{"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":"2016-12-09T08:57:27Z","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/265964905","html_url":"https://github.com/TGAC/KAT/issues/68#issuecomment-265964905","issue_url":"https://api.github.com/repos/TGAC/KAT/issues/68","id":265964905,"user":{"login":"maplesond","id":3940628,"avatar_url":"https://avatars.githubusercontent.com/u/3940628?v=3","gravatar_id":"","url":"https://api.github.com/users/maplesond","html_url":"https://github.com/maplesond","followers_url":"https://api.github.com/users/maplesond/followers","following_url":"https://api.github.com/users/maplesond/following{/other_user}","gists_url":"https://api.github.com/users/maplesond/gists{/gist_id}","starred_url":"https://api.github.com/users/maplesond/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/maplesond/subscriptions","organizations_url":"https://api.github.com/users/maplesond/orgs","repos_url":"https://api.github.com/users/maplesond/repos","events_url":"https://api.github.com/users/maplesond/events{/privacy}","received_events_url":"https://api.github.com/users/maplesond/received_events","type":"User","site_admin":false},"created_at":"2016-12-09T08:57:27Z","updated_at":"2016-12-09T08:57:27Z","body":"Thanks for the log @shyamrallapalli .  I still don't have a definitive answer to this but I think I've narrowed the problem down to an incompatibility with the toolchains that were used to build the various dependencies.  Most likely the dependency that's causing the issue is python.  I've made some modifications to the configuration script.  Could you checkout the top of the develop branch, then run `./autogen.sh && ./configure --disable-plotting && make`.  Hopefully, that bypasses the issue your facing, although it will mean that the plotting functionality is disabled.  If that fixes the problem, I'll try and make further changes, or suggest workarounds, that can avoid the issue you are facing while still retaining the plotting functionality."}}
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