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build fail - can't find libstdc++ #101

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Gracklewolf opened this issue May 9, 2017 · 1 comment
Open

build fail - can't find libstdc++ #101

Gracklewolf opened this issue May 9, 2017 · 1 comment

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@Gracklewolf
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Gracklewolf commented May 9, 2017

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 ..

@ckingsford
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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).

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