make error with gvcftools-0.17.0

[kgerman73]

I have an AWS instance running Amazon linux and I get the following error when running make with gvcftools-0.17.0:

g++ -L/root/gvcftools-0.17.0/redist/boost/stage/lib -L/root/gvcftools-0.17.0/redist/tabix trio.o /root/gvcftools-0.17.0/src/libtrio/libtrio.a /root/gvcftools-0.17.0/src/libutil/libutil.a -ltabix_and_faidx -lz -lm -lboost_program_options -o trio
/usr/bin/ld: cannot find -lboost_program_options
collect2: error: ld returned 1 exit status

If I install the boost and boost-devel packages I get a different error:

g++ -L/root/gvcftools-0.17.0/redist/boost/stage/lib -L/root/gvcftools-0.17.0/redist/tabix trio.o /root/gvcftools-0.17.0/src/libtrio/libtrio.a /root/gvcftools-0.17.0/src/libutil/libutil.a -ltabix_and_faidx -lz -lm -lboost_program_options -o trio
trio.o: In function boost::program_options::typed_value<double, char>::xparse(boost::any&, std::vector<std::string, std::allocator<std::string> > const&) const': trio.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE6xparseERNS_3anyERKSt6vectorISsSaISsEE[_ZNK5boost15program_options11typed_valueIdcE6xparseERNS_3anyERKSt6vectorISsSaISsEE]+0xbb): undefined reference to boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&)'
trio.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE6xparseERNS_3anyERKSt6vectorISsSaISsEE[_ZNK5boost15program_options11typed_valueIdcE6xparseERNS_3anyERKSt6vectorISsSaISsEE]+0x20a): undefined reference to boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&)' trio.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x20): undefined reference to boost::program_options::validation_error::what() const'
trio.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x20): undefined reference to boost::program_options::validation_error::what() const' trio.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x20): undefined reference to boost::program_options::validation_error::what() const'
trio.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x20): undefined reference to boost::program_options::validation_error::what() const' trio.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x20): undefined reference to boost::program_options::validation_error::what() const'
/root/gvcftools-0.17.0/src/libtrio/libtrio.a(trio_option_util.o): In function validate(boost::any&, std::vector<std::string, std::allocator<std::string> > const&, std::vector<info_filter, std::allocator<info_filter> >*, int)': trio_option_util.cpp:(.text+0x23d): undefined reference to boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&)'
trio_option_util.cpp:(.text+0x35d): undefined reference to `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::string const&, std::string const&)'
collect2: error: ld returned 1 exit status

Doesn't boost come included in the install package? Any idea why it can't find it out of the box?

[serge2016]

Same here...
Any ideas?

[kalylian]

I had the same issue. Solved it by putting gvcftools in a container running CentOS 6 (which, according to the docs, is a tested OS). I guess it needs a pretty old gcc.