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building gadgetron on VM with boost 1.68 causes undefined reference to `boost::system::detail::generic_category_instance' #161

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evgueni-ovtchinnikov opened this issue Dec 7, 2018 · 5 comments · Fixed by #429
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building gadgetron on VM with boost 1.68 causes undefined reference to `boost::system::detail::generic_category_instance' #161

evgueni-ovtchinnikov opened this issue Dec 7, 2018 · 5 comments · Fixed by #429
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v3.2

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@evgueni-ovtchinnikov
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Building Gadgetron needs gcc6 and boost 1.65.0 We tried with 1.68.0, but then got

undefined reference to `boost::system::detail::generic_category_instance'

This might be related to boostorg/system#26 as g++-6 defaults to C++-14 and therefore resolved by making sure that boost is built with gcc-6. This is actually #14.
@KrisThielemans
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@evgueni-ovtchinnikov please try again with the new versiono fthe Superbuild. It works for me.

@evgueni-ovtchinnikov
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update_VM.sh runs gcc-5.4.0

linking executable test_ismrmrd failed with error messages

undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'

had to use the same trick of setting (after failed update) USE_SYSTEM_ISMRMRD=ON to build

@KrisThielemans
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Confirmed that this also happens with gcc 5.4 and older Gadgetron, e.g. gadgetron/gadgetron@e7eb430

It disappears when editing gadgetron's CMakeLists.txt to force use std=c++11 and not 14 (although this gives some warnings)

It seems therefore that we cannot use a packaged system boost 1.68, and that we'd have to build Boost ourselves, making sure that c++-14 is used.

sigh.

@KrisThielemans KrisThielemans changed the title building recent gadgetron on VM causes undefined reference to `boost::system::detail::generic_category_instance' building gadgetron on VM with boost 1.68 causes undefined reference to `boost::system::detail::generic_category_instance' Dec 17, 2018
@KrisThielemans KrisThielemans mentioned this issue Dec 17, 2018
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@KrisThielemans
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Lengthy discussion at https://groups.google.com/forum/#!topic/boost-developers-archive/EWG5NVOZo_g Conclusion is that you need to build boost (or any C++ library) with the same C++ standard version as you own code.

This seems to imply that we need to figure out what compiler options Gadgetron used, and then always build boost ourselves, using e.g. cxxstd=14.

Note that boost.system is header-only from 1.69, which might help a bit (but could still throw up problems for other boost libraries)

This was referenced Dec 18, 2018
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@KrisThielemans KrisThielemans mentioned this issue Jan 10, 2019
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@KrisThielemans
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Current Gadgetron master attempts to use C++ 20 (CMake will downgrade if it is not supported by the compiler)

@KrisThielemans KrisThielemans added this to the v2.1 milestone Feb 15, 2019
@KrisThielemans KrisThielemans modified the milestones: v2.1, v2.2 Oct 14, 2019
KrisThielemans added a commit to KrisThielemans/SIRF-SuperBuild that referenced this issue Jul 26, 2020
@KrisThielemans
set preprocessor define BOOST_ERROR_CODE_HEADER_ONLY
0bfc080 
We get linking problems with boost system if the C++ versions
don't match (i.e. the one used to compile boost, and the current one),
specifically with boost::system::detail::generic_category_instance

Setting this variable forces Boost to use an inline variable, as opposed to
the instantiated variable in the library

Fixes SyneRBI#161
@KrisThielemans KrisThielemans mentioned this issue Jul 26, 2020
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KrisThielemans added a commit to KrisThielemans/SIRF-SuperBuild that referenced this issue Jul 27, 2020
@KrisThielemans
set preprocessor defines for boost system to be header only
9a18058 
We get linking problems with boost system if the C++ versions
don't match (i.e. the one used to compile boost, and the current one),
specifically with boost::system::detail::generic_category_instance

Setting these preprocessor variables forces Boost to use inline variables, as opposed to
the instantiated variables in the library

Fixes SyneRBI#161
KrisThielemans added a commit that referenced this issue Jul 27, 2020
@KrisThielemans
Merge pull request #429 from KrisThielemans/BOOST_ERROR_CODE (fix #161)
37335e7 
set preprocessor defines BOOST_ERROR_CODE_HEADER_ONLY and BOOST_SYSTEM_NO_DEPRECATED

Fixes #161
@KrisThielemans KrisThielemans mentioned this issue Dec 23, 2020
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set preprocessor define BOOST_ERROR_CODE_HEADER_ONLY KrisThielemans/SIRF-SuperBuild
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