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thuem / THUNDER

A particle-filter framework for robust cryoEM 3D reconstruction
GNU General Public License v2.0
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jsoncpp compilation error #1

Closed jianSG closed 6 years ago

jianSG commented 6 years ago

I ran into following error when compiling jsoncpp. jsoncpp Github page suggests it may related to gcc/g++ version and/or standard, but I do not understand the way to solve it in the context of THUNDER. I am using gcc/g++ 7.3 on Ubuntu 18.04 LTS, cuda 9.1. Thanks for your help in advance.

[ 71%] Linking CXX static library libcore.a [ 71%] Built target core Scanning dependencies of target jsoncpp [ 72%] Building CXX object external/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:234:14: error: ‘scoped_ptr’ in namespace ‘std’ does not name a template type typedef std::scoped_ptr const CharReaderPtr; ^~~~~~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp: In function ‘bool Json::parseFromStream(const Json::CharReader::Factory&, std::istream&, Json::Value, std::__cxx11::string)’: /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:2007:3: error: ‘CharReaderPtr’ was not declared in this scope CharReaderPtr const reader(fact.newCharReader()); ^~~~~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:2007:3: note: suggested alternative: ‘CharReader’ CharReaderPtr const reader(fact.newCharReader()); ^~~~~ CharReader /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:2008:10: error: ‘reader’ was not declared in this scope return reader->parse(begin, end, root, errs); ^~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:2008:10: note: suggested alternative: ‘Reader’ return reader->parse(begin, end, root, errs); ^~ Reader /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp: At global scope: /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:3803:14: error: ‘scoped_ptr’ in namespace ‘std’ does not name a template type typedef std::scoped_ptr const StreamWriterPtr; ^~~~~~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp: In function ‘std::__cxx11::string Json::writeString(const Json::StreamWriter::Factory&, const Json::Value&)’: /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4924:3: error: ‘StreamWriterPtr’ was not declared in this scope StreamWriterPtr const writer(builder.newStreamWriter()); ^~~~~~~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4924:3: note: suggested alternative: ‘StreamWriter’ StreamWriterPtr const writer(builder.newStreamWriter()); ^~~~~~~ StreamWriter /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4925:3: error: ‘writer’ was not declared in this scope writer->write(root, &sout); ^~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4925:3: note: suggested alternative: ‘Writer’ writer->write(root, &sout); ^~ Writer /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp: In function ‘std::ostream& Json::operator<<(std::ostream&, const Json::Value&)’: /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4931:3: error: ‘StreamWriterPtr’ was not declared in this scope StreamWriterPtr const writer(builder.newStreamWriter()); ^~~~~~~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4931:3: note: suggested alternative: ‘StreamWriter’ StreamWriterPtr const writer(builder.newStreamWriter()); ^~~~~~~ StreamWriter /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4932:3: error: ‘writer’ was not declared in this scope writer->write(root, &sout); ^~ /home/jianshi/Downloads/THUNDER-master/external/jsoncpp/jsoncpp.cpp:4932:3: note: suggested alternative: ‘Writer’ writer->write(root, &sout); ^~ Writer external/jsoncpp/CMakeFiles/jsoncpp.dir/build.make:62: recipe for target 'external/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o' failed make[2]: [external/jsoncpp/CMakeFiles/jsoncpp.dir/jsoncpp.cpp.o] Error 1 CMakeFiles/Makefile2:588: recipe for target 'external/jsoncpp/CMakeFiles/jsoncpp.dir/all' failed make[1]: [external/jsoncpp/CMakeFiles/jsoncpp.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2

paradoxstar commented 6 years ago

It is caused by the version of gcc/g++. Since there are the selections of CharReaderPtr in jsoncpp.cpp as below: 233 #if __GNC__ >= 6 234 typedef std::scoped_ptr<CharReader> const CharReaderPtr; 235 #else 236 typedef std::auto_ptr<CharReader> CharReaderPtr 237 #endif For better compatibility to clusters with old version compilers(gcc/g++ 4.x, usually using these versions for stability), THUNDER does not use c++11 standard library (without '-std=c++11'), and we only test on gcc/g++4.x, 5.x, which make the selection to be std::auto_ptr<CharReader>. Under your condition(gcc/g++ 7.3)，it may select std::scoped_ptr<CharReader>. So c++11 standard library is necessary.

There are two solutions:

  1. You can easily comment this selection, like: 233 //#if __GNC__ >= 6 234 //typedef std::scoped_ptr<CharReader> const CharReaderPtr; 235 //#else 236 typedef std::auto_ptr<CharReader> CharReaderPtr 237 //#endif
  2. You can add the c++11 standard library in cmake: cmake -DADDITIONAL_FLAGS="-std=c++11" ..

We will fix this bug soon. :)

jianSG commented 6 years ago

Great. By comment off the lines actually worked. Thanks a lot for the help.