problem compiling on mac os x

[yannickspill]

I am unable to build the latest IMP on my mac. However, XCode was also updated so I don't know whose fault it is.

[7/154] Linking CXX shared library lib/libimp_base.dylib
FAILED: : && /usr/bin/c++  -fcolor-diagnostics -w  -g  -dynamiclib -Wl,-headerpad_max_install_names -framework CoreFoundation -fsanitize=undefined -fsanitize=undefined -o lib/libimp_base.dylib -install_name /Users/Yannick/Documents/imp/build-debug/lib/libimp_base.dylib modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_all.cpp.o modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_config.cpp.o  /usr/local/lib/libboost_filesystem-mt.dylib /usr/local/lib/libboost_program_options-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libprofiler.dylib /usr/local/lib/libboost_random-mt.dylib && :
ld: file not found: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.ubsan_osx.a
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ninja: build stopped: subcommand failed.

For a start, if you know how to remove the fsanitize and framework flags, that would help me a lot. I am using the mavericks clang and the rest is an up-to-date homebrew. Here's my cmake.

cmake -DCMAKE_BUILD_TYPE=Debug -G Ninja -DIMP_DISABLED_MODULES="domino:multifit:system:example:misc:em2d:modeller:cgal:membrane" ../src/  -DIMP_PER_CPP_COMPILATION="isd2:isd:saxs:core" -DCMAKE_CXX_FLAGS="-fcolor-diagnostics" -DPYTHON_LIBRARY="/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib" -DPYTHON_INCLUDE_DIR="/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/include/python2.7/"

[benmwebb]

Works fine on our Mavericks build machine: http://salilab.org/imp/nightly/logs/develop/20140420/mac10v9-intel/base.build.log

However that is running XCode 5.1. I just updated it to 5.1.1 so we'll see tomorrow whether we get the same problem here.

[yannickspill]

thanks. can you tell me how to turn off the frameworks in the meantime?

[benmwebb]

Nope. Why would you want to do that anyway?

[yannickspill]

oh because libclang_rt.ubsan_osx.a is related to -framework CoreFoundation -fsanitize=undefined

[cgreenberg]

I'm getting a related error, but only on a debug build (Mavericks, latest Xcode, ...)

FAILED: /usr/local/Cellar/open-mpi/1.7.3/bin/mpicxx   -DIMPBASE_COMPILATION -DIMPBASE_EXPORTS -DIMP_base_lib_EXPORTS -w  -g -fPIC -Iinclude -I/usr/local/include    --std=c++11 -fsanitize=undefined -fno-sanitize-recover -MMD -MT modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o -MF "modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o.d" -o modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o -c src/base/paths.cpp
clang: error: unsupported argument 'undefined' to option 'fsanitize='
ninja: build stopped: subcommand failed.

[yannickspill]

it's in debug mode in my case as well. fast builds fine.

Le 22/04/14 02:51, Charles Greenberg a écrit :

I'm getting a related error, but only on a debug build (Mavericks, latest Xcode, ...)

FAILED: /usr/local/Cellar/open-mpi/1.7.3/bin/mpicxx -DIMPBASE_COMPILATION -DIMPBASE_EXPORTS -DIMP_base_lib_EXPORTS -w -g -fPIC -Iinclude -I/usr/local/include --std=c++11 -fsanitize=undefined -fno-sanitize-recover -MMD -MT modules/base/src/CMakeFiles/IMP.base-lib.dir////src/base/paths.cpp.o -MF "modules/base/src/CMakeFiles/IMP.base-lib.dir////src/base/paths.cpp.o.d" -o modules/base/src/CMakeFiles/IMP.base-lib.dir///__/src/base/paths.cpp.o -c src/base/paths.cpp clang: error: unsupported argument 'undefined' to option 'fsanitize=' ninja: build stopped: subcommand failed.

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