Unable to successfully compile using ubuntu virtual machine

[Anonymous]

Hello, I am currently unable to correclty compile. I am running a ubuntu virtual machine on win10 (ubuntu 14.04 LTS, GCC version 4.8.4). 

The version I am currently using is Rosetta 3.12.

Then try to compile using with the following…

./scons.py mode=release bin

The following error is given

scons: Building targets …

mpiCC -o build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/jd3/pose_outputters/mmTFPoseOutputter.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -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 -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/jd3/pose_outputters/mmTFPoseOutputter.cc

mpiCC -o build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/environment/claims/ClaimStrength.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -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 -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/environment/claims/ClaimStrength.cc

mpiCC -o build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/environment/claims/CutBiasClaim.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -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 -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/environment/claims/CutBiasClaim.cc

mpiCC -o build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/environment/claims/EnvClaim.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -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 -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/environment/claims/EnvClaim.cc

mpiCC -o build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/environment/claims/EnvLabelSelector.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -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 -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/environment/claims/EnvLabelSelector.cc

In file included from src/core/io/mmtf/util.hh:26:0,

                 from src/core/io/mmtf/mmtf_writer.hh:25,

                 from src/protocols/jd3/pose_outputters/mmTFPoseOutputter.cc:31:

external/include/mmtf.hpp:1:1: error: expected unqualified-id before ‘.’ token

 ../mmtf/include/mmtf.hpp

 ^

scons: *** [build/src/release/linux/4.4/64/x86/gcc/4.8/mpi/protocols/jd3/pose_outputters/mmTFPoseOutputter.os] Error 1

 

[Anonymous]

The Rosetta distribution relies on symlinks. This works fine on Mac and Linux, but Windows filesystems don’t have the same symlink support. Depending on how you did the extraction of the Rosetta distribution, extracting things on a Windows machine may result in those symlinks being converted to text files with the contents being the destination file. If you have that, you’ll get the error messages like the ones you’re seeing.

My recommendation is not to extract the file in the external Windows environment, but rather extract things within the virtual machine, on a filesystem set up for that virtual machine (not one which is co-mounted with the host Windows operating system). That should preserve the symlinks properly.

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