[BioC] package xps

[Dan Tenenbaum]

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
echo $ROOTSYS
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:

source("http://bioconductor.org/biocLite.R")
biocLite("xps")

Dan


>
>
> 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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