This is a problem with your compiler: it should be linking against a shared version of libstdc++. Please take this up with your OS support.
On Wed, 14 Jun 2006, Dan Lipsitt wrote: > I am unable to install the gmp package on an x86_64 (Xeon) machine. I > have had the same problem with other packages (eg. MCMCpack) as well. > I am running Red Hat Enterprise Linux 4.1. > I get the following error: > > g++ -shared -L/usr/local/lib64 -o gmp.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o -L/usr/local/lib/ -lgmp > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > > However, I have found that if I run "R CMD SHLIB" twice in the src/ > directory, once to build the .o files, and once to link, I can build > the shared library. If I run it on the .o files instead of the .cc > files it uses gcc instead of g++. This appears to be the change that > allows the lib to build. "-fPIC" seems to have nothing to do with it. > > So my question is: How do I get "R CMD INSTALL" to link with gcc > instead of g++? I have tried adding "LINK.cc = $(LINK.c)" to the top > of src/Makevars.in and then running "R CMD check" in the top dir of > the package, but it uses g++ anyway. Any other fix or workaround > suggestions would be appreciated as well. > > A commandline transcript follows below. > > Thanks, > Dan > > $ sudo R CMD INSTALL gmp_0.3-4.tar.gz > * Installing *source* package 'gmp' ... > creating cache ./config.cache > checking for __gmpz_ui_sub in -lgmp... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c biginteger.cc -o biginteger.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c biginteger_operator.cc -o > biginteger_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigintegerR.cc -o > bigintegerR.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrational.cc -o > bigrational.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrational_operator.cc -o > bigrational_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrationalR.cc -o > bigrationalR.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c factor.cc -o factor.o > g++ -shared -L/usr/local/lib64 -o gmp.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o -L/usr/local/lib/ -lgmp > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > collect2: ld returned 1 exit status > make: *** [gmp.so] Error 1 > ERROR: compilation failed for package 'gmp' > > $ tar xzf gmp_0.3-4.tar.gz > $ cd gmp/src > $ R CMD SHLIB *.cc > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > biginteger.cc -o biginteger.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > biginteger_operator.cc -o biginteger_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigintegerR.cc -o bigintegerR.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrational.cc -o bigrational.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrational_operator.cc -o bigrational_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrationalR.cc -o bigrationalR.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > factor.cc -o factor.o > g++ -shared -L/usr/local/lib64 -o biginteger.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > collect2: ld returned 1 exit status > make: *** [biginteger.so] Error 1 > $ R CMD SHLIB *.o > gcc -shared -L/usr/local/lib64 -o biginteger.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o > $ > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
