[BioC] package xps

[cstrato]

Dear Steven,

You mentioned that you added 2 lines to .bashrc. However, the README 
file says that you need to add the following 3 lines to .bashrc:

               export ROOTSYS=<path>/root
               export PATH=$ROOTSYS/bin:$PATH
               export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH

Could you try this setting and let me know?

Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 8/3/12 10:55 AM, Steven wrote:
> 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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>
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