xps- not being able to load

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Juehua Yu ▴ 20

@juehua-yu-6029

Last seen 10.3 years ago

Hi all, I have read all online instructions for how to install and load xps in R, but keep getting the following error: 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/library/ 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 Root has been built. 5.99/02 R 3.0.1 Mac 10.8.4 Root installed in /users/juehuayu/Documents/root with ./configure macosx64 Also, I generated a bashrc file in /users/juehuayu/Documents/root # .bashrc # User specific aliases and functions #svn export PATH=$PATH:/usr/local/bin # ROOT settings export ROOTSYS=/users/juehuayu/Documents/root/root export PATH=$ROOTSYS/bin:$PATH export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi Please help. -- Juehua Yu Department of Surgery and Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California, Los Angeles California 90095 [[alternative HTML version deleted]]

xps xps • 1.5k views

ADD COMMENT • link updated 11.5 years ago by cstrato ★ 3.9k • written 11.5 years ago by Juehua Yu ▴ 20

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cstrato ★ 3.9k

@cstrato-908

Last seen 6.2 years ago

Austria

Dear Juehua Yu, The error indicates that xps does not find ROOT. Can you please tell me which version of ROOT you did compile? (Please note that version 5.99/02 does not exist.) When compiling ROOT yourself I would suggest that you check first if typing 'root' in a new xterm (or Terminal) will start ROOT. How did you install xps? I would suggest to compile xps, e.g.: R CMD INSTALL xps_1.20.2.tar.gz Which version of X did you install? Best regards, Christian On 7/6/13 3:19 AM, Juehua Yu wrote: > Hi all, > > I have read all online instructions for how to install and load xps in R, > but keep getting the following error: > > 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/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/l ibs/xps.so > Reason: image not found > Error: package or namespace load failed for ?xps? > > > Root has been built. 5.99/02 > R 3.0.1 > Mac 10.8.4 > > Root installed in /users/juehuayu/Documents/root > with ./configure macosx64 > > Also, I generated a bashrc file in /users/juehuayu/Documents/root > # .bashrc > > # User specific aliases and functions > > #svn > export PATH=$PATH:/usr/local/bin > > # ROOT settings > > export ROOTSYS=/users/juehuayu/Documents/root/root > export PATH=$ROOTSYS/bin:$PATH > export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH > > # Source global definitions > if [ -f /etc/bashrc ]; then > . /etc/bashrc > fi > > Please help. > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 11.5 years ago cstrato ★ 3.9k

