Date: Sun, 12 Nov 2017 09:46:15 -0600 From: Jason Bacon <bacon4000@gmail.com> To: Jan Beich <jbeich@FreeBSD.org> Cc: office@FreeBSD.org, luis.camp0.2009@gmail.com Subject: Re: Link issue Message-ID: <49134cf3-8b8b-ee43-ac64-250adeb1f5e0@gmail.com> In-Reply-To: <8tfc-j1p5-wny@FreeBSD.org> References: <06535286-a5c8-3809-8679-920b4a837dfd@gmail.com> <y3nc-lwpx-wny@FreeBSD.org> <aa080174-8395-7053-f97d-244af95a95c7@gmail.com> <8tfc-j1p5-wny@FreeBSD.org>
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On 11/11/17 09:05, Jan Beich wrote: > Jason Bacon<bacon4000@gmail.com> writes: > >> On 11/11/17 08:24, Jan Beich wrote: >> >>> Jason Bacon<bacon4000@gmail.com> writes: >>> >>>> BoltParams.o: In function >>>> `LMM::BoltParams::processCommandLineArgs(int, char**)': >>>> BoltParams.cpp:(.text+0x1a01): undefined reference to >>>> `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, >>>> std::char_traits<char>, std::allocator<char> > const&, unsigned int, >>>> unsigned int)' >>> Try replacing USE_GCC=yes with USES=compiler:gcc-c++11-lib to make the >>> port use GCC/libc++ rather than GCC/libstdc++. >> Hmm, I had tried that before to no avail. I think maybe I forgot to >> comment out compiler:openmp and hence gcc-c++11-lib was silently >> ignored. > Due tohttps://bugs.freebsd.org/bugzilla/show_bug.cgi?id=199603 > sometimes one has to be careful about order of USES arguments. > >> At any rate, it's working now. >> >> Thanks! The following results in link errors: USES= compiler:openmp compiler:gcc-c++11-lib gmake The following works, but I suspect that compiler:openmp is actually being ignored: USES= compiler:gcc-c++11-lib compiler:openmp gmake It also works if I omit compiler:openmp, but I'll leave it in just to document the requirement for now. This is all on 11.1-RELEASE. On 10.3 there's another issue. Maybe due to the older clang base? Heading out the door now, but will investigate this later if you don't have a quick answer... Thanks again. g++6 -L/usr/ports/wip/bolt-lmm/work -fstack-protector -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -fopenmp -o bolt BoltMain.o Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lnlopt -lboost_program_options -lboost_iostreams -lz -llapack -lopenblas -lgfortran -lpthread -lm Bolt.o: In function `long double boost::math::detail::full_igamma_prefix<long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> >(long double, long double, boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy> const&)': Bolt.cpp:(.text._ZN5boost4math6detail18full_igamma_prefixIeNS0_8policies6policyINS3_13promote_floatILb0EEENS3_14promote_doubleILb0EEENS3_14default_policyES9_S9_S9_S9_S9_S9_S9_S9_S9_S9_EEEET_SB_SB_RKT0_[_ZN5boost4math6detail18full_igamma_prefixIeNS0_8policies6policyINS3_13promote_floatILb0EEENS3_14promote_doubleILb0EEENS3_14default_policyES9_S9_S9_S9_S9_S9_S9_S9_S9_S9_EEEET_SB_SB_RKT0_]+0x55): warning: powl has lower than advertised precision BoltMain.o: In function `boost::iostreams::access_control<boost::iostreams::detail::chain_client<boost::iostreams::chain<boost::iostreams::input, char, std::__1::char_traits<char>, std::__1::allocator<char> > >, boost::iostreams::public_, boost::iostreams::detail::pub_<boost::iostreams::detail::chain_client<boost::iostreams::chain<boost::iostreams::input, char, std::__1::char_traits<char>, std::__1::allocator<char> > > > >::~access_control()': BoltMain.cpp:(.text._ZN5boost9iostreams14access_controlINS0_6detail12chain_clientINS0_5chainINS0_5inputEcNSt3__111char_traitsIcEENS6_9allocatorIcEEEEEENS0_7public_ENS2_4pub_ISC_EEED0Ev[_ZN5boost9iostreams14access_controlINS0_6detail12chain_clientINS0_5chainINS0_5inputEcNSt3__111char_traitsIcEENS6_9allocatorIcEEEEEENS0_7public_ENS2_4pub_ISC_EEED5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)' BoltMain.o: In function `boost::iostreams::access_control<boost::iostreams::detail::chain_client<boost::iostreams::chain<boost::iostreams::output, char, std::__1::char_traits<char>, std::__1::allocator<char> > >, boost::iostreams::public_, boost::iostreams::detail::pub_<boost::iostreams::detail::chain_client<boost::iostreams::chain<boost::iostreams::output, char, std::__1::char_traits<char>, std::__1::allocator<char> > > > >::~access_control()': BoltMain.cpp:(.text._ZN5boost9iostreams14access_controlINS0_6detail12chain_clientINS0_5chainINS0_6outputEcNSt3__111char_traitsIcEENS6_9allocatorIcEEEEEENS0_7public_ENS2_4pub_ISC_EEED0Ev[_ZN5boost9iostreams14access_controlINS0_6detail12chain_clientINS0_5chainINS0_6outputEcNSt3__111char_traitsIcEENS6_9allocatorIcEEEEEENS0_7public_ENS2_4pub_ISC_EEED5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)' BoltMain.o: In function `boost::detail::sp_counted_impl_p<boost::iostreams::detail::chain_base<boost::iostreams::chain<boost::iostreams::output, char, std::__1::char_traits<char>, std::__1::allocator<char> >, char, std::__1::char_traits<char>, std::__1::allocator<char>, boost::iostreams::output>::chain_impl>::~sp_counted_impl_p()': BoltMain.cpp:(.text._ZN5boost6detail17sp_counted_impl_pINS_9iostreams6detail10chain_baseINS2_5chainINS2_6outputEcNSt3__111char_traitsIcEENS7_9allocatorIcEEEEcS9_SB_S6_E10chain_implEED0Ev[_ZN5boost6detail17sp_counted_impl_pINS_9iostreams6detail10chain_baseINS2_5chainINS2_6outputEcNSt3__111char_traitsIcEENS7_9allocatorIcEEEEcS9_SB_S6_E10chain_implEED5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)' BoltMain.o: In function `boost::detail::sp_counted_impl_p<boost::iostreams::detail::chain_base<boost::iostreams::chain<boost::iostreams::input, char, std::__1::char_traits<char>, std::__1::allocator<char> >, char, std::__1::char_traits<char>, std::__1::allocator<char>, boost::iostreams::input>::chain_impl>::~sp_counted_impl_p()': BoltMain.cpp:(.text._ZN5boost6detail17sp_counted_impl_pINS_9iostreams6detail10chain_baseINS2_5chainINS2_5inputEcNSt3__111char_traitsIcEENS7_9allocatorIcEEEEcS9_SB_S6_E10chain_implEED0Ev[_ZN5boost6detail17sp_counted_impl_pINS_9iostreams6detail10chain_baseINS2_5chainINS2_5inputEcNSt3__111char_traitsIcEENS7_9allocatorIcEEEEcS9_SB_S6_E10chain_implEED5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)' BoltMain.o: In function `boost::numeric::ublas::bad_size::~bad_size()': BoltMain.cpp:(.text._ZN5boost7numeric5ublas8bad_sizeD0Ev[_ZN5boost7numeric5ublas8bad_sizeD5Ev]+0x21): undefined reference to `operator delete(void*, unsigned long)' BoltMain.o:BoltMain.cpp:(.text._ZN5boost7numeric5ublas14external_logicD0Ev[_ZN5boost7numeric5ublas14external_logicD5Ev]+0x21): more undefined references to `operator delete(void*, unsigned long)' follow collect2: error: ld returned 1 exit status gmake[2]: *** [Makefile:126: bolt] Error 1 gmake[2]: Leaving directory '/usr/ports/wip/bolt-lmm/work/BOLT-LMM_v2.3/src' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make[1]: stopped in /usr/ports/wip/bolt-lmm *** Error code 1 Stop. make: stopped in /usr/ports/wip/bolt-lmm -- Earth is a beta site.
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