[BioC] Problems installing bioconductor on ubuntu

Bio Sam biosam at gmail.com
Fri Jul 11 22:29:31 CEST 2008

Hi Rebecca,
   as a big fan of Ubuntu and Bioconductor, I've gone through a number
of installs, and run into many similar headaches.  As Steve pointed
out, you are missing gcc and associated libraries, which you can get
from build-essentials.  This will get many packages working, but I
typically also run into many additional missing requirements when I
try to install other components of Bioconductor using the biocLite()
script.  To avoid these problems, I usually go through a checklist of
steps to get R/Bioconductor working smoothly.

1. Install dependencies:
This command will install most of the Ubuntu package that
R/Bioconductor will need later.  You can also use Synaptic Package
Manager and install each one (I haven't updated this list for a few
months, so some might have newer versions, also this list was compiled
for ubuntu 7.10.):

sudo apt-get install sun-java6-jdk libgtk2.0-dev graphviz-dev
libgtk1.2-dev curl ggobi libxml2-dev mesa-common-dev libglu1-mesa-dev
libgd2-xpm-dev libmysqlclient15-dev gfortran-4.2 refblas3-dev
libcurl4-gnutls-dev libboost-dev g++-4.2 unixodbc-dev build-essential

2. I then add the Cran Ubuntu repository as explained here:

This ensures that I'm running the latest version of R, which usually
isn't available from the Ubuntu software repositories.  I have had
very good luck with this repository in the ~2 years I've been using

3. Install R:
After adding the repository above, I install the following packages
using either the command line "apt-get install" or Synaptic Package
r-base-core r-base-html r-base-latex r-base-dev r-base-core
r-cran-rgtk2 r-cran-rggobi r-cran-rgl

4: Fix Java
To make sure that R will use the Sun version of java installed above
(sun-java6-jdk) run:
R CMD javareconf

5: run biocLite()
After doing this, you should be able to install most packages from the
Cran/Bioconductor repositories without any problems with missing

Again, some of these steps might not be necessary depending on which
Bioconductor packages you plan to use (although build-essential is
essential), but if you run into problems installing the packages above
might help.


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