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/lib rary/xps/libs/xps.so, > 6): Library not loaded: @rpath/libGui.so > Referenced from: > /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/l ibs/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/0 53690.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/libra ry/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/librar y/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. >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> >> > > >