[BioC] xps- not being able to load
cstrato
cstrato at aon.at
Sat Jul 6 19:53:22 CEST 2013
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/__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.
>
>
>
>
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>
>
>
> --
> 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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