when donging 'make', it appeared 'collect2: ld returned 1 exit status'

[maolingfengZJU]

Samtools 0.1.18. Boost 1.63.
When donging 'make', it appeared 'collect2: ld returned 1 exit status', like the message below.
[root@tc6000 LACHESIS-master]# make
Making all in src/include/gtools
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include/gtools'
Making all in src/include/markov
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include/markov'
Making all in src/include
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include' make[1]: Nothing to be done for all'.
make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include' Making all in src make[1]: Entering directory /public/software/apps/LACHESIS-master/src'
make all-am
make[2]: Entering directory /public/software/apps/LACHESIS-master/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/lib -Wl,-R,/usr/local/lib -L/usr/local/lib -Wl,-R,/usr/local/lib -L/public/software/apps/samtools-0.1.18 -lz -lpthread -lm -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz libtool: link: g++ -g -O2 -Wl,-R -Wl,/usr/local/lib -Wl,-R -Wl,/usr/local/lib -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/lib -L/public/software/apps/samtools-0.1.18 -lpthread -lm -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz include/libJmarkov.a(WDAG.o): In function WDAG::ReadFromFile(std::basic_string<char, std::char_traits, std::allocator > const&)':
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::error_info_injectorstd::overflow_error::~error_info_injector()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::overflow_error >::~clone_impl()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::error_info_injectorstd::overflow_error::~error_info_injector()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::overflow_error >::~clone_impl()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function error_info_injector':
/usr/local/include/boost/exception/exception.hpp:348: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o):/usr/local/include/boost/exception/exception.hpp:348: more undefined references to std::overflow_error::~overflow_error()' follow
Lachesis-ChromLinkMatrix.o: In function is_regular_file': /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
Lachesis-GenomeLinkMatrix.o: In function is_regular_file': /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-GenomeLinkMatrix.o:/usr/local/include/boost/filesystem/operations.hpp:456: more undefined references to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' follow
collect2: ld returned 1 exit status
make[2]: *** [Lachesis] Error 1
make[2]: Leaving directory /public/software/apps/LACHESIS-master/src' make[1]: *** [all] Error 2 make[1]: Leaving directory /public/software/apps/LACHESIS-master/src'
make: *** [all-recursive] Error 1

Can you give some advices to solve this problem.

[WenchaoLin]

Try boost 1.52.0 and samtools 0.1.19.

[andysw90]

Any joy? Having same issue (with samtools 0.1.19)

[milkcookie]

Did you solve the problem? I come cross the same problem when I run "make".

[liyang16859]

Did you solve it? Same here too.

[Huangtianyu-caas]

Hi @maolingfengZJU ,

Did you fix this issue? Thanks a lot.

My best,
Tianyu