Unable to load xps
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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/Versio ns/3.0/Resources/library/xps/libs/xps.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/librar y/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resour ces/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.
xps xps • 1.9k views
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cstrato ★ 3.9k
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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/Ver sions/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/Res ources/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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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/libra ry/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 Perif?rico Sur No. 4809, Col. Arenal Tepepan, Delegaci?n Tlalpan. M?xico, D.F. C.P. 14610 Tel. 535019200 ext 1126
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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/xp s/libs/xps.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libr ary/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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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/05369 0.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/x ps/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/xp s/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 Perif?rico Sur No. 4809, Col. Arenal Tepepan, Delegaci?n Tlalpan. M?xico, D.F. C.P. 14610 Tel. 535019200 ext 1126
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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/0536 90.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/li brary/xps/libs/xps.so, >>>>> 6): Library not loaded: @rpath/libGui.so >>>>> Referenced from: >>>>> >>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/x ps/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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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/053 690.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/l ibrary/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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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/li bs/xps.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/librar y/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/lib s/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/05 3690.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/librar y/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 Perif?rico Sur No. 4809, Col. Arenal Tepepan, Delegaci?n Tlalpan. M?xico, D.F. C.P. 14610 Tel. 535019200 ext 1126
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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. >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> >> > > >
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