Error in Ubuntu 20.10

Hi, sorry for disturbing you but  I have problems installing Rosetta.  In Ubuntu 20.10.

I have also tried with clans, but it did not work.  I follow all the classical error list, but still no success. Also I am not sure what is the error. 

Could someone help me, please?

regards

JP

tar -xvzf rosetta_src_2020.50.61505_bundle.tgz

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ubuntu@ubuntu-MS-7C75:~$ python -V

Python 2.7.18

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ubuntu@ubuntu-MS-7C75:~/Rosetta/main/source$ sudo apt-get install build-essential

Reading package lists… Done

Building dependency tree       

Reading state information… Done

build-essential is already the newest version (12.8ubuntu3).

0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

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ubuntu@ubuntu-MS-7C75:~/Rosetta/main/source$ gcc -v

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper

OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa

OFFLOAD_TARGET_DEFAULT=1

Target: x86_64-linux-gnu

Configured with: ../src/configure -v –with-pkgversion=’Ubuntu 10.2.0-13ubuntu1′ –with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs –enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 –prefix=/usr –with-gcc-major-version-only –program-suffix=-10 –program-prefix=x86_64-linux-gnu- –enable-shared –enable-linker-build-id –libexecdir=/usr/lib –without-included-gettext –enable-threads=posix –libdir=/usr/lib –enable-nls –enable-clocale=gnu –enable-libstdcxx-debug –enable-libstdcxx-time=yes –with-default-libstdcxx-abi=new –enable-gnu-unique-object –disable-vtable-verify –enable-plugin –enable-default-pie –with-system-zlib –enable-libphobos-checking=release –with-target-system-zlib=auto –enable-objc-gc=auto –enable-multiarch –disable-werror –with-arch-32=i686 –with-abi=m64 –with-multilib-list=m32,m64,mx32 –enable-multilib –with-tune=generic –enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,hsa –without-cuda-driver –enable-checking=release –build=x86_64-linux-gnu –host=x86_64-linux-gnu –target=x86_64-linux-gnu

Thread model: posix

Supported LTO compression algorithms: zlib zstd

gcc version 10.2.0 (Ubuntu 10.2.0-13ubuntu1) 

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/scons.py -j8 mode=release bin

scons: Reading SConscript files …

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 4522 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/5.8/64/x86/gcc/10/default/core/io/silent/SilentStruct.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/io/silent/SilentStruct.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/NamedAtomPairConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/NamedAtomPairConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/NamedDihedralConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/NamedDihedralConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/NonResidueTypeConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/NonResidueTypeConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/ResidueCouplingConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/ResidueCouplingConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/ResidueTypeConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/ResidueTypeConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/ResidueTypeLinkingConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/ResidueTypeLinkingConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/RTConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/RTConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/SequenceProfileConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/SequenceProfileConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

src/core/io/silent/SilentStruct.cc: In member function ‘void core::io::silent::SilentStruct::energies_into_pose(core::pose::Pose&) const’:

src/core/io/silent/SilentStruct.cc:801:13: error: redeclaration of ‘typedef class std::__cxx11::basic_string<char> std::string’

  801 |  using std::string;

      |             ^~~~~~

In file included from /usr/include/c++/10/iosfwd:39,

                 from /usr/include/c++/10/ios:38,

                 from /usr/include/c++/10/ostream:38,

                 from /usr/include/c++/10/iostream:39,

                 from src/core/io/silent/SilentStruct.cc:16:

/usr/include/c++/10/bits/stringfwd.h:79:33: note: previous declaration ‘typedef class std::__cxx11::basic_string<char> std::string’

   79 |   typedef basic_string<char>    string;

      |                                 ^~~~~~

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/SiteConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/SiteConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/SiteConstraintResidues.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/SiteConstraintResidues.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/constraints/util.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/constraints/util.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/pack_basic/RotamerSetsBase.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/pack_basic/RotamerSetsBase.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/io/external/PsiPredInterface.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/io/external/PsiPredInterface.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/aa_composition_energy/AACompositionConstraint.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/aa_composition_energy/AACompositionConstraint.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/core/scoring/aa_composition_energy/AACompositionEnergySetup.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/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/scoring/aa_composition_energy/AACompositionEnergySetup.cc

g++: warning: switch ‘-ffor-scope’ is no longer supported

scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/core/io/silent/SilentStruct.os] Error 1

scons: building terminated because of errors.