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Error when compiling Rosetta 3.13

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Error when compiling Rosetta 3.13
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Hey everyone:

I am trying to compile Rosetta3.13 on Ubuntu 22.04, and I got some error messages. I have tried GNU11 and Clang but neither of them worked. Would you please give me some hint to fix this problem. Here is the error message:

  if len(operation_list) is not 2:
scons: Reading SConscript files ...
Copy("user.options", "user.options.template")
Copy("user.settings", "user.settings.template")
Copy("/home/shinlab/Downloads/rosetta_src_3/rosetta_src_2021.16.61629_bundle/main/source/src/pilot_apps.src.settings", "/home/shinlab/Downloads/rosetta_src_3/rosetta_src_2021.16.61629_bundle/main/source/src/pilot_apps.src.settings.template")
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 4580 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/5.19/64/x86/gcc/11/default/apps/public/AbinitioRelax.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/AbinitioRelax.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/devel/init.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/init.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/init/init.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/init.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/init/register1.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register1.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/init/register2.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register2.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/init/register3.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register3.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/init/register4.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register4.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/AntibodyClass.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/AntibodyClass.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/AntibodyModeler.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/AntibodyModeler.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/CDRH3Modeler.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/CDRH3Modeler.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/LHRepulsiveRampLegacy.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/LHRepulsiveRampLegacy.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/LHSnugFitLegacy.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/LHSnugFitLegacy.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/GraftMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/GraftMover.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody_legacy/Ubiquitin_E2C_Modeler.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/Ubiquitin_E2C_Modeler.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/Ab_TemplateInfo.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/Ab_TemplateInfo.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyCDRGrafter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyCDRGrafter.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyEnumManager.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyEnumManager.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyInfo.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyInfo.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyFeatures.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyFeatures.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyFeaturesCreator.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyFeaturesCreator.cc
g++: warning: switch '-ffor-scope' is no longer supported
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyModelerProtocol.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyModelerProtocol.cc
g++: warning: switch '-ffor-scope' is no longer supported
In file included from src/protocols/features/FeaturesReporterCreator.hh:21,
                 from src/protocols/antibody/AntibodyFeaturesCreator.hh:18,
                 from src/protocols/antibody/AntibodyFeaturesCreator.cc:15:
src/protocols/features/FeaturesReporter.fwd.hh:27:14: error: 'uint64_t' in namespace 'std' does not name a type; did you mean 'wint_t'?
   27 | typedef std::uint64_t StructureID;
      |              ^~~~~~~~
      |              wint_t
In file included from src/protocols/features/InterfaceFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeaturesCreator.cc:21:
src/protocols/features/FeaturesReporter.hh:99:17: error: 'StructureID' has not been declared
   99 |                 StructureID /*parent id*/,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:109:17: error: 'StructureID' has not been declared
  109 |                 StructureID /*parent id*/,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:124:17: error: 'StructureID' has not been declared
  124 |                 StructureID,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:130:17: error: 'StructureID' has not been declared
  130 |                 StructureID,
      |                 ^~~~~~~~~~~
In file included from src/protocols/features/InterfaceFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeaturesCreator.cc:21:
src/protocols/features/FeaturesReporter.hh:185:17: error: 'StructureID' has not been declared
  185 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyNumberingParser.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyNumberingParser.cc
g++: warning: switch '-ffor-scope' is no longer supported
In file included from src/protocols/features/FeaturesReporter.hh:19,
                 from src/protocols/features/InterfaceFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.cc:14:
src/protocols/features/FeaturesReporter.fwd.hh:27:14: error: 'uint64_t' in namespace 'std' does not name a type; did you mean 'wint_t'?
   27 | typedef std::uint64_t StructureID;
      |              ^~~~~~~~
      |              wint_t
In file included from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeaturesCreator.cc:21:
src/protocols/features/InterfaceFeatures.hh:71:17: error: 'StructureID' has not been declared
   71 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:126:17: error: 'StructureID' has not been declared
  126 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:135:17: error: 'StructureID' has not been declared
  135 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:144:17: error: 'StructureID' has not been declared
  144 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:156:17: error: 'StructureID' has not been declared
  156 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:181:17: error: 'StructureID' has not been declared
  181 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
