[BioC] Unable to load xps

[cstrato]

Dear Jorge,

I am sorry that my suggestions did not help you, and I do not know R.app 
well enough to have an idea what might be the cause.

For this reason I am cc to Simon, who is the author of R.app and is 
always very helpful. Maybe he has a suggestion.

Best regards,
Christian


On 9/11/13 5:14 PM, Jorge Melendez wrote:
> Hi
> I deleted DYLD_LIBRARY_PATH, changed to .bashrc and reinstalled xps
> with R CMD INSTALL. Still the same problem. Perhaps is something
> related to M.lion ( changing bashrc gives me the warning: dyld: DYLD_
> environment variables being ignored because main executable
> (/usr/bin/sudo) is setuid or setgid in terminal when using sudo).
>
> Best and thank you!
> Jorge
>
>
> 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’
>
> On Wed, Sep 11, 2013 at 8:45 AM, cstrato <cstrato at aon.at> wrote:
>> 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.
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>
>
>
>