scons: building terminated because of errors.

[Anonymous]

Hello everyone,

I’m new here. I’m want to install and run rosetta. First I want to ask about the difference between Rosetta 2017.36 source + binaries for Linux  and Rosetta 2017.36 source .

Secondly, and most importantly, unfortunately, I can’t get it installed according to this guide here (log is below):

https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build

I tried it with both the src and src+binaries versions. I would appreciate if someone  takes a little time to assist me, specially that I’m also new to linux. 

I might be getting ahead of myself here but feel free to direct me to any tutorials or guides to get up and running with rosetta as fast as possible. BUT let’s actually get it installed first. 

Thanks in advance

 

[labusr@luxor source]$ ./scons.py -j 4 mode=release bin

scons: Reading SConscript files ...

Running versioning script ... Release package detected, using rosetta/main/.release.json to acquire version information...

Done. (0.0 seconds)

file ./options.dox being updated

file ./full-options-list.md being updated

Number of option files updated: 2

Total 4041 options.

Finished updating ResidueProperty code -- no changes needed

Finished updating VariantType code -- no changes needed

scons: done reading SConscript files.

scons: Building targets ...

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/libObjexxFCL.so -Wl,-rpath=/home/labusr/Downloads/rosetta_src_2017.36.59679_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default -Wl,-rpath=$ORIGIN -Wl,-rpath=$ORIGIN/../lib -shared build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/char.functions.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Cstring.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Dimension.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DimensionExpression.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DimensionExpressionRef.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DynamicIndexRange.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/format.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Fstring.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/IndexRange.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Observer.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverGraph.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverMediator.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverMulti.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Star.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/string.functions.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Time_Date.os -Lexternal/lib -Lbuild/src/release/linux/3.10/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -lz -lcppdb -lsqlite3 -lcifparse -lxml2

/usr/bin/ld: cannot find -lz

collect2: error: ld returned 1 exit status

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/RNA_Info.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DOLDER_GCC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/RNA_Info.cc

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/RNA_FittedTorsionInfo.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DOLDER_GCC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/RNA_FittedTorsionInfo.cc

scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/default/libObjexxFCL.so] Error 1

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/RNA_SamplerUtil.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DOLDER_GCC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/RNA_SamplerUtil.cc

scons: building terminated because of errors.

 

 

Below is the log for the src+binaries version:

 

[labusr@luxor source]$ ./scons.py -j 4 mode=release bin

scons: Reading SConscript files ...

Running versioning script ... fatal: Not a git repository (or any parent up to mount point /home)

Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

Done. (0.0 seconds)

file ./options.dox being updated

file ./full-options-list.md being updated

Number of option files updated: 2

Total 3922 options.

Finished updating ResidueProperty code -- no changes needed

Finished updating VariantType code -- no changes needed

scons: done reading SConscript files.

scons: Building targets ...

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/libObjexxFCL.so -Wl,-rpath=/home/labusr/Downloads/rosetta_bin_linux_2017.08.59291_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/default -Wl,-rpath=$ORIGIN -Wl,-rpath=$ORIGIN/../lib -shared build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/char.functions.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Cstring.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Dimension.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DimensionExpression.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DimensionExpressionRef.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/DynamicIndexRange.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/format.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Fstring.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/IndexRange.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Observer.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverGraph.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverMediator.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/ObserverMulti.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Star.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/string.functions.os build/src/release/linux/3.10/64/x86/gcc/4.8/default/ObjexxFCL/Time_Date.os -Lexternal/lib -Lbuild/src/release/linux/3.10/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -lz -lcppdb -lsqlite3 -lcifparse -lxml2

/bin/ld: cannot find -lz

collect2: error: ld returned 1 exit status

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/RNA_FittedTorsionInfo.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/RNA_FittedTorsionInfo.cc

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/RNA_SamplerUtil.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/RNA_SamplerUtil.cc

g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/default/core/chemical/rna/util.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/chemical/rna/util.cc

scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/default/libObjexxFCL.so] Error 1

scons: building terminated because of errors.

 

[Anonymous]

The src+binaries version should already have a compiled version of Rosetta availible in the bin/ directory. So you don’t necessarily *need* to compile this version, as the pre-compiled binaries may already work for your computer. — They may not, though, or you may want a different style of compilation, so you may need to run the compilation anyway. Aside from their already being a compiled version in the +binaries download, the two should be the same.