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Dear Christian, Thank you so much for your information. The root is 5.24.00. I tried both root_v5.24.00.macosx105-i386-gcc-4.0.tar.gz and root_v5.24.00.source.tar.gz I can start root anywhere and in a new terminal. When I did R CMD INSTALL xps_1.20.2.tar.gz I got this following errors. dhcp-10-47-221-155:Downloads juehuayu$ R CMD INSTALL xps_1.20.2.tar.gz * installing to library /Library/Frameworks/R.framework/Versions/3.0/Resources/library * installing *source* package xps ... checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... none needed checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E checking for gcc... (cached) llvm-gcc-4.2 -arch x86_64 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... (cached) none needed found ROOT version 5.99/02 in directory /Users/juehuayu/Documents/root ** libs ** arch - Unknown argument "--dicttype"! Usage: root-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] [--cflags] [--auxcflags] [--ldflags] [--new] [--nonew] [--libs] [--glibs] [--evelibs] [--bindir] [--libdir] [--incdir] [--etcdir] [--noauxcflags] [--noauxlibs] [--noldflags] [--has-<feature>] [--arch] [--platform] [--config] [--features] [--svn-revision] [--python-version] [--cc] [--cxx] [--f77] [--ld ] [--help] clang++ -I/Users/juehuayu/Documents/root/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/Users/juehuayu/Documents/root/include -c TMLMath.cxx TMLMath.cxx:123:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::Expm1------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:123:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::Expm1------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:159:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::Log1p------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:159:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::Log1p------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:253:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::Pow------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:253:51: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::Pow------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:301:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::PowDi------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:301:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::PowDi------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:390:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::PBeta------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:390:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::PBeta------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:410:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::DNorm------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:410:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::DNorm------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:445:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::PNorm------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:445:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::PNorm------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:490:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::QNorm------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:490:53: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::QNorm------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:646:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::PT------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ TMLMath.cxx:646:50: error: use of undeclared identifier 'endl'; did you mean 'std::endl'? if(kCSa) cout << "------TMLMath::PT------" << endl; ^~~~ std::endl /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here endl(basic_ostream<_CharT, _Traits>& __os) ^ TMLMath.cxx:690:13: error: use of undeclared identifier 'cout'; did you mean 'std::cout'? if(kCSa) cout << "------TMLMath::QT------" << endl; ^~~~ std::cout /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here extern ostream cout; ///< Linked to standard output ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make: *** [TMLMath.o] Error 1 ERROR: compilation failed for package xps * removing /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps * restoring previous /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps Best wishes, Juehua On Sat, Jul 6, 2013 at 7:54 AM, cstrato <cstrato@aon.at> wrote: > Dear Juehua Yu, > > The error indicates that xps does not find ROOT. > > Can you please tell me which version of ROOT you did compile? (Please note > that version 5.99/02 does not exist.) > > When compiling ROOT yourself I would suggest that you check first if > typing 'root' in a new xterm (or Terminal) will start ROOT. > > How did you install xps? > I would suggest to compile xps, e.g.: > R CMD INSTALL xps_1.20.2.tar.gz > > Which version of X did you install? > > Best regards, > Christian > > > > On 7/6/13 3:19 AM, Juehua Yu wrote: > >> Hi all, >> >> I have read all online instructions for how to install and load xps in R, >> but keep getting the following error: >> >> 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 >> >> >> Root has been built. 5.99/02 >> R 3.0.1 >> Mac 10.8.4 >> >> Root installed in /users/juehuayu/Documents/root >> with ./configure macosx64 >> >> Also, I generated a bashrc file in /users/juehuayu/Documents/root >> # .bashrc >> >> # User specific aliases and functions >> >> #svn >> export PATH=$PATH:/usr/local/bin >> >> # ROOT settings >> >> export ROOTSYS=/users/juehuayu/**Documents/root/root >> export PATH=$ROOTSYS/bin:$PATH >> export LD_LIBRARY_PATH=$ROOTSYS/lib:$**LD_LIBRARY_PATH >> >> # Source global definitions >> if [ -f /etc/bashrc ]; then >> . /etc/bashrc >> fi >> >> Please help. >> >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> -- Juehua Yu Department of Surgery and Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California, Los Angeles California 90095 [[alternative HTML version deleted]]

