[BioC] Installing Bioconductor under Linux

Seth Falcon sfalcon at fhcrc.org
Tue Jun 7 20:08:04 CEST 2005

On  7 Jun 2005, fhong at salk.edu wrote:

> Thank Seth
>>> 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
> I tried this, it looks OK ( no error message). Then I copied
> shell-script 'R' to '/usr/local/bin/R'again.

Hrm.  I would expect make install to copy the shell-script for you.
The default install path is /usr/local.

>  But it still gave me
> the same thing when I typed in R
>> source("http://www.bioconductor.org/getBioC.R")
> X connection to localhost:10.0 broken (explicit kill or server

> I also unset the DISPLAY environment variable using "unset DISPLAY",
> but the problem is still there. 

> I am accessing the linux (at my
> laptop) via ssh as a super user. The linux machine information
> returned by "uname -a" is

And what happens if you access the machine as a normal user and run R
that way?  Running R as super user is not the best of ideas and may be
related to your X11 troubles.  

The error message you are seeing is telling you that applications on
the remote machine can't properly connect to an X server --- this sort
of configuration is, I'm afraid, beyond the scope of bioC.

> As I mentioned before, there was an old version R installed before,
> it didn't gave me that error when I typed
> "source("http://www.bioconductor.org/getBioC.R")", which make me
> think there may be something wrong with my installation.

Even as super user?  That is odd.

+ seth

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