BreakDancer make error

Question

[Peter]

~/bin/breakdancer/build$make
[ 14%] Built target boost-libs
[ 28%] Built target samtools-lib
[ 28%] Built target deps
[ 42%] Built target gtest160
[ 49%] Built target breakdancer
[ 52%] Built target common
[ 71%] Built target io
Linking CXX executable ../../../../bin/breakdancer-max
../../../../vendor/boost/boost/lib/libboost_serialization.a(xml_grammar.o): In function `std::bitset<256ul>::_M_check(unsigned long, char const*) const [clone .isra.27] [clone .part.28]':
xml_grammar.cpp:(.text.unlikely+0x11): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const':
instances.cpp:(.text._ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_[_ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_]+0x31f): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
instances.cpp:(.text._ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_[_ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_]+0x3e3): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
instances.cpp:(.text._ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_[_ZNK5boost9re_detail31cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_]+0x3f7): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::re_detail::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const':
instances.cpp:(.text._ZNK5boost9re_detail31cpp_regex_traits_implementationIcE9transformEPKcS4_[_ZNK5boost9re_detail31cpp_regex_traits_implementationIcE9transformEPKcS4_]+0xb3): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o):instances.cpp:(.text._ZN5boost9re_detail18basic_regex_parserIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE20parse_perl_extensionEv[_ZN5boost9re_detail18basic_regex_parserIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE20parse_perl_extensionEv]+0x1da1): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [bin/breakdancer-max] Error 1
make[1]: *** [build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/all] Error 2
make: *** [all] Error 2

[ernfrid]

That seems odd. Can you post the output from cmake on the initial run when the compiler etc is detected?

[Peter]

It works well on Ubuntu system. But not Centos 6.4 system.

Answer 1

[Peter]

~/bin/breakdancer/build$cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
Score floating point type: double
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXX11_FLAG0
-- Performing Test CXX11_FLAG0 - Success
-- C++11 support enabled via -std=c++11
-- Performing Test CXX11_STDLIB_FLAG0
-- Performing Test CXX11_STDLIB_FLAG0 - Success
-- Sufficient C++11 library support found with flag ' '
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/peter/bin/breakdancer/build

[ernfrid]

I tried to replicate this on a fresh CentOS6.4 virtual machine. I get an older compiler and breakdancer compiles without issues. Has your CentOS system been customized with a newer compiler? Or is it a newer CentOS?