[BioC] package xps
Dan Tenenbaum
dtenenba at fhcrc.org
Fri Aug 3 19:05:52 CEST 2012
On Fri, Aug 3, 2012 at 9:19 AM, Steven <steven.wink at gmail.com> wrote:
> 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?
I doubt it.
There is an alternative to setting LD_LIBRARY_PATH which most modern
linuxes (including Ubuntu) support. Instead of modifying
LD_LIBRARY_PATH, create a file /etc/ld.so.conf.d/ROOT.conf which just
contains:
(assuming your home directory is /home/winks as ~ won't work here):
/home/winks/ROOT/root/lib
Then run sudo /sbin/ldconfig to make the system aware of this file.
Try doing this, removing the LD_LIBRARY_PATH from you .bashrc, and
sourcing it again. See if you can now install xps.
Dan
>
> 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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>>
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