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g++ -o build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os -c -std=c++11 -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 -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 -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4 -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 -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])'
  pose_asu.dump_pdb( pdbout , "1" );
                                  ^
In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:
src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const
  dump_pdb(std::string const & file_name) const;
  ^
src/core/pose/Pose.hh:1518:2: note:   candidate expects 1 argument, 2 provided
src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const
  dump_pdb(std::ostream & out) const;
  ^
src/core/pose/Pose.hh:1521:2: note:   candidate expects 1 argument, 2 provided
src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const
  dump_pdb(
  ^
src/core/pose/Pose.hh:1525:2: note:   no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])'
  pose_asu.dump_pdb( buffer , "1" );
                                  ^
In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:
src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const
  dump_pdb(std::string const & file_name) const;
  ^
src/core/pose/Pose.hh:1518:2: note:   candidate expects 1 argument, 2 provided
src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const
  dump_pdb(std::ostream & out) const;
  ^
src/core/pose/Pose.hh:1521:2: note:   candidate expects 1 argument, 2 provided
src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const
  dump_pdb(
  ^
src/core/pose/Pose.hh:1525:2: note:   no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir("..");
             ^
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir("..");
             ^
src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::__cxx11::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)':
src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  chdir("..");
             ^
scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os] Error 1
scons: building terminated because of errors.

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