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January 2015

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Problems compiling IMP on mac OS X version 10.9.5
by Marco Di Stefano 30 Jan '15

30 Jan '15

Dear IMP users, I am having problems in compiling IMP on my mac (OS X version 10.9.5). These are the steps I followed in some details and I hope you can help me to fix my problem. 1 - I downloaded IMP from github with this command in a directory in my home folder ~/IMP git clone git@github.com:salilab/imp.git 2 - I renamed the downloaded imp directory as src mv imp/ src 3 - In the src folder I executed the python script ./setup_git.py 4 - In ~/IMP I created the directory build-fast and from the latter directory I launched . ../prep_env_fast.sh where prep_env_fast.sh contains the following: cmake ../src/ -G Ninja -DIMP_DISABLED_MODULES=domino:multifit:system:example:misc:em3d:modeller:membrane -DCMAKE_POLICY_DEFAULT_CMP0054=OLD -DCMAKE_POLICY_DEFAULT_CMP0042=OLD -DCM\ AKE_BUILD_TYPE=Release -DIMP_MAX_LOG=SILENT -DIMP_MAX_CHECKS=NONE -DCMAKE_INSTALL_PREFIX=$HOME -DIMP_PER_CPP_COMPILATION="core:isd" It is meant to run the cmake command excluding some of the modules and tuning some other flags. The output of the script is: -- The C compiler identification is AppleClang 6.0.0.6000056 -- The CXX compiler identification is AppleClang 6.0.0.6000056 -- Check for working C compiler using: Ninja -- Check for working C compiler using: Ninja -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler using: Ninja -- Check for working CXX compiler using: Ninja -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Running check_common_problems -- Running clean_build_dir -- Running setup_cmake -- Enabling clang C++11 support -- Wrong doxygen version at /usr/local/bin/doxygen. Found 1.8.9.1, but needed 1.8.6 -- core is percpp -- isd is percpp -- Python binary is /usr/bin/python (version 2.7.5) -- Found PythonLibs: /usr/lib/libpython2.7.dylib (found suitable exact version "2.7.5") -- Running setup -- Running setup_all -- Running making containers -- Running setup_module_alias for kernel -- Setting up alias for module kernel as -- Boost version: 1.57.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Performing Test IMP_COMPILER_HAS_AUTO -- Performing Test IMP_COMPILER_HAS_AUTO - Success -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Failed -- Found GPERFTOOLS -- Performing Test GPerfTools_found -- Performing Test GPerfTools_found - Success -- Found GPerfTools -- Found LOG4CXX -- Performing Test Log4CXX_found -- Performing Test Log4CXX_found - Success -- Found Log4CXX -- Performing Test TCMalloc_HeapChecker_found -- Performing Test TCMalloc_HeapChecker_found - Failed TCMalloc_HeapChecker not found -- Performing Test TCMalloc_HeapProfiler_found -- Performing Test TCMalloc_HeapProfiler_found - Failed TCMalloc_HeapProfiler not found -- Running generate paths.cpp Configuring module base ... yes -- Running setup_swig_wrappers base -- Running IMP.base making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/base.h Configuring module benchmark ... yes -- Running setup_swig_wrappers benchmark -- Running IMP.benchmark making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/benchmark.h -- Build type: Release -- USING CXXFLAGS = ' -w -O3 -DNDEBUG' -- USING EXEFLAGS = ' -framework CoreFoundation ' -- Targetting Ninja -- Using /usr/bin/c++ compiler. -- DARWIN_VERSION=13 -- Mac Leopard detected -- Requested component: MPFR -- Requested component: GMP Configuring module cgal ... yes -- Running setup_swig_wrappers cgal -- Running IMP.cgal making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/cgal.h Configuring module kmeans ... yes -- Running setup_swig_wrappers kmeans -- Running IMP.kmeans making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/kmeans.h Configuring module module_template ... yes -- Running setup_swig_wrappers module_template -- Running IMP.module_template making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/module_template.h -- Found MPI_C: /usr/local/Cellar/open-mpi/1.8.4/lib/libmpi.dylib -- Found MPI_CXX: /usr/local/Cellar/open-mpi/1.8.4/lib/libmpi_cxx.dylib;/usr/local/Cellar/open-mpi/1.8.4/lib/libmpi.dylib -- MPI found Configuring module mpi ... yes -- Running setup_swig_wrappers mpi -- Running IMP.mpi making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/mpi.h Configuring module test ... yes -- Running setup_swig_wrappers test -- Running IMP.test making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/test.h -- Found ANN -- Performing Test ANN_found -- Performing Test ANN_found - Success -- Found ANN Configuring module algebra ... yes -- Running setup_swig_wrappers algebra -- Running IMP.algebra making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/algebra.h Configuring module kernel ... yes -- Running setup_swig_wrappers kernel -- Running IMP.kernel making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/kernel.h Configuring module display ... yes -- Running setup_swig_wrappers display -- Running IMP.display making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/display.h -- Found GSL -- Performing Test GSL_found -- Performing Test GSL_found - Success -- Found GSL Configuring module gsl ... yes -- Running setup_swig_wrappers gsl -- Running IMP.gsl making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/gsl.h Configuring module parallel ... yes -- Running setup_swig_wrappers parallel -- Running IMP.parallel making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/parallel.h -- Found HDF5 -- Performing Test HDF5_found -- Performing Test HDF5_found - Success -- Found HDF5 Configuring module score_functor ... yes -- Running setup_swig_wrappers score_functor -- Running IMP.score_functor making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/score_functor.h Configuring module statistics ... yes -- Running setup_swig_wrappers statistics -- Running IMP.statistics making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/statistics.h Configuring module core ... yes -- Running setup_swig_wrappers core -- Running IMP.core making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/core.h