[BioC] Unable to load xps

[cstrato]

Dear Jorge,

I am, glad to hear that xps works fine from terminal.

I must admit that I gave up long time ago to adopt xps for R.app. At the 
moment, on my Mac running Lion I cannot even open R.app, I get simply an 
error message.

Best regards,
Christian


On 9/10/13 7:59 PM, Jorge Melendez wrote:
> 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.
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
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