[BioC] package xps

[Steven]

Hi Dan,




2012/8/3 Dan Tenenbaum <dtenenba at fhcrc.org>:
> 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?
>
I also installed with ./configure linuxx8664gcc
make

I can run root by typing root.


>
>>               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?
>

I also sourced it.
by typing  echo $ROOTSYS I get:
winks at ubuntu:~/ROOT/root$


> To make sure root is properly installed, what happens if you do this:
>
> $ROOTSYS/bin/root --help
> You should see a usage message describing the various options for root.
>
Indeed I do, this is the output:
winks at ubuntu:~/ROOT/root$ $ROOTSYS/bin/root --help
Usage: /home/winks/ROOT/root/bin/root [-l] [-b] [-n] [-q] [dir]
[[file:]data.root] [file1.C ... fileN.C]
Options:
  -b : run in batch mode without graphics
  -n : do not execute logon and logoff macros as specified in .rootrc
  -q : exit after processing command line macro files
  -l : do not show splash screen
  -x : exit on exception
 dir : if dir is a valid directory cd to it before executing

  -?       : print usage
  -h       : print usage
  --help   : print usage
  -config  : print ./configure options
  -memstat : run with memory usage monitoring



>
>
>>
>> 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?
I normally get acces problems when installing packages in R when I
don't initiate R with sudo rights. I didn't try R CMD INSTALL
xps_1.16.0.tar.gz without sudo.


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


No, I am running R version 2.14.1.
I installed R version 2.15.

Still get the same error, this is the output:

checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... no

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

   Please consult the README file for more information

ERROR: configuration failed for package ‘xps’
* removing ‘/usr/local/lib/R/site-library/xps’


Thanks so far for your help!

Steven



>
> 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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