[BioC] Installing Bioconductor under Linux

fhong at salk.edu fhong at salk.edu
Tue Jun 7 18:51:39 CEST 2005

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.  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"

Linux qtlpc.salk.edu 2.4.20-31.9bigmem #1 SMP Tue Apr 13 17:11:51 EDT 2004
i686 i686 i386 GNU/Linux

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.

thanks for your help.


>> 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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105

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