[BioC] package xps

Dan Tenenbaum dtenenba at fhcrc.org
Fri Aug 3 00:55:08 CEST 2012

Hi Steven,

On Thu, Aug 2, 2012 at 3:48 PM, Steven <steven.wink at gmail.com> wrote:
> Hi all,
> I am having trouble getting package xps to work, and would really
> appreciate any help I can get.
> I have succesfully installed root_v5.34.01 on my ubuntu 12.04 OS
> as described on in the xps package readme file I added ROOTSYS to PATH
> and LD_LIBRARY_PATH by entering these lines in the terminal:
> export ROOTSYS=~/ROOT/root  (I make a folder ROOT in which I unpacked root.)

Did you just unpack the source tarball of root into /ROOT, or did you
install root there?

>               export PATH=$ROOTSYS/bin:$PATH
>               export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
>  I also added above 2 lines in .bashrc

Did you source the .bashrc after adding these lines?
What happens if you type
at the command line?

To make sure root is properly installed, what happens if you do this:

$ROOTSYS/bin/root --help
You should see a usage message describing the various options for root.

> root seems to run fine.
> next, I download xps_1.16.0.tar.gz and run:
> sudo R CMD INSTALL xps_1.16.0.tar.gz

Why are you using sudo here?

Are you running R 2.15? This is the version of R you will need with xps 1.16.0.

We recommend you install xps like this, within R:



> I get the following error message:
> xps configuration error:
>    You must set the shell variable ROOTSYS to the
>    directory where ROOT resides and re-run R CMD INSTALL
>    e.g., (using Bourne shell syntax):
>       export ROOTSYS=/opt/root
>       export "PATH=$ROOTSYS/bin:$PATH"
>       R CMD INSTALL xps
> So apparently ROOTSYS variables are not set right? I tried anything I
> could think of but I am lacking in understanding here.
> Thanks alot!
> sincerely
> Steven Wink
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