search

dina-lab3D / CombFold

Apache License 2.0
68 stars 12 forks source link

Make compilation Error #3

Closed CalvinKlein96 closed 7 months ago

CalvinKlein96 commented 7 months ago

Hi Ben,

here is Calvin, we just met at the EMBO Structural Computational Biology workshop. As I am quite excited to test your software I directly tried to install CombFold on our system:

Rocky Linux release 8.6 (Green Obsidian) gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18)

I compiled boost 1.47.0 from source, which seemingly worked fine, as I do have all the necessary hpp files and libs in the end. Also, I changed the BOOST_INCLUDE and BOOST_LIB in the Makefile. However, when trying to make CombFold I get the follwoing error after some time.

What version of boost are you using? I am wondering if this comes from a compatibilty issue, or whether I am doing something wrong.

I attached the full log file as well.

make.log

In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp: At global scope:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:38:33: error: \u2018template<class T, class A> std::size_t boost::hash_value\u2019 redeclared as different kind of symbol
     std::size_t hash_value(std::list<T, A> const& v);
                                 ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:343:24: note: previous declaration \u2018std::size_t boost::hash_value(std::type_index)\u2019
     inline std::size_t hash_value(std::type_index v)
                        ^~~~~~~~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:38:28: error: reference to \u2018list\u2019 is ambiguous
     std::size_t hash_value(std::list<T, A> const& v);
                            ^~~
In file included from /usr/include/c++/8/list:63,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string/std/list_traits.hpp:15,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string/std_containers_traits.hpp:20,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string.hpp:18,
                 from libs_DockingLib/ResidueIndexedMolecule.h:8,
                 from libs_DockingLib/ChemMolecule.h:5,
                 from libs_DockingLib/connolly_surface.h:5,
                 from libs_DockingLib/connolly_surface.cc:7:
/usr/include/c++/8/bits/stl_list.h:564:11: note: candidates are: \u2018template<class _Tp, class _Alloc> class std::__cxx11::list\u2019
     class list : protected _List_base<_Tp, _Alloc>
           ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/detail/container_fwd.hpp:86:47: note:                 \u2018template<class T, class Allocator> class std::list\u2019
     template <class T, class Allocator> class list;
                                               ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:38:39: error: expected primary-expression before \u2018,\u2019 token
     std::size_t hash_value(std::list<T, A> const& v);
                                       ^
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:38:42: error: expected primary-expression before \u2018>\u2019 token
     std::size_t hash_value(std::list<T, A> const& v);
                                          ^
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:38:44: error: expected primary-expression before \u2018const\u2019
     std::size_t hash_value(std::list<T, A> const& v);
                                            ^~~~~
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:69:33: error: \u2018template<class T, class A> std::size_t boost::hash_value\u2019 redeclared as different kind of symbol
     std::size_t hash_value(std::list<T, A> const& v)
                                 ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:343:24: note: previous declaration \u2018std::size_t boost::hash_value(std::type_index)\u2019
     inline std::size_t hash_value(std::type_index v)
                        ^~~~~~~~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:69:28: error: reference to \u2018list\u2019 is ambiguous
     std::size_t hash_value(std::list<T, A> const& v)
                            ^~~
In file included from /usr/include/c++/8/list:63,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string/std/list_traits.hpp:15,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string/std_containers_traits.hpp:20,
                 from /ibmm_data/kleinc/software/libs/include/boost/algorithm/string.hpp:18,
                 from libs_DockingLib/ResidueIndexedMolecule.h:8,
                 from libs_DockingLib/ChemMolecule.h:5,
                 from libs_DockingLib/connolly_surface.h:5,
                 from libs_DockingLib/connolly_surface.cc:7:
/usr/include/c++/8/bits/stl_list.h:564:11: note: candidates are: \u2018template<class _Tp, class _Alloc> class std::__cxx11::list\u2019
     class list : protected _List_base<_Tp, _Alloc>
           ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/detail/container_fwd.hpp:86:47: note:                 \u2018template<class T, class Allocator> class std::list\u2019
     template <class T, class Allocator> class list;
                                               ^~~~
In file included from /ibmm_data/kleinc/software/libs/include/boost/functional/hash/hash.hpp:535,
                 from /ibmm_data/kleinc/software/libs/include/boost/functional/hash.hpp:6,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered/unordered_map.hpp:17,
                 from /ibmm_data/kleinc/software/libs/include/boost/unordered_map.hpp:16,
                 from libs_DockingLib/connolly_surface.cc:11:
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:69:39: error: expected primary-expression before \u2018,\u2019 token
     std::size_t hash_value(std::list<T, A> const& v)
                                       ^
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:69:42: error: expected primary-expression before \u2018>\u2019 token
     std::size_t hash_value(std::list<T, A> const& v)
                                          ^
/ibmm_data/kleinc/software/libs/include/boost/functional/hash/extensions.hpp:69:44: error: expected primary-expression before \u2018const\u2019
     std::size_t hash_value(std::list<T, A> const& v)
                                            ^~~~~
make: *** [Makefile:29: libs_DockingLib/connolly_surface.o] Error 1

Cheers Calvin

CalvinKlein96 commented 7 months ago

After testing multiple versions of boost it compiled with boost 1.66.0