[BioC] Problems installing bioconductor on ubuntu

Rebecca griffithsr at performanceplants.com
Thu Aug 7 21:30:45 CEST 2008

Bio Sam <biosam at ...> writes:

> 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:
> http://cran.r-project.org/bin/linux/ubuntu/
> 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
> it.
> 3. Install R:
> After adding the repository above, I install the following packages
> using either the command line "apt-get install" or Synaptic Package
> Manager:
> 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
> dependencies.
> 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.
> Sam
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I installed all the dependencies and then tried to install the newest version 
of r-base-core and I now get the following error message:

sudo apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.

Since you only requested a single operation it is extremely likely that
the package is simply not installable and a bug report against
that package should be filed.
The following information may help resolve the situation:

The following packages have unmet dependencies:
  r-base-core: Depends: libpango1.0-0 (>= 1.18.3) but 1.18.2-0ubuntu1 is to be 
E: Broken packages

I think this a ubuntu issue, but was wondering whether anyone has come across 
it while trying to install R?


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