

// Commands pasted above  were taken as typed in the  ubuntu terminal .

Suggestions to resolve this would be really helpful to me . Thanking You  in advance .

R.Sarvotham

India

In Ubuntu, if you install R using say 'apt get', then you will install in a system directory that is not writeable by a regular user. This includes the library directory and recommended packages. Then if you try to install packages as a regular user, R will create a personal library directory in your home directory (which is where all of your Bioconductor packages were installed).

One step for biocLite() is to look at the installed packages, and see if they can be updated. If some of the recommended packages in the system directory can be updated, then biocLite() will note that and tell you that you don't have privileges to update them, which is what that warning is telling you.

If you really care to update the recommended packages, you can run R under sudo and then biocLite() will have privileges to install in the system directories.

Hi,

I would really encourage you to install the current version of R:

1. That will solve the "installed directory not writable" problems.

2. That will allow you to use the current version of Bioconductor (3.0). Passed versions are not supported. 

3. It's easy:

Make sure you have the following deb packages on your system (you should already have most of them):

gfortran
g++
libreadline6-dev
libx11-dev
libxt-dev
tk-dev
libpng12-dev
libjpeg-dev
libtiff4-dev
libcairo2-dev

Then from your user account (no sudo):

cd ~/Downloads
wget http://cran.fhcrc.org/src/base/R-3/R-3.1.2.tar.gz
tar zxf R-3.1.2.tar.gz
cd
mkdir R-3.1.2
cd R-3.1.2
~/Downloads/R-3.1.2/configure && make

Done. (don't run make install)

Start R with ~/R-3.1.2/bin/R or create a symlink in ~/bin

Then:

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

should run smoothly.

H.