[BioC] package xps
Steven
steven.wink at gmail.com
Fri Aug 3 18:19:23 CEST 2012
Hi Christian,
sorry about that, a bit sloppy of me but I did in fact add all 3 lines:
export ROOTSYS=~/ROOT/root
export PATH=$ROOTSYS/bin:$PATH
export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
Also it seems the variable has been set correctly based on the "echo"
output. Makes the error all the stranger.
Could it be that I a installed ubuntu 12:04 with a windows installer
(Wubi) have anything to do with it?
Best regards,
Steven
2012/8/3 cstrato <cstrato at aon.at>:
> 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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