problem occured when running make all_analysis

[Anonymous]

Dear Professor,

When I run make all_analysis, problem occured as below. My boost version boost_1_59_0.

[huzi@huzi analysis]$ make all_analysis
tar xz -C ../../vendor -f ../../vendor/wn_matrix.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/wn_matrix/0.18/src/WnMatrix.c -o ../../obj/WnMatrix.o
tar xz -C ../../vendor -f ../../vendor/libnucnet.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/libnucnet/0.28/src/LibnucnetNuc.c -o ../../obj/LibnucnetNuc.o
tar xz -C ../../vendor -f ../../vendor/libnucnet.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/libnucnet/0.28/src/LibnucnetReac.c -o ../../obj/LibnucnetReac.o
tar xz -C ../../vendor -f ../../vendor/libnucnet.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/libnucnet/0.28/src/Libnucnet.c -o ../../obj/Libnucnet.o
tar xz -C ../../vendor -f ../../vendor/libstatmech.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/libstatmech/0.9/src/Libstatmech.c -o ../../obj/Libstatmech.o
tar xz -C ../../vendor -f ../../vendor/libnuceq.tar.gz
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c ../../vendor/libnuceq/0.6/src/Libnuceq.c -o ../../obj/Libnuceq.o
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/auxiliary.o ../../nnt/auxiliary.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/iter.o ../../nnt/iter.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/math.o ../../nnt/math.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/two_d_weak_rates.o ../../nnt/two_d_weak_rates.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/wrappers.o ../../nnt/wrappers.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/user_rate_functions.o ../../user/user_rate_functions.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/flow_utilities.o ../../user/flow_utilities.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/aa522a25.o ../../user/aa522a25.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/neutrino_rate_functions.o ../../user/neutrino_rate_functions.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/network_utilities.o ../../user/network_utilities.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/rate_modifiers.o ../../user/rate_modifiers.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/screen.o ../../user/screen.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/thermo.o ../../user/thermo.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/nse_corr.o ../../user/nse_corr.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/weak_utilities.o ../../user/weak_utilities.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. -c -o ../../obj/remove_duplicate.o ../../user/remove_duplicate.cpp
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o -o ./compute_flows compute_flows.cpp -lboost_program_options xml2-config --libs gsl-config --libs
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o -o ./compute_abundance_moment_in_zones compute_abundance_moment_in_zones.cpp -lboost_program_options xml2-config --libs gsl-config --libs
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o -o ./compute_Ycdot compute_Ycdot.cpp -lboost_program_options xml2-config --libs gsl-config --libs
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o -o ./compute_zone_mu compute_zone_mu.cpp -lboost_program_options xml2-config --libs gsl-config --libs
g++ -Werror -Wall -Wpointer-arith -Wcast-qual -Wwrite-strings -fshort-enums -fno-common -g -ansi -Wconversion -DWN_XML_CHAR=xmlChar -O0 -fopenmp -Wno-deprecated xml2-config --cflags gsl-config --cflags -I../../vendor/libnucnet/0.28/src -I../../vendor/wn_matrix/0.18/src -I../../vendor/libstatmech/0.9/src -I../../vendor/libnuceq/0.6/src -I../.. ../../obj/WnMatrix.o ../../obj/LibnucnetNuc.o ../../obj/LibnucnetReac.o ../../obj/Libnucnet.o ../../obj/Libstatmech.o ../../obj/Libnuceq.o ../../obj/auxiliary.o ../../obj/iter.o ../../obj/math.o ../../obj/two_d_weak_rates.o ../../obj/wrappers.o ../../obj/user_rate_functions.o ../../obj/flow_utilities.o ../../obj/aa522a25.o ../../obj/neutrino_rate_functions.o ../../obj/network_utilities.o ../../obj/rate_modifiers.o ../../obj/screen.o ../../obj/thermo.o ../../obj/nse_corr.o ../../obj/weak_utilities.o ../../obj/remove_duplicate.o -o ./compare_equil compare_equil.cpp -lboost_program_options xml2-config --libs gsl-config --libs
/tmp/ccgz370a.o: In function get_input(int, char**)': /home/huzi/nucnet-tools-code/examples/analysis/compare_equil.cpp:66: undefined reference toboost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&, unsigned int, unsigned int)'
/tmp/ccgz370a.o: In function ~error_with_option_name': /usr/local/include/boost/program_options/errors.hpp:119: undefined reference tovtable for boost::program_options::error_with_option_name'
/tmp/ccgz370a.o: In function boost::program_options::basic_command_line_parser<char>::run()': /usr/local/include/boost/program_options/detail/parsers.hpp:108: undefined reference toboost::program_options::detail::cmdline::get_canonical_option_prefix()'
/tmp/ccgz370a.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x10): undefined reference to boost::program_options::error_with_option_name::what() const' /tmp/ccgz370a.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x18): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&) const'
/tmp/ccgz370a.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x10): undefined reference to boost::program_options::error_with_option_name::what() const' /tmp/ccgz370a.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x18): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&) const'
/tmp/ccgz370a.o:(.rodata._ZTIN5boost15program_options16validation_errorE[typeinfo for boost::program_options::validation_error]+0x8): undefined reference to typeinfo for boost::program_options::error_with_option_name' /tmp/ccgz370a.o: In functionerror_with_option_name':
/usr/local/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name' /tmp/ccgz370a.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x14): undefined reference toboost::program_options::error_with_option_name::what() const'
/tmp/ccgz370a.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x1c): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /tmp/ccgz370a.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x10): undefined reference toboost::program_options::error_with_option_name::what() const'
/tmp/ccgz370a.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x18): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&) const'
collect2: ld returned 1 exit status
make: *** [compare_equil] Error 1

[Bradley S. Meyer]

It looks like you are compiling with gcc but trying to link to libraries compiled with clang. Try following the steps at this blog post carefully. Let me know if you still have trouble. Best wishes.