Question: BreakDancer make error
0
gravatar for Peter
2.7 years ago by
Peter0
China
Peter0 wrote:

~/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

breakdancer • 1.2k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Peter0

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

ADD REPLYlink written 2.7 years ago by ernfrid180

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

ADD REPLYlink written 2.7 years ago by Peter0
0
gravatar for Peter
2.7 years ago by
Peter0
China
Peter0 wrote:

~/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

ADD COMMENTlink written 2.7 years ago by Peter0

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?

ADD REPLYlink written 2.6 years ago by ernfrid180
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