ADD REPLY • link 11.5 years ago Juehua Yu ▴ 20

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Dear Juehua, The problem is that root_5.24/00 is much too old, so it does not work with Mountain Lion. For Mountain Lion you need at least version 5.34/xx. I suggest that you use the version which was used by the Bioconductor maintainers to build xps, i.e. root_v5.34.05. You can download from CERN the version compiled for Mountain Lion: ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz Best regards, Christian On 7/6/13 7:35 PM, Juehua Yu wrote: > Dear Christian, > Thank you so much for your information. > The root is 5.24.00. I tried both > root_v5.24.00.macosx105-i386-gcc-4.0.tar.gz and root_v5.24.00.source.tar.gz > I can start root anywhere and in a new terminal. > > When I did R CMD INSTALL xps_1.20.2.tar.gz > I got this following errors. > > dhcp-10-47-221-155:Downloads juehuayu$ R CMD INSTALL xps_1.20.2.tar.gz > > * installing to library > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > > * installing *source* package ?xps? ... > > checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99 > > checking for C compiler default output file name... a.out > > checking whether the C compiler works... yes > > checking whether we are cross compiling... no > > checking for suffix of executables... > > checking for suffix of object files... o > > checking whether we are using the GNU C compiler... yes > > checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes > > checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI > C... none needed > > checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 > -std=gnu99 -E > > checking for gcc... (cached) llvm-gcc-4.2 -arch x86_64 -std=gnu99 > > checking whether we are using the GNU C compiler... (cached) yes > > checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... > (cached) yes > > checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI > C... (cached) none needed > > found ROOT version 5.99/02 in directory /Users/juehuayu/Documents/root > > ** libs > > ** arch - > > Unknown argument "--dicttype"! > > Usage: root-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] > [--cflags] [--auxcflags] [--ldflags] [--new] [--nonew] [--libs] > [--glibs] [--evelibs] [--bindir] [--libdir] [--incdir] [--etcdir] > [--noauxcflags] [--noauxlibs] [--noldflags] [--has-<feature>] [--arch] > [--platform] [--config] [--features] [--svn-revision] [--python- version] > [--cc] [--cxx] [--f77] [--ld ] [--help] > > clang++ -I/Users/juehuayu/Documents/root/include -O2 -pipe -Wall -W > -Woverloaded-virtual -pthread -m64 > -I/Users/juehuayu/Documents/root/include -c TMLMath.cxx > > TMLMath.cxx:123:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::Expm1------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:123:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::Expm1------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:159:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::Log1p------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:159:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::Log1p------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:253:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::Pow------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:253:51: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::Pow------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:301:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::PowDi------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:301:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::PowDi------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:390:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::PBeta------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:390:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::PBeta------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:410:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::DNorm------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:410:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::DNorm------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:445:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::PNorm------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:445:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::PNorm------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:490:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::QNorm------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:490:53: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::QNorm------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:646:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::PT------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > TMLMath.cxx:646:50: error: use of undeclared identifier 'endl'; did you > mean 'std::endl'? > > if(kCSa) cout << "------TMLMath::PT------" << endl; > > ^~~~ > > std::endl > > /usr/include/c++/4.2.1/ostream:607:5: note: 'std::endl' declared here > > endl(basic_ostream<_CharT, _Traits>& __os) > > ^ > > TMLMath.cxx:690:13: error: use of undeclared identifier 'cout'; did you > mean 'std::cout'? > > if(kCSa) cout << "------TMLMath::QT------" << endl; > > ^~~~ > > std::cout > > /usr/include/c++/4.2.1/iostream:63:18: note: 'std::cout' declared here > > extern ostream cout; ///< Linked to standard output > > ^ > > fatal error: too many errors emitted, stopping now [-ferror-limit=] > > 20 errors generated. > > make: *** [TMLMath.o] Error 1 > > ERROR: compilation failed for package ?xps? > > * removing > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps? > > * restoring previous > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps? > > > Best wishes, > Juehua > > > On Sat, Jul 6, 2013 at 7:54 AM, cstrato <cstrato at="" aon.at=""> <mailto:cstrato at="" aon.at="">> wrote: > > Dear Juehua Yu, > > The error indicates that xps does not find ROOT. > > Can you please tell me which version of ROOT you did compile? > (Please note that version 5.99/02 does not exist.) > > When compiling ROOT yourself I would suggest that you check first if > typing 'root' in a new xterm (or Terminal) will start ROOT. > > How did you install xps? > I would suggest to compile xps, e.g.: > R CMD INSTALL xps_1.20.2.tar.gz > > Which version of X did you install? > > Best regards, > Christian > > > > On 7/6/13 3:19 AM, Juehua Yu wrote: > > Hi all, > > I have read all online instructions for how to install and load > xps in R, > but keep getting the following error: > > 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/__Reso urces/library/xps/libs/__xps.so, > 6): Library not loaded: @rpath/libGui.so > Referenced from: > /Library/Frameworks/R.__framework/Versions/3.0/__Resources/l ibrary/xps/libs/__xps.so > Reason: image not found > Error: package or namespace load failed for ?xps? > > > Root has been built. 5.99/02 > R 3.0.1 > Mac 10.8.4 > > Root installed in /users/juehuayu/Documents/root > with ./configure macosx64 > > Also, I generated a bashrc file in /users/juehuayu/Documents/root > # .bashrc > > # User specific aliases and functions > > #svn > export PATH=$PATH:/usr/local/bin > > # ROOT settings > > export ROOTSYS=/users/juehuayu/__Documents/root/root > export PATH=$ROOTSYS/bin:$PATH > export LD_LIBRARY_PATH=$ROOTSYS/lib:$__LD_LIBRARY_PATH > > # Source global definitions > if [ -f /etc/bashrc ]; then > . /etc/bashrc > fi > > Please help. > > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > Juehua Yu > Department of Surgery and Department of Pathology and Laboratory Medicine > David Geffen School of Medicine at University of California, Los Angeles > California 90095

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