[BioC] Unable to load xps

[Jorge Melendez]

Thank you!
I called xps from terminal instead and now it is working.
Best
Jorge

On Tue, Sep 10, 2013 at 11:56 AM, cstrato <cstrato at aon.at> wrote:
> Dear Jorge,
>
> Could you please answer the following questions and/or try the following:
>
> - I assume that you have installed XQuartz?
>
> - Are you running R from xterm or from Terminal.app?
> (Using R.app will probably not work.)
>
> - Is the absolute path to libGui.so:
> /Users/jorgemelendez/my_rnaseq_exp/root/libGui.so
>
> - I see that you did export ROOTSYS etc in .bash_profile. I do not know if
> this may be the reason but I am always putting this in .bashrc in my home
> directory.
>
> - Probably for Mountain Lion the following line is no longer necessary:
> export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH
>
> - You probably refer to this thread:
> https://www.stat.math.ethz.ch/pipermail/bioconductor/2013-July/053690.html
> In this case the user told me that downloading the compiled version from:
> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz
> did finally solve his problem.
>
> - Maybe you could try to compile root from source, i.e. unpack root in e.g.
> your home directory and then do:
> $ cd root
> $ ./configure macosx64
> $ make
> $ . bin/thisroot.sh
>
> - How did you install xps? Maybe it will help to compile xps, e.g.:
> R CMD INSTALL xps_1.20.3.tar.gz
>
> Best regards,
> Christian
>
>
>
> On 9/10/13 5:36 PM, Jorge Melendez wrote:
>>
>> Hello Christian
>> Thanks for the quick response!
>> Yes, I am using root_v5.34.05.macosx64-10.8-i386.tar
>> Best
>> Jorge
>>
>> On Tue, Sep 10, 2013 at 10:29 AM, cstrato <cstrato at aon.at> wrote:
>>>
>>> Dear Jorge,
>>>
>>> Which file did you download from the ROOT website?
>>>
>>> Please note that the README file says:
>>>     For Mountain Lion there exists a 64 bit binary:
>>>     root_v5.34.05.macosx64-10.8-i386.tar.gz
>>>
>>> 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 9/10/13 5:04 PM, Jorge Melendez [guest] wrote:
>>>>
>>>>
>>>> Hi!
>>>> As someone else on the list, I am having trouble loading xps in a mac. I
>>>> am using OSX 10.8, R 3.0.1.  I used the latest precompiled binary and
>>>> installed root at ~/my_rnaseq_exp/root. I changed my .bash_profile with
>>>> export ROOTSYS=/Users/jorgemelendez/my_rnaseq_exp/root
>>>> export PATH=$ROOTSYS/bin:$PATH
>>>> export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
>>>> export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH
>>>> Root root runs fine, but when trying to load xps in R:
>>>>
>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>     unable to load shared object
>>>>
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so':
>>>>
>>>>
>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so,
>>>> 6): Library not loaded: @rpath/libGui.so
>>>>     Referenced from:
>>>>
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so
>>>>     Reason: image not found
>>>> Error: package or namespace load failed for ‘xps’
>>>>
>>>>
>>>> Can you help?
>>>> Thanks a lot
>>>>
>>>>    -- output of sessionInfo():
>>>>
>>>> R version 3.0.1 (2013-05-16)
>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_3.0.1
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>>>
>>>
>>
>>
>>
>



-- 
Jorge Melendez Zajgla MD PhD
Functional Cancer Genomics Laboratory
Deputy Director of Basic Research
National Institute of Genomic Medicine
Mexico
Periférico Sur No. 4809, Col. Arenal Tepepan,
Delegación Tlalpan. México, D.F. C.P. 14610
Tel. 535019200 ext 1126