As to your particular error, the “cannot find -lz” means that you need to install the development headers for the zlib compression library. You don’t mention which Linux distribution you use (how to install is different for each), but for Ubuntu it would be something like `sudo apt-get install zlib1g-dev`. Again, the package name and how to install it may be different if you’re on a different Linux distribution.

[Anonymous]

Hello, everyone.

I a novice to use Rosetta. I met a similar problem while I am installing the Rosetta.

My installation was also terminated due to errors, but I really do not know how to solve it. I am wondering whether you guys could help me out. Thank you very much!!!

The command I used is ./scons.py -j 6 mode=release bin

What follows is the partial display while installation.

 

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: In destructor ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = core::pose::signals::DestructionEvent, _Alloc = std::allocator<core::pose::signals::DestructionEvent>]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:314:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::DestructionEvent, _Alloc = std::allocator<core::pose::signals::DestructionEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:132: error: invalid use of incomplete type ‘struct core::pose::signals::DestructionEvent’

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘struct core::pose::signals::DestructionEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: In destructor ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = core::pose::signals::GeneralEvent, _Alloc = std::allocator<core::pose::signals::GeneralEvent>]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:314:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::GeneralEvent, _Alloc = std::allocator<core::pose::signals::GeneralEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:132: error: invalid use of incomplete type ‘struct core::pose::signals::GeneralEvent’

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::GeneralEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: In destructor ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = core::pose::signals::EnergyEvent, _Alloc = std::allocator<core::pose::signals::EnergyEvent>]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:314:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::EnergyEvent, _Alloc = std::allocator<core::pose::signals::EnergyEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:132: error: invalid use of incomplete type ‘struct core::pose::signals::EnergyEvent’

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::EnergyEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: In destructor ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = core::pose::signals::ConformationEvent, _Alloc = std::allocator<core::pose::signals::ConformationEvent>]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:314:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::ConformationEvent, _Alloc = std::allocator<core::pose::signals::ConformationEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:132: error: invalid use of incomplete type ‘struct core::pose::signals::ConformationEvent’

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::ConformationEvent’

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:63,

                 from src/utility/vectorL.hh:27,

                 from src/utility/vector1.hh:23,

                 from src/core/init/init.hh:21,

                 from src/protocols/init/init.cc:17:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: In function ‘void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::DestructionEvent*]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:149:   instantiated from ‘void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = core::pose::signals::DestructionEvent*, _Tp = core::pose::signals::DestructionEvent]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:313:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::DestructionEvent, _Alloc = std::allocator<core::pose::signals::DestructionEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:123: error: incomplete type ‘std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::DestructionEvent*]::_Value_type’ not allowed

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: In function ‘void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::GeneralEvent*]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:149:   instantiated from ‘void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = core::pose::signals::GeneralEvent*, _Tp = core::pose::signals::GeneralEvent]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:313:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::GeneralEvent, _Alloc = std::allocator<core::pose::signals::GeneralEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:123: error: incomplete type ‘std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::GeneralEvent*]::_Value_type’ not allowed

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: In function ‘void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::EnergyEvent*]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:149:   instantiated from ‘void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = core::pose::signals::EnergyEvent*, _Tp = core::pose::signals::EnergyEvent]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:313:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::EnergyEvent, _Alloc = std::allocator<core::pose::signals::EnergyEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:123: error: incomplete type ‘std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::EnergyEvent*]::_Value_type’ not allowed

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: In function ‘void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::ConformationEvent*]’:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:149:   instantiated from ‘void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = core::pose::signals::ConformationEvent*, _Tp = core::pose::signals::ConformationEvent]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:313:   instantiated from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = core::pose::signals::ConformationEvent, _Alloc = std::allocator<core::pose::signals::ConformationEvent>]’

src/utility/signals/BufferedSignalHub.hh:93:   instantiated from ‘std::__shared_count<_Lp>::__shared_count(_Ptr) [with _Ptr = core::pose::Pose*, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:568:   instantiated from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose, __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/shared_ptr.h:1244:   instantiated from ‘std::shared_ptr<_Tp>::shared_ptr(_Tp1*) [with _Tp1 = core::pose::Pose, _Tp = core::pose::Pose]’

src/core/pose/Pose.hh:2081:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:123: error: incomplete type ‘std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = core::pose::signals::ConformationEvent*]::_Value_type’ not allowed

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘bool utility::signals::BufferedSignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:168: error: ‘s’ has incomplete type

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::ConformationEvent’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:239: error: ‘s’ has incomplete type

