{"action":"created","issue":{"url":"https://api.github.com/repos/TGAC/KAT/issues/68","repository_url":"https://api.github.com/repos/TGAC/KAT","labels_url":"https://api.github.com/repos/TGAC/KAT/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/TGAC/KAT/issues/68/comments","events_url":"https://api.github.com/repos/TGAC/KAT/issues/68/events","html_url":"https://github.com/TGAC/KAT/issues/68","id":194091904,"number":68,"title":"make fails - undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'","user":{"login":"shyamrallapalli","id":3543099,"avatar_url":"https://avatars.githubusercontent.com/u/3543099?v=3","gravatar_id":"","url":"https://api.github.com/users/shyamrallapalli","html_url":"https://github.com/shyamrallapalli","followers_url":"https://api.github.com/users/shyamrallapalli/followers","following_url":"https://api.github.com/users/shyamrallapalli/following{/other_user}","gists_url":"https://api.github.com/users/shyamrallapalli/gists{/gist_id}","starred_url":"https://api.github.com/users/shyamrallapalli/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shyamrallapalli/subscriptions","organizations_url":"https://api.github.com/users/shyamrallapalli/orgs","repos_url":"https://api.github.com/users/shyamrallapalli/repos","events_url":"https://api.github.com/users/shyamrallapalli/events{/privacy}","received_events_url":"https://api.github.com/users/shyamrallapalli/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-07T16:09:45Z","updated_at":"2016-12-07T17:10:16Z","closed_at":null,"body":"Hi,\r\n\r\nmake fails with following errors \r\nI have tried v 2.2.0 and 2.3.0 and both result in the same errors.\r\n\r\nI don't understand the errors, complete logs are attached at the end of the post.\r\nCould you please help me to fix this.\r\n\r\n```\r\n  CXX      kat-kat.o\r\n  CXXLD    kat\r\nkat-plot_spectra_mx.o: In function `_M_check':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/basic_string.h:324: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/basic_string.h:324: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\nkat-plot.o: In function `kat::Plot::convertCharToWideChar(char const*)':\r\n/gpfs/home/veb06hwu/programs/kat-2.3.0/kat-2.3.0/src/plot.cc:112: undefined reference to `__cxa_throw_bad_array_new_length'\r\nkat-filter_kmer.o: In function `_M_check':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/basic_string.h:324: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\nkat-filter_sequence.o: In function `_M_check':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/basic_string.h:324: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\nkat-histogram.o: In function `at':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/stl_vector.h:803: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\nkat-sect.o: In function `at':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/stl_vector.h:803: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/stl_vector.h:803: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\nkat-sect.o:/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/stl_vector.h:803: more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow\r\n../lib/.libs/libkat.a(libkat_la-jellyfish_helper.o): In function `jflib::basic_circular_buffer<unsigned long, 32u, 4294967295ul>::basic_circular_buffer(unsigned long)':\r\n/gpfs/home/veb06hwu/programs/kat-2.3.0/kat-2.3.0/lib/../deps/jellyfish-2.2.0/include/jellyfish/circular_buffer.hpp:51: undefined reference to `__cxa_throw_bad_array_new_length'\r\n../lib/.libs/libkat.a(libkat_la-jellyfish_helper.o): In function `jellyfish::mer_heap::heap<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, jellyfish::large_hash::region_iterator_base<jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> > > >::initialize(unsigned long)':\r\n/gpfs/home/veb06hwu/programs/kat-2.3.0/kat-2.3.0/lib/../deps/jellyfish-2.2.0/include/jellyfish/mer_heap.hpp:72: undefined reference to `__cxa_throw_bad_array_new_length'\r\n../deps/jellyfish-2.2.0/.libs/libkat_jellyfish.a(misc.o): In function `_M_check':\r\n/gpfs/software/compilers/gcc/4.9.3/include/c++/4.9.3/bits/basic_string.h:324: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'\r\ncollect2: error: ld returned 1 exit status\r\nmake[2]: *** [kat] Error 1\r\nmake[2]: Leaving directory `/gpfs/home/veb06hwu/programs/kat-2.3.0/kat-2.3.0/src'\r\nmake[1]: *** [all-recursive] Error 1\r\nmake[1]: Leaving directory `/gpfs/home/veb06hwu/programs/kat-2.3.0/kat-2.3.0'\r\nmake: *** [all] Error 2\r\n```\r\n\r\ngrep \"no\" in configure log\r\n```\r\ngrep \"no$\" kat_configure_log.txt\r\nchecking whether we are cross compiling... no\r\nchecking whether g++ supports C++11 features by default... no\r\nchecking for dlltool... no\r\nchecking for sysroot... no\r\nchecking for mt... no\r\nchecking if : is a manifest tool... no\r\nchecking if gcc supports -fno-rtti -fno-exceptions... no\r\nchecking if gcc static flag -static works... no\r\nchecking whether -lc should be explicitly linked in... no\r\nchecking if g++ static flag -static works... no\r\nchecking if compiler needs -Werror to reject unknown flags... no\r\nchecking for the pthreads library -lpthreads... no\r\nchecking whether pthreads work without any flags... no\r\nchecking whether pthreads work with -Kthread... no\r\nchecking whether pthreads work with -kthread... no\r\nchecking for the pthreads library -llthread... no\r\nchecking if more special flags are required for pthreads... no\r\nchecking for PTHREAD_PRIO_INHERIT... no\r\nchecking whether we are cross compiling... no\r\nchecking for dlltool... no\r\nchecking for sysroot... no\r\nchecking for mt... no\r\nchecking if : is a manifest tool... no\r\nchecking if gcc supports -fno-rtti -fno-exceptions... no\r\nchecking if gcc static flag -static works... no\r\nchecking whether -lc should be explicitly linked in... no\r\nchecking if g++ static flag -static works... no\r\nchecking for _NSGetExecutablePath... no\r\n\r\n```\r\n\r\n#### complete logs\r\n[kat_configure_log.txt](https://github.com/TGAC/KAT/files/637043/kat_configure_log.txt)\r\n[kat_make_log.txt](https://github.com/TGAC/KAT/files/637045/kat_make_log.txt)\r\n\r\nMany thanks"},"comment":{"url":"https://api.github.com/repos/TGAC/KAT/issues/comments/265508246","html_url":"https://github.com/TGAC/KAT/issues/68#issuecomment-265508246","issue_url":"https://api.github.com/repos/TGAC/KAT/issues/68","id":265508246,"user":{"login":"shyamrallapalli","id":3543099,"avatar_url":"https://avatars.githubusercontent.com/u/3543099?v=3","gravatar_id":"","url":"https://api.github.com/users/shyamrallapalli","html_url":"https://github.com/shyamrallapalli","followers_url":"https://api.github.com/users/shyamrallapalli/followers","following_url":"https://api.github.com/users/shyamrallapalli/following{/other_user}","gists_url":"https://api.github.com/users/shyamrallapalli/gists{/gist_id}","starred_url":"https://api.github.com/users/shyamrallapalli/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shyamrallapalli/subscriptions","organizations_url":"https://api.github.com/users/shyamrallapalli/orgs","repos_url":"https://api.github.com/users/shyamrallapalli/repos","events_url":"https://api.github.com/users/shyamrallapalli/events{/privacy}","received_events_url":"https://api.github.com/users/shyamrallapalli/received_events","type":"User","site_admin":false},"created_at":"2016-12-07T17:10:16Z","updated_at":"2016-12-07T17:10:16Z","body":"ok solved it by including lib folder of gcc\r\n```-L/gpfs/software/compilers/gcc/4.9.3/lib64 -L/gpfs/software/compilers/gcc/4.9.3/lib```\r\nin the above command in the log\r\n\r\nso it appears in my case i may have to provide LD_LIBRARY_PATH to the gcc i have source, right?\r\n"}}
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