ckingsford
commented
7 years ago Not sure what is going on here. Are you able to compile other C++ programs? It seems like a compiler installation error (or configuration/path issue).
Open Gracklewolf opened 7 years ago
ckingsford
commented
7 years ago Not sure what is going on here. Are you able to compile other C++ programs? It seems like a compiler installation error (or configuration/path issue).
Trying to build sailfish on a Redhat 7.2 server. Make fails with the following:
/usr/lib64/ccache/g++ -pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type -static-libstdc++ -Wno-deprecated-register -Wno-unused-local-typedefs -L/usr/lib64 CMakeFiles/sailfish.dir/Sailfish.cpp.o -o sailfish -L/cluster/app/source/sailfish/lib -L/cluster/app/source/sailfish/external/install/lib -rdynamic libsailfish_core.a -lpthread -Wl,-Bstatic -lboost_iostreams-mt -lboost_filesystem-mt -lboost_system-mt -lboost_thread-mt -lboost_timer-mt -lboost_chrono-mt -lboost_program_options-mt -lboost_serialization-mt -Wl,-Bdynamic -lgff -lz ../../external/install/lib/libdivsufsort.a ../../external/install/lib/libdivsufsort64.a ../../external/install/lib/libjellyfish-2.0.a -lm -ltbb -ltbbmalloc -lgomp -lrt ../../external/install/lib/libjemalloc.a -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" /bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/sailfish] Error 1 make[2]: Leaving directory `/cluster/app/source/sailfish/build' make[1]: [src/CMakeFiles/sailfish.dir/all] Error 2 make[1]: Leaving directory `/cluster/app/source/sailfish/build' make: *** [all] Error 2
This makes no sense as the stdc++ library is clearly on the system. Here is my initial cmake:
cmake -DCMAKE_INSTALL_PREFIX=/cluster/app/sailfish ..