[BioC] Installing Bioconductor under Linux

[Saurin Jani]

Hi Hong,

Seth is correct..! 

On Linux:

Download: R-2.1.0.tar.gz

$ tar xvfz R-2.1.0.tar.gz
$ ./configure
$ make
$ make check-all

Now login as super user or root to your Linux computer
$ su   

$ make install


$ exit

$ R 


Your are good to go.



Saurin





  


--- Seth Falcon <sfalcon at fhcrc.org> wrote:

> 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
> 
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