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Rosetta 2017.08 compile fails

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Rosetta 2017.08 compile fails
#1

Hi,

I'm trying to compile Rosetta 2017.08, but I get the following error. Does anyone have suggestions on where to start looking for a fix?

[?1034hscons: Reading SConscript files ...
Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git
Done. (0.0 seconds)
Number of option files updated: 0
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/2.6/64/x86/gcc/5.2/default/apps/public/AbinitioRelax.o -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 -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/5.2 -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/apps/public/AbinitioRelax.cc
In file included from src/utility/options/Option.hh:25,
                 from src/utility/options/OptionCollection.hh:23,
                 from src/basic/options/option.hh:17,
                 from src/apps/public/AbinitioRelax.cc:20:
src/utility/excn/Exceptions.hh:66: error: expected ';' before 'override'
src/utility/excn/Exceptions.hh:67: error: expected ';' before 'override'
In file included from src/utility/options/OptionCollection.hh:23,
                 from src/basic/options/option.hh:17,
                 from src/apps/public/AbinitioRelax.cc:20:
src/utility/options/Option.hh: In member function 'void utility::options::Option::check_restricted_access(bool) const':
src/utility/options/Option.hh:449: error: cannot allocate an object of abstract type 'utility::excn::EXCN_Msg_Exception'
src/utility/excn/Exceptions.hh:63: note:   because the following virtual functions are pure within 'utility::excn::EXCN_Msg_Exception':
src/utility/excn/EXCN_Base.hh:69: note:     virtual void utility::excn::EXCN_Base::show(std::ostream&) const
In file included from src/utility/options/ScalarOption_T_.hh:25,
                 from src/utility/options/BooleanOption.hh:23,
                 from src/utility/options/OptionCollection.hh:24,
                 from src/basic/options/option.hh:17,
                 from src/apps/public/AbinitioRelax.cc:20:
src/utility/options/ScalarOption.hh: At global scope:
src/utility/options/ScalarOption.hh:62: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:89: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:95: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:101: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:107: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:112: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:119: error: expected ';' before 'ScalarOption'
src/utility/options/ScalarOption.hh:120: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:126: error: expected ';' before 'override'
src/utility/options/ScalarOption.hh:130: error: expected ';' before '}' token
In file included from src/utility/options/BooleanOption.hh:23,
                 from src/utility/options/OptionCollection.hh:24,
                 from src/basic/options/option.hh:17,
                 from src/apps/public/AbinitioRelax.cc:20:
src/utility/options/ScalarOption_T_.hh:123: error: expected ';' before 'override'
src/utility/options/ScalarOption_T_.hh:161: error: expected ';' before 'override'
src/apps/public/AbinitioRelax.cc:65: error: expected ';' at end of input
src/apps/public/AbinitioRelax.cc:65: error: expected '}' at end of input
In file included from src/utility/options/BooleanOption.hh:23,
                 from src/utility/options/OptionCollection.hh:24,
                 from src/basic/options/option.hh:17,
                 from src/apps/public/AbinitioRelax.cc:20:
src/utility/options/ScalarOption_T_.hh: In constructor 'utility::options::ScalarOption_T_<K, T>::ScalarOption_T_()':
src/utility/options/ScalarOption_T_.hh:77: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_state_'
src/utility/options/ScalarOption_T_.hh:78: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_value_'
src/utility/options/ScalarOption_T_.hh:79: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'state_'
src/utility/options/ScalarOption_T_.hh:80: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'value_'
src/utility/options/ScalarOption_T_.hh: In copy constructor 'utility::options::ScalarOption_T_<K, T>::ScalarOption_T_(const utility::options::ScalarOption_T_<K, T>&)':
src/utility/options/ScalarOption_T_.hh:88: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'key_'
src/utility/options/ScalarOption_T_.hh:89: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'description_'
src/utility/options/ScalarOption_T_.hh:90: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'short_description_'
src/utility/options/ScalarOption_T_.hh:91: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'legal_'
src/utility/options/ScalarOption_T_.hh:92: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'lower_'
src/utility/options/ScalarOption_T_.hh:93: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'upper_'
src/utility/options/ScalarOption_T_.hh:94: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_state_'
src/utility/options/ScalarOption_T_.hh:95: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_value_'
src/utility/options/ScalarOption_T_.hh:96: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'state_'
src/utility/options/ScalarOption_T_.hh:97: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'value_'
src/utility/options/ScalarOption_T_.hh: In constructor 'utility::options::ScalarOption_T_<K, T>::ScalarOption_T_(const K&, const std::string&)':
src/utility/options/ScalarOption_T_.hh:107: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'key_'
src/utility/options/ScalarOption_T_.hh:108: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'description_'
src/utility/options/ScalarOption_T_.hh:109: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'short_description_'
src/utility/options/ScalarOption_T_.hh:110: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_state_'
src/utility/options/ScalarOption_T_.hh:111: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'default_value_'
src/utility/options/ScalarOption_T_.hh:112: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'state_'
src/utility/options/ScalarOption_T_.hh:113: error: class 'utility::options::ScalarOption_T_<K, T>' does not have any field named 'value_'
src/utility/options/ScalarOption_T_.hh: In member function 'utility::options::ScalarOption_T_<K, T>& utility::options::ScalarOption_T_<K, T>::operator=(const utility::options::ScalarOption_T_<K, T>&)':
src/utility/options/ScalarOption_T_.hh:143: error: 'key_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:144: error: 'description_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:145: error: 'short_description_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:146: error: 'legal_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:147: error: 'lower_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:148: error: 'upper_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:149: error: 'default_state_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:150: error: 'default_value_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:151: error: 'state_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh:152: error: 'value_' was not declared in this scope
src/utility/options/ScalarOption_T_.hh: At global scope:
src/utility/options/ScalarOption_T_.hh:155: error: expected unqualified-id at end of input
src/utility/options/ScalarOption_T_.hh:155: error: expected '}' at end of input
src/utility/options/ScalarOption_T_.hh:155: error: expected '}' at end of input
scons: *** [build/src/release/linux/2.6/64/x86/gcc/5.2/default/apps/public/AbinitioRelax.o] Error 1
scons: building terminated because of errors.

