Link issue

[Jason Bacon]

On 11/11/17 09:05, Jan Beich wrote:
> Jason Bacon<bacon4000 at gmail.com>  writes:
>
>> On 11/11/17 08:24, Jan Beich wrote:
>>
>>> Jason Bacon<bacon4000 at 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

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