simtk.org

Guys,

I am now further along. Now when compiling MMB I am getting a hard error in ClonePtr.h, appended below. It seems like something that should have come up when I compiled simbody or molmodel, but those all compiled just fine. Thanks in advance for any advice.

Sam

nl110-99-73:build Sam$ /usr/bin/g++ -DMMBlib_EXPORTS -I/Users/Sam/svn/RNAToolbox/trunk/include -isystem /usr/local/SimTK/include/simbody -I/usr/local/SimTK/include -I/usr/local/openmm/include/openmm/reference -I/usr/local/openmm/include/openmm -I/usr/local/openmm/include -I/usr/local/seqan-library-1.4.1/include -std=c++11 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.5 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /Users/Sam/svn/RNAToolbox/trunk/src/DisplacementContainer.cpp
In file included from /Users/Sam/svn/RNAToolbox/trunk/src/DisplacementContainer.cpp:12:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/DisplacementContainer.h:14:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/BiopolymerClass.h:18:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/Mutation.h:4:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/Utils.h:22:
In file included from /usr/local/SimTK/include/simbody/SimTKsimbody.h:43:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon.h:32:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon/basics.h:44:
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:72:19: error: non-friend class member 'nullptr_t' cannot have a qualified name
ClonePtr(std::nullptr_t) noexcept : ClonePtr() {}
~~~~~^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:72:29: error: expected ';' at end of declaration list
ClonePtr(std::nullptr_t) noexcept : ClonePtr() {}
^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:358:53: error: no type named 'nullptr_t' in namespace 'std'
inline bool operator==(const ClonePtr<T>& lhs, std::nullptr_t)
~~~~~^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:364:29: error: no type named 'nullptr_t' in namespace 'std'
inline bool operator==(std::nullptr_t, const ClonePtr<T>& rhs)
~~~~~^

I wonder if you need to include <cstddef> (http://en.cppreference.com/w/cpp/types/nullptr_t).

I did include it in my Utils.h:

21 #include <cstddef>
22 #include "SimTKsimbody.h"
23 #include "SimTKmolmodel.h"

Based on your comment I also added it to ClonePtr.h , though I would think that would have come up before if that were the issue:

27 #include "SimTKcommon/internal/common.h"
28
29 #include <cstddef>
30 #include <memory>

Neither of these changes fixed the issue (see compiler output below). I was able to get rid of the error by declaring nullptr_t in ClonePtr.h:

36 namespace std {
37 typedef decltype(nullptr) nullptr_t;
38 }

.. However then I had other namespace issues elsewhere (see below). I feel like the problem must be something very simple and fundamental.

/usr/bin/c++ -DMMBlib_EXPORTS -I/Users/Sam/svn/RNAToolbox/trunk/include -isystem /usr/local/SimTK/include/simbody -I/usr/local/SimTK/include -I/openmm -I/openmm/reference -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.5 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /Users/Sam/svn/RNAToolbox/trunk/src/DisplacementContainer.cpp
In file included from /Users/Sam/svn/RNAToolbox/trunk/src/Utils.cpp:11:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/Utils.h:22:
In file included from /usr/local/SimTK/include/simbody/SimTKsimbody.h:43:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon.h:32:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon/basics.h:38:
/usr/local/SimTK/include/simbody/SimTKcommon/internal/common.h:792:1: error: unknown type name 'constexpr'
constexpr bool detect64BitPlatform() { return (sizeof(size_t) > sizeof(int)); }
^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/common.h:792:11: error: expected unqualified-id
constexpr bool detect64BitPlatform() { return (sizeof(size_t) > sizeof(int)); }
^


I find it interesting that the first namespace issue does not come up until ClonePtr.h, line 359. There is some commentary in there about namespace lookups.

321 //==============================================================================
322 // SimTK namespace-scope functions
323 //==============================================================================
324 // These namespace-scope functions will be resolved by the compiler using
325 // "Koenig lookup" which examines the arguments' namespaces first.
326 // See Herb Sutter's discussion here: http://www.gotw.ca/publications/mill08.htm.


Thanks

Sam

/usr/bin/g++ -DMMBlib_EXPORTS -I/Users/Sam/svn/RNAToolbox/trunk/include -isystem /usr/local/SimTK/include/simbody -I/usr/local/SimTK/include -I/usr/local/openmm/include/openmm/reference -I/usr/local/openmm/include/openmm -I/usr/local/openmm/include -I/usr/local/seqan-library-1.4.1/include -std=c++11 -O3 -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.5 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Utils.cpp.o -c /Users/Sam/svn/RNAToolbox/trunk/src/Utils.cpp
In file included from /Users/Sam/svn/RNAToolbox/trunk/src/Utils.cpp:11:
In file included from /Users/Sam/svn/RNAToolbox/trunk/include/Utils.h:22:
In file included from /usr/local/SimTK/include/simbody/SimTKsimbody.h:43:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon.h:32:
In file included from /usr/local/SimTK/include/simbody/SimTKcommon/basics.h:44:
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:73:19: error: non-friend class member 'nullptr_t' cannot have a qualified name
ClonePtr(std::nullptr_t) noexcept : ClonePtr() {}
~~~~~^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:73:29: error: expected ';' at end of declaration list
ClonePtr(std::nullptr_t) noexcept : ClonePtr() {}
^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:359:53: error: no type named 'nullptr_t' in namespace 'std'
inline bool operator==(const ClonePtr<T>& lhs, std::nullptr_t)
~~~~~^
/usr/local/SimTK/include/simbody/SimTKcommon/internal/ClonePtr.h:365:29: error: no type named 'nullptr_t' in namespace 'std'
inline bool operator==(std::nullptr_t, const ClonePtr<T>& rhs)
~~~~~^

Turns out it wanted me to set -stdlib=libc++ for some reason..

having some additional problems, but the above seems to be fixed now

thanks
sam

I'm glad you resolved the issue. The correct C++ standard library to use with Clang (which is what you are using on a Mac; g++ is simply a symlink to clang++) is libc++ (this standard library is created by LLVM and goes with Clang). The libstdc++ standard library goes with GCC.