The output of rosetta_compiler_test.py is good:

Testing compiler 'g++', reporting as:
    g++ (GCC) 5.2.0

Main tests:

AUTO:                       Pass.
BIND:                       Pass.
CHRONO:                     Pass.
DELEGATING CONSTRUCTORS:    Pass.
DELETED CONSTRUCTORS:       Pass.
IN-CLASS INITIALIZATION:    Pass.
INHERITING CONSTRUCTORS:    Pass.
INITIALIZER LIST:           Pass.
LAMBDA:                     Pass.
MAP AT():                   Pass.
MOVE:                       Pass.
NULLPTR:                    Pass.
OVERRIDE:                   Pass.
RANGE FOR:                  Pass.
SMART POINTERS:             Pass.
UNORDERED MAP:              Pass.

Optional tests (not needed for standard compiles, but for extra features like multithreading):

ATOMIC:                     Pass.
CONDITION VARIABLE:         Pass.
MUTEX:                      Pass.
REGEX:                      Pass.
THREAD:                     Pass.
THREAD LOCAL:               Pass.

Summary:
Main Tests:                 16 of 16 passed
Optional Tests:             6 of 6 passed

Congratulations! Your compiler should support Rosetta!

 

Category: 
Post Situation: 
Tue, 2017-10-31 09:50
ipetrik_ambry

It looks like the compiler that scons is finding is not the same as the compiler you're using on the command line.

Try copying Rosetta/main/source/tools/build/site.settings.killdevil  to Rosetta/main/source/tools/build/site.settings and then recompiling.

Tue, 2017-10-31 09:56
rmoretti

That seems to have done it. Thanks!

Tue, 2017-10-31 10:05
ipetrik_ambry