[BioC] package xps

[Steven]

2012/8/3 Steven <steven.wink at gmail.com>:
> 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:
>>
>> $ROOTSYS/bin/root --help
>> You should see a usage message describing the various options for root.
>>
> Indeed I do, this is the output:
> winks at ubuntu:~/ROOT/root$ $ROOTSYS/bin/root --help
> Usage: /home/winks/ROOT/root/bin/root [-l] [-b] [-n] [-q] [dir]
> [[file:]data.root] [file1.C ... fileN.C]
> Options:
>   -b : run in batch mode without graphics
>   -n : do not execute logon and logoff macros as specified in .rootrc
>   -q : exit after processing command line macro files
>   -l : do not show splash screen
>   -x : exit on exception
>  dir : if dir is a valid directory cd to it before executing
>
>   -?       : print usage
>   -h       : print usage
>   --help   : print usage
>   -config  : print ./configure options
>   -memstat : run with memory usage monitoring
>
>
>
>>
>>
>>>
>>> root seems to run fine.
>>>
>>> next, I download xps_1.16.0.tar.gz and run:
>>> sudo R CMD INSTALL xps_1.16.0.tar.gz
>>
>> Why are you using sudo here?
> I normally get acces problems when installing packages in R when I
> don't initiate R with sudo rights. I didn't try R CMD INSTALL
> xps_1.16.0.tar.gz without sudo.
I just tried without SUDO rights, and this is the output:
winks at ubuntu:~/ROOT/root$ R CMD INSTALL xps_1.16.0.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
Error: ERROR: no permission to install to directory
‘/usr/local/lib/R/site-library’


ps: I also tried installing the recommended way with biocLite -I get
the same ROOTSYS shell variable problem


>
>
>>
>> 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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