In file included from src/protocols/features/InterfaceFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.cc:14:
src/protocols/features/FeaturesReporter.hh:99:17: error: 'StructureID' has not been declared
   99 |                 StructureID /*parent id*/,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:109:17: error: 'StructureID' has not been declared
  109 |                 StructureID /*parent id*/,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:124:17: error: 'StructureID' has not been declared
  124 |                 StructureID,
      |                 ^~~~~~~~~~~
src/protocols/features/FeaturesReporter.hh:130:17: error: 'StructureID' has not been declared
  130 |                 StructureID,
      |                 ^~~~~~~~~~~
In file included from src/protocols/features/InterfaceFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.cc:14:
src/protocols/features/FeaturesReporter.hh:185:17: error: 'StructureID' has not been declared
  185 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
In file included from src/protocols/antibody/AntibodyFeatures.hh:18,
                 from src/protocols/antibody/AntibodyFeatures.cc:14:
src/protocols/features/InterfaceFeatures.hh:71:17: error: 'StructureID' has not been declared
   71 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:126:17: error: 'StructureID' has not been declared
  126 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:135:17: error: 'StructureID' has not been declared
  135 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:144:17: error: 'StructureID' has not been declared
  144 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:156:17: error: 'StructureID' has not been declared
  156 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
src/protocols/features/InterfaceFeatures.hh:181:17: error: 'StructureID' has not been declared
  181 |                 StructureID struct_id,
      |                 ^~~~~~~~~~~
In file included from src/protocols/antibody/AntibodyFeaturesCreator.cc:21:
src/protocols/antibody/AntibodyFeatures.hh:84:27: error: 'protocols::features::StructureID' has not been declared
   84 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:92:27: error: 'protocols::features::StructureID' has not been declared
   92 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:98:27: error: 'protocols::features::StructureID' has not been declared
   98 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:104:27: error: 'protocols::features::StructureID' has not been declared
  104 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:111:27: error: 'protocols::features::StructureID' has not been declared
  111 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:119:27: error: 'protocols::features::StructureID' has not been declared
  119 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
g++ -o build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyNumberingConverterMover.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -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 -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody/AntibodyNumberingConverterMover.cc
g++: warning: switch '-ffor-scope' is no longer supported
scons: *** [build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyFeaturesCreator.os] Error 1
In file included from src/protocols/antibody/AntibodyFeatures.cc:14:
src/protocols/antibody/AntibodyFeatures.hh:84:27: error: 'protocols::features::StructureID' has not been declared
   84 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:92:27: error: 'protocols::features::StructureID' has not been declared
   92 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:98:27: error: 'protocols::features::StructureID' has not been declared
   98 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:104:27: error: 'protocols::features::StructureID' has not been declared
  104 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:111:27: error: 'protocols::features::StructureID' has not been declared
  111 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.hh:119:27: error: 'protocols::features::StructureID' has not been declared
  119 |                 features::StructureID struct_id,
      |                           ^~~~~~~~~~~
In file included from src/protocols/antibody/AntibodyFeatures.cc:30:
src/protocols/features/util.hh:79:9: error: 'StructureID' was not declared in this scope
   79 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/features/util.hh:80:42: error: expected primary-expression before 'db_session'
   80 |         utility::sql_database::sessionOP db_session
      |                                          ^~~~~~~~~~
src/protocols/features/util.hh:81:1: error: expression list treated as compound expression in initializer [-fpermissive]
   81 | );
      | ^
src/protocols/features/util.hh:83:18: error: 'StructureID' was not declared in this scope
   83 | utility::vector1<StructureID>
      |                  ^~~~~~~~~~~
src/protocols/features/util.hh:83:29: error: template argument 1 is invalid
   83 | utility::vector1<StructureID>
      |                             ^
src/protocols/features/util.hh:83:29: error: template argument 2 is invalid
src/protocols/antibody/AntibodyFeatures.cc:118:9: error: 'StructureID' has not been declared
  118 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.cc:321:9: error: 'StructureID' has not been declared
  321 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.cc:443:9: error: 'StructureID' has not been declared
  443 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.cc:540:9: error: 'StructureID' has not been declared
  540 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.cc:557:9: error: 'StructureID' has not been declared
  557 |         StructureID struct_id,
      |         ^~~~~~~~~~~
src/protocols/antibody/AntibodyFeatures.cc:623:9: error: 'StructureID' has not been declared
  623 |         StructureID struct_id,
      |         ^~~~~~~~~~~
scons: *** [build/src/release/linux/5.19/64/x86/gcc/11/default/protocols/antibody/AntibodyFeatures.os] Error 1

 

Category: 
Compilation
Post Situation: 
Unsolved
Wed, 2023-02-22 14:23
Sihan_Li
Top

You're using a more recent compiler than existed when Rosetta 3.13 was released. Something which worked on the older compilers is no longer working.

This has been corrected in more recent weekly releases, but if you still want to use Rosetta 3.13, the fix is simple. Simply add the line 

#include <cstdint>

To the top of the file `src/protocols/features/FeaturesReporter.fwd.hh` (After the owning_ptr.hh #include line would work.) Then re-launch the Rosetta compile process.

Wed, 2023-02-22 14:31
rmoretti
(Reply to #3)
Top

That worked! Thank you so much for your help :D

Thu, 2023-02-23 06:14
Sihan_Li