[BioC] Unable to load xps

[Jorge Melendez]

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.
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>



-- 
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