[BioC] Installing Bioconductor under Linux

[Seth Falcon]

Hi Fangxin,

On  6 Jun 2005, fhong at salk.edu wrote:
> I am trying to install Bioconductor under linux. By following the
> manual, I first installed R 2.1.0 from R-2.1.0.tar.gz downloaded
> from R website
>
> tar xvfz R-2.1.0.tar.gz
>
> Then I have successfully run
> ./configure
> make
>
> I met errors and wouldn't go through when I tried
> make check  (or make check FORCE=FORCE or make check-devel)

If 'make check' reports errors, it is usually prudent to resolve them
before proceeding.  It may be that solving the issue you report below
relating to X11 will also solve the make check errors.

> But it looks like R is installed. After I copied shell-script 'R' to
> 'usr/local/bin/R', typing 'R' on the command line invokes the R of
> current version. ( there is an old version R installed, I just
> simple replace the old R at 'usr/local/bin' by the new one)

Why not just use:
make install

> But when I tried to install Bioconductor, I met the problem
>> source("http://www.bioconductor.org/getBioC.R")
> X connection to localhost:10.0 broken (explicit kill or server
> shutdown).

I'm assuming you are accessing the Linux server via ssh (we'd need
more detail on exactly what your setup is and how you are using it).
You may want to try a fresh ssh connection.  The X11 error is unlikely
to be related to R.

An alternative is to unset the DISPLAY environment variable.  In bash
(default Linux shell):

    unset DISPLAY

This will turn off the X11 capability for R (and other apps), but
should avoid the error message you saw.


> This didn't happen when I used the old version R. Any suggestion is
> greatly appreciated!!

Lastly, you may want to install R in your home directory instead of at
the system level.  This way, you have the most control over the
version and what packages are and are not installed.  

Here's one way to accomplish this:

mkdir ~/R-2.1.0
mkdir ~/src
cd ~/src
tar xzvf ~/R-2.1.0.tar.gz
cd R-2.1.0
./configure --prefix=~/R-2.1.0 && make && make install

Then add ~/R-2.1.0/bin to your path.

Many of us developers skip the install step and run from the build
directory.  I think some of the help may not get built with this
approach, but it is a bit faster which can be useful when one is often
recompiling R.

Hope these suggestions are useful.

Best,

+ seth