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::ConformationEvent’

src/utility/signals/SignalHub.hh: In member function ‘bool utility::signals::SignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:230: error: ‘<anonymous>’ has incomplete type

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::ConformationEvent’

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘bool utility::signals::BufferedSignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:168: error: ‘s’ has incomplete type

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::EnergyEvent’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:239: error: ‘s’ has incomplete type

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::EnergyEvent’

src/utility/signals/SignalHub.hh: In member function ‘bool utility::signals::SignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:230: error: ‘<anonymous>’ has incomplete type

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::EnergyEvent’

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘bool utility::signals::BufferedSignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:168: error: ‘s’ has incomplete type

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::GeneralEvent’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:239: error: ‘s’ has incomplete type

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::GeneralEvent’

src/utility/signals/SignalHub.hh: In member function ‘bool utility::signals::SignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:230: error: ‘<anonymous>’ has incomplete type

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘const struct core::pose::signals::GeneralEvent’

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘bool utility::signals::BufferedSignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:168: error: ‘s’ has incomplete type

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘const struct core::pose::signals::DestructionEvent’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:239: error: ‘s’ has incomplete type

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘struct core::pose::signals::DestructionEvent’

src/utility/signals/SignalHub.hh: In member function ‘bool utility::signals::SignalHub<ResultType, Signal>::signal_allowed(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’:

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:230: error: ‘<anonymous>’ has incomplete type

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘const struct core::pose::signals::DestructionEvent’

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’:

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:156: error: invalid use of incomplete type ‘struct core::pose::signals::ConformationEvent’

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::ConformationEvent’

src/utility/signals/BufferedSignalHub.hh:156: error:   initializing argument 1 of ‘void utility::signals::SignalHub<ResultType, Signal>::operator()(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send(Signal, std::vector<std::shared_ptr<utility::signals::LinkUnit>, std::allocator<std::shared_ptr<utility::signals::LinkUnit> > >&) const [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’:

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:332: error: ‘s’ has incomplete type

src/core/pose/signals/ConformationEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::ConformationEvent’

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:344: warning: suggest parentheses around assignment used as truth value

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’:

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:156: error: invalid use of incomplete type ‘struct core::pose::signals::EnergyEvent’

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::EnergyEvent’

src/utility/signals/BufferedSignalHub.hh:156: error:   initializing argument 1 of ‘void utility::signals::SignalHub<ResultType, Signal>::operator()(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send(Signal, std::vector<std::shared_ptr<utility::signals::LinkUnit>, std::allocator<std::shared_ptr<utility::signals::LinkUnit> > >&) const [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’:

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:332: error: ‘s’ has incomplete type

src/core/pose/signals/EnergyEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::EnergyEvent’

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:344: warning: suggest parentheses around assignment used as truth value

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’:

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:156: error: invalid use of incomplete type ‘struct core::pose::signals::GeneralEvent’

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::GeneralEvent’

src/utility/signals/BufferedSignalHub.hh:156: error:   initializing argument 1 of ‘void utility::signals::SignalHub<ResultType, Signal>::operator()(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send(Signal, std::vector<std::shared_ptr<utility::signals::LinkUnit>, std::allocator<std::shared_ptr<utility::signals::LinkUnit> > >&) const [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’:

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:332: error: ‘s’ has incomplete type

src/core/pose/signals/GeneralEvent.fwd.hh:30: error: forward declaration of ‘struct core::pose::signals::GeneralEvent’

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:344: warning: suggest parentheses around assignment used as truth value

In file included from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/BufferedSignalHub.hh: In member function ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’:

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/BufferedSignalHub.hh:156: error: invalid use of incomplete type ‘struct core::pose::signals::DestructionEvent’

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘struct core::pose::signals::DestructionEvent’

src/utility/signals/BufferedSignalHub.hh:156: error:   initializing argument 1 of ‘void utility::signals::SignalHub<ResultType, Signal>::operator()(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

In file included from src/utility/signals/BufferedSignalHub.hh:29,

                 from src/core/pose/Pose.hh:86,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalRequirement.hh:30,

                 from src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementFactory.hh:22,

                 from src/protocols/init/init.LegacyRequirementCreators.ihh:11,

                 from src/protocols/init/init.cc:21:

src/utility/signals/SignalHub.hh: In member function ‘void utility::signals::SignalHub<ResultType, Signal>::send(Signal, std::vector<std::shared_ptr<utility::signals::LinkUnit>, std::allocator<std::shared_ptr<utility::signals::LinkUnit> > >&) const [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’:

