[BioC] Unable to load xps

[cstrato]

Dear Jorge,

FYI, after updating to R-3.0.1 I have just tested R.app on my Mac 
running Lion again and realized that R.app now woks just fine.

I can also start library(xps) w/o problems and run my examples. I am 
even able to set 'verbose=TRUE' so that the output of 'cout' is 
displayed in R Console immediately.

Thus at the moment I am not sure why you are not able to run xps with 
R.app. Maybe it has to do that you are using .bash_profile instead of 
.bashrc, but I am not sure.

Since you can run xps from the terminal but not from R.app this would 
mean that in your case R.app does not recognize ROOTSYS or 
LD_LIBRARY_PATH. (Maybe you need to delete DYLD_LIBRARY_PATH?)

Did you use the Package Manager in the R.app to install xps? Maybe you 
need to install xps with R CMD INSTALL?

Best regards,
Christian


On 9/10/13 8:18 PM, cstrato wrote:
> 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.
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>