Error during compile – Rosetta Commons

This topic has 3 replies, 2 voices, and was last updated 9 years, 6 months ago by Anonymous.

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- June 7, 2015 at 11:29 pm #2209
  Anonymous
  I have the rosetta git repository checked out and am getting an error when I try to compile. The error states that many files are missing. I’m not sure how to trouble shoot this. Thanks!
  
  > git pull
  etc etc 100% complete
  
  > cd /Rosetta/main/source
  > ./scons.py -j4 mode=release bin
  
  scons: Reading SConscript files …
  Running versioning script … Done. (0.1 seconds)
  Number of option files updated: 0
  Total 3350 options.
  Finished updating ResidueProperty code — no changes needed
  Finished updating VariantType code — no changes needed
  scons: done reading SConscript files.
  scons: Building targets …
  clang++ -o build/src/release/macos/10.10/64/x86/clang/4.0/default/apps/public/AbinitioRelax.o -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCXX11 -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/4.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/apps/public/AbinitioRelax.cc
  In file included from src/apps/public/AbinitioRelax.cc:20:
  In file included from src/basic/options/option.hh:18:
  In file included from src/utility/options/OptionCollection.hh:23:
  In file included from src/utility/options/Option.hh:24:
  In file included from src/utility/options/keys/OptionKey.hh:26:
  In file included from src/utility/keys/AutoKey.hh:36:
  In file included from src/utility/down_cast.hh:23:
  In file included from src/utility/assert.hh:19:
  In file included from src/utility/backtrace.hh:30:
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cassert:21:10: fatal error: ‘assert.h’ file not found
  #include
  ^
  1 error generated.
  clang++ -o build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/domain_assembly.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCXX11 -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/4.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/devel/domain_assembly/domain_assembly.cc
  In file included from src/devel/domain_assembly/domain_assembly.cc:14:
  In file included from src/core/types.hh:22:
  src/platform/macos/platform/types.hh:21:10: fatal error: ‘sys/types.h’ file not found
  #include
  ^
  clang++ -o build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/domain_assembly_setup.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCXX11 -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/4.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/devel/domain_assembly/domain_assembly_setup.cc
  In file included from src/devel/domain_assembly/domain_assembly_setup.cc:14:
  In file included from src/core/types.hh:22:
  src/platform/macos/platform/types.hh:21:10: fatal error: ‘sys/types.h’ file not found
  #include
  ^
  scons: *** [build/src/release/macos/10.10/64/x86/clang/4.0/default/apps/public/AbinitioRelax.o] Error 1
  clang++ -o build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/DomainAssemblyMover.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCXX11 -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/macos/64/clang/4.0 -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/devel/domain_assembly/DomainAssemblyMover.cc
  In file included from src/devel/domain_assembly/DomainAssemblyMover.cc:14:
  In file included from src/devel/domain_assembly/DomainAssemblyMover.hh:18:
  In file included from src/devel/domain_assembly/DomainAssemblyMover.fwd.hh:18:
  In file included from src/utility/pointer/owning_ptr.hh:15:
  In file included from src/utility/pointer/std/owning_ptr.hh:20:
  In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:596:
  In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator:319:
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:90:10: fatal error: ‘wchar.h’ file not found
  #include // for mbstate_t
  ^
  1 error generated.
  scons: *** [build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/domain_assembly_setup.os] Error 1
  1 error generated.
  scons: *** [build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/domain_assembly.os] Error 1
  1 error generated.
  scons: *** [build/src/release/macos/10.10/64/x86/clang/4.0/default/devel/domain_assembly/DomainAssemblyMover.os] Error 1
  scons: building terminated because of errors.
- June 8, 2015 at 2:35 am #11046
  Anonymous
  The files which are missing (assert.h; sys/types.h; wchar.h) are all part of the standard C++ library, and not specific to Rosetta. It sounds like the full development packages have not been installed on your system, particularly those standard libraries.
  
  It looks like this is on a Mac – you may want to check your Xcode installation and make sure that eveything needed for C++ compilation is installed. Try updating it if necessary. (If you’re on Linux, normally there’s something like “build-essentials” on your package manager.)
- June 8, 2015 at 3:23 am #11047
  Anonymous
  Thank you. I am running Mac OS X Yosemite. There is something wrong with my Xcode now that I look at it – it crashes instead of opening – so maybe this is the source of the issue?
- June 9, 2015 at 11:14 pm #11050
  Anonymous
  As I replied earlier, Xcode was crashing instead of opening. I deleted and reinstalled from the app store, and now Rosetta is compiling with no errors.
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