Link problem

[mianbaozhai]

Hi,
I tried to install armatus using cmake
cmake CMakeLists.txt -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=~/software/armatus/
That's OK.

But, I have a problem when make install

Linking CXX executable armatus
cd /public/home/liuyanlin/download/armatus-2.2/src && /public/home/liuyanlin/anaconda2/bin/cmake -E cmake_link_script CMakeFiles/armatus.dir/link.txt --verbose=1
/public/home/liuyanlin/anaconda2/bin/c++ -O3 -g -std=c++11 -Wall -Wno-unused-local-typedefs CMakeFiles/armatus.dir/Armatus.cpp.o CMakeFiles/armatus.dir/ArmatusUtil.cpp.o CMakeFiles/armatus.dir/ArmatusParams.cpp.o CMakeFiles/armatus.dir/ArmatusDAG.cpp.o CMakeFiles/armatus.dir/IntervalScheduling.cpp.o -o armatus -rdynamic -lboost_program_options-mt -lboost_iostreams -lboost_graph -lboost_system -lboost_regex -lz -Wl,-rpath,/public/home/liuyanlin/anaconda2/lib:
/usr/bin/ld: skipping incompatible /usr/lib/../lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/../lib/libc.so when searching for -lc
/usr/bin/ld: warning: libicui18n.so.54, needed by /public/home/liuyanlin/anaconda2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/../../../../lib/libboost_graph.so, not found (try using -rpath or -rpath-link)
/public/home/liuyanlin/anaconda2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crt1.o: In function _start': (.text+0x12): undefined reference to __libc_csu_fini'
/public/home/liuyanlin/anaconda2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crt1.o: In function _start': (.text+0x19): undefined reference to __libc_csu_init'
CMakeFiles/armatus.dir/Armatus.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&, int)':
...

I added a parameter “-L/usr/lib/x86_64-redhat-linux5E/lib64” in link.txt and set up "ln /public/home/liuyanlin/anaconda2/lib/libicui18n.so.54.1 /public/home/liuyanlin/anaconda2/lib/libicui18n.so.54"

But still some part of the problem is not resolved

Linking CXX executable armatus
cd /public/home/liuyanlin/download/armatus-2.2/src && /public/home/liuyanlin/anaconda2/bin/cmake -E cmake_link_script CMakeFiles/armatus.dir/link.txt --verbose=1
/public/home/liuyanlin/anaconda2/bin/c++ -O3 -g -std=c++11 -Wall -Wno-unused-local-typedefs -L/usr/lib/x86_64-redhat-linux5E/lib64 CMakeFiles/armatus.dir/Armatus.cpp.o CMakeFiles/armatus.dir/ArmatusUtil.cpp.o CMakeFiles/armatus.dir/ArmatusParams.cpp.o CMakeFiles/armatus.dir/ArmatusDAG.cpp.o CMakeFiles/armatus.dir/IntervalScheduling.cpp.o -o armatus -rdynamic -lboost_program_options-mt -lboost_iostreams -lboost_graph -lboost_system -lboost_regex -lz -Wl,-rpath-link,/public/home/liuyanlin/anaconda2/lib:
/public/home/liuyanlin/anaconda2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crt1.o: In function _start': (.text+0x12): undefined reference to __libc_csu_fini'
/public/home/liuyanlin/anaconda2/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.8.5/crt1.o: In function _start': (.text+0x19): undefined reference to __libc_csu_init'
CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&, int)': /public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:373: undefined reference to boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)'
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:373: undefined reference to boost::program_options::error_with_option_name::error_with_option_name(std::string const&, std::string const&, std::string const&, int)' CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::error_with_option_name::~error_with_option_name()':
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::validation_error::~validation_error()':
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::invalid_option_value::~invalid_option_value()':
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::error_with_option_name::~error_with_option_name()':
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::validation_error::~validation_error()':
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o:/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:119: more undefined references to vtable for boost::program_options::error_with_option_name' follow
CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::basic_command_line_parser<char>::run()': /public/home/liuyanlin/anaconda2/include/boost/program_options/detail/parsers.hpp:108: undefined reference to boost::program_options::detail::cmdline::get_canonical_option_prefix()'
CMakeFiles/armatus.dir/Armatus.cpp.o: In function main': /public/home/liuyanlin/download/armatus-2.2/src/Armatus.cpp:55: undefined reference to boost::program_options::options_description::options_description(std::string const&, unsigned int, unsigned int)'
CMakeFiles/armatus.dir/Armatus.cpp.o: In function boost::program_options::error_with_option_name::error_with_option_name(boost::program_options::error_with_option_name const&)': /public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name'
CMakeFiles/armatus.dir/Armatus.cpp.o: In function error_with_option_name': /public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name'
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name' /public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name'
/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o:/public/home/liuyanlin/anaconda2/include/boost/program_options/errors.hpp:89: more undefined references to vtable for boost::program_options::error_with_option_name' follow
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x28): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x28): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorE[_ZTIN5boost15program_options16validation_errorE]+0x10): undefined reference to typeinfo for boost::program_options::error_with_option_name' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x20): undefined reference to boost::program_options::error_with_option_name::what() const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const' CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x20): undefined reference to boost::program_options::error_with_option_name::what() const'
CMakeFiles/armatus.dir/Armatus.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::string const&) const' /lib64//librt.so.1: undefined reference to __fortify_fail@GLIBC_PRIVATE'
/lib64//libpthread.so.0: undefined reference to __vdso_clock_gettime@GLIBC_PRIVATE' collect2: error: ld returned 1 exit status make[2]: *** [src/armatus] Error 1 make[2]: Leaving directory /public/home/liuyanlin/download/armatus-2.2'
make[1]: *** [src/CMakeFiles/armatus.dir/all] Error 2
make[1]: Leaving directory `/public/home/liuyanlin/download/armatus-2.2'
make: *** [all] Error 2

Do you have any suggestions?
Thank you！

[ckingsford]

Someone else who is also using conda suggested doing the following:

  export LD_LIBRARY_PATH=$CONDA_PREFIX/lib/

and also you could try adding -L$CONDA_PREFIX/lib/ to your link command line. E.g. add that directory to the src/CMakeLists.txt file at the link_directories line.