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:332: error: ‘s’ has incomplete type

src/core/pose/signals/DestructionEvent.fwd.hh:24: error: forward declaration of ‘struct core::pose::signals::DestructionEvent’

src/utility/signals/SignalHub.hh:240:   instantiated from ‘void utility::signals::SignalHub<ResultType, Signal>::send_signal(Signal) [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

src/utility/signals/SignalHub.hh:344: warning: suggest parentheses around assignment used as truth value

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:69,

                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:41,

                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:42,

                 from src/protocols/init/init.hh:23,

                 from src/protocols/init/init.cc:16:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: In member function ‘__gnu_cxx::__normal_iterator<_Iterator, _Container>& __gnu_cxx::__normal_iterator<_Iterator, _Container>::operator++() [with _Iterator = core::pose::signals::ConformationEvent*, _Container = std::vector<core::pose::signals::ConformationEvent, std::allocator<core::pose::signals::ConformationEvent> >]’:

src/utility/signals/BufferedSignalHub.hh:155:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::ConformationEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:708: error: cannot increment a pointer to incomplete type ‘core::pose::signals::ConformationEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: In member function ‘__gnu_cxx::__normal_iterator<_Iterator, _Container>& __gnu_cxx::__normal_iterator<_Iterator, _Container>::operator++() [with _Iterator = core::pose::signals::EnergyEvent*, _Container = std::vector<core::pose::signals::EnergyEvent, std::allocator<core::pose::signals::EnergyEvent> >]’:

src/utility/signals/BufferedSignalHub.hh:155:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::EnergyEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:708: error: cannot increment a pointer to incomplete type ‘core::pose::signals::EnergyEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: In member function ‘__gnu_cxx::__normal_iterator<_Iterator, _Container>& __gnu_cxx::__normal_iterator<_Iterator, _Container>::operator++() [with _Iterator = core::pose::signals::GeneralEvent*, _Container = std::vector<core::pose::signals::GeneralEvent, std::allocator<core::pose::signals::GeneralEvent> >]’:

src/utility/signals/BufferedSignalHub.hh:155:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::GeneralEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:708: error: cannot increment a pointer to incomplete type ‘core::pose::signals::GeneralEvent’

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: In member function ‘__gnu_cxx::__normal_iterator<_Iterator, _Container>& __gnu_cxx::__normal_iterator<_Iterator, _Container>::operator++() [with _Iterator = core::pose::signals::DestructionEvent*, _Container = std::vector<core::pose::signals::DestructionEvent, std::allocator<core::pose::signals::DestructionEvent> >]’:

src/utility/signals/BufferedSignalHub.hh:155:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::release_buffer() [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

src/utility/signals/BufferedSignalHub.hh:124:   instantiated from ‘void utility::signals::BufferedSignalHub<ResultType, Signal>::unblock() [with ReturnType = void, Signal = core::pose::signals::DestructionEvent]’

src/protocols/evaluation/PoseEvaluator.hh:128:   instantiated from here

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:708: error: cannot increment a pointer to incomplete type ‘core::pose::signals::DestructionEvent’

scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.4/default/protocols/init/init.os] Error 1

scons: building terminated because of errors.

 

[Anonymous]

It looks like you’re using GCC 4.4 to compile Rosetta. Unfortunatly, that won’t work. Rosetta needs a compiler which has support for C++11. In practice, this means GCC 4.8 or later (5.2 or later is better). (see https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation and https://www.rosettacommons.org/docs/latest/build_documentation/Cxx11Support)

You don’t necessarily have to update the system compiler. You should be able to install an updated version of GCC in a different location from the system compiler. You would just then need to adjust your PATH settings such that the directory the updated compiler binary are installed into come before the system compiler. (Do a `g++ –version` in the shell prior to running scons to check.)

You can also use a version of Clang more recent than 3.3, but there’s complications with the C++ standard library. Whereas GCC comes with its own version of the C++ standard library, on Linux, Clang uses the version provided by GCC. If that’s from the default system GCC 4.4, then the library doesn’t have sufficient C++11 support to work with Rosetta.

The library version adds a slight complication to running Rosetta. If you use an alternate install location for GCC, you may need to alter your LD_LIBRARY_PATH environment variables to include the location where GCC installed the compiled version of the C++ standard library for that version of GCC.

[Author]

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