Configuring module container ... yes -- Running setup_swig_wrappers container -- Running IMP.container making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/container.h modeller is disabled Different data/build_info/sorted_modules -modeller Module IMP.modeller disabled Configuring module symmetry ... yes -- Running setup_swig_wrappers symmetry -- Running IMP.symmetry making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/symmetry.h Configuring module atom ... yes -- Running setup_swig_wrappers atom -- Running IMP.atom making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/atom.h Configuring module pmi ... yes -- Running setup_swig_wrappers pmi -- Running IMP.pmi making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/pmi.h Configuring module scratch ... yes -- Running setup_swig_wrappers scratch -- Running IMP.scratch making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/scratch.h Configuring module em ... yes -- Running setup_swig_wrappers em -- Running IMP.em making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/em.h Configuring module kinematics ... yes -- Running setup_swig_wrappers kinematics -- Running IMP.kinematics making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/kinematics.h misc is disabled Different data/build_info/sorted_modules -misc Module IMP.misc disabled -- Building internal RMF -- Boost version: 1.57.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- iostreams -- Found HDF5: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libhdf5.dylib;/usr/local/Cellar/hdf5/1.8.14/lib/libhdf5.dylib;/usr/local/opt/szip/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib -- Found HDF5: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libhdf5.dylib;/usr/local/Cellar/hdf5/1.8.14/lib/libhdf5.dylib;/usr/local/opt/szip/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (Required is at least version "1.8") -- Deprecated backends (and hdf5) are enabled -- Found Log4CXX -- Enabling clang C++11 support -- Running Making RMF/HDF5.h -- Updating /Users/marco/IMP/build-fast/src/dependency/RMF/include/RMF/HDF5.h -- Running Making RMF.h -- Updating /Users/marco/IMP/build-fast/src/dependency/RMF/include/RMF.h -- Running setup_cmake.py -- Running Running setup_cmake.py -- Logging enabled -- Using VMD headers found in /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/plugins/vmd/include -- Found SWIG: swig (found suitable version "3.0.2", minimum required is "1.3.40") -- Wrong doxygen version at /usr/local/bin/doxygen. Found 1.8.9.1, but needed 1.8.6 -- RMF doc disabled Configuring module rmf ... yes -- Running setup_swig_wrappers rmf -- Running IMP.rmf making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/rmf.h Configuring module rotamer ... yes -- Running setup_swig_wrappers rotamer -- Running IMP.rotamer making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/rotamer.h Configuring module saxs ... yes -- Running setup_swig_wrappers saxs -- Running IMP.saxs making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/saxs.h -- Found HDF5 -- Found HDF5 domino is disabled Different data/build_info/sorted_modules -domino Module IMP.domino disabled Configuring module isd ... yes -- Running setup_swig_wrappers isd -- Running IMP.isd making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/isd.h -- Found FFTW3 -- Performing Test FFTW3_found -- Performing Test FFTW3_found - Success -- Found FFTW3 OpenCV21 not found -- Found OPENCV22 -- Performing Test OpenCV22_found -- Performing Test OpenCV22_found - Success -- Found OpenCV22 Configuring module em2d ... IMP.domino not found Different data/build_info/sorted_modules -em2d Module IMP.em2d disabled ExampleDependency not found example is disabled Different data/build_info/sorted_modules -example Module IMP.example disabled -- Found FFTW3 -- Found FFTW3 multifit is disabled Different data/build_info/sorted_modules -multifit Module IMP.multifit disabled Configuring module pepdock ... IMP.domino not found Different data/build_info/sorted_modules -pepdock Module IMP.pepdock disabled Configuring module probC ... yes -- Running setup_swig_wrappers probC -- Running IMP.probC making all header -- Updating /Users/marco/IMP/build-fast/include/IMP/probC.h -- Found LIBTAU -- Performing Test libTau_found -- Performing Test libTau_found - Success -- Found libTau Configuring module cnmultifit ... IMP.multifit not found Different data/build_info/sorted_modules -cnmultifit Module IMP.cnmultifit disabled -- Running setup_swig_dependencies -- Creating thread pool with 8 Configuring application EMageFit ... no Different data/build_info/applications -EMageFit Application EMageFit disabled Configuring application cnmultifit_tools ... no Different data/build_info/applications -cnmultifit_tools Application cnmultifit_tools disabled Configuring application em_tools ... yes Configuring application example_app ... yes Configuring application foxs ... yes Configuring application integrative_docking ... no Different data/build_info/applications -integrative_docking Application integrative_docking disabled Configuring application ligand_score ... yes Configuring application multifit_tools ... no Different data/build_info/applications -multifit_tools Application multifit_tools disabled Configuring application pdb_tools ... yes Configuring application rmf_tools ... yes Configuring application saxs_merge ... yes Configuring application saxs_tools ... yes -- Running setup_imppy -- Documentation disabled as doxygen not found -- Configuring done -- Generating done -- Build files have been written to: /Users/marco/IMP/build-fast 5 - Then I launch from build-fast the command ninja -j1 RMF and I obtained the following error. [98/118] Swig source FAILED: cd /Users/marco/IMP/build-fast/src/dependency/RMF/swig && /usr/local/Cellar/cmake/3.1.0/bin/cmake -E make_directory /Users/marco/IMP/build-fast/lib && swig -python -castmode -naturalvar -Wextra -fvirtual -DPySwigIterator=RMF_PySwigIterator -c++ -DSwigPyIterator=RMF_SwigPyIterator -DRMFEXPORT -outdir /Users/marco/IMP/build-fast/lib -c++ -I/Users/marco/IMP/build-fast/include -I/usr/local/include -I/Users/marco/IMP/build-fast/src/dependency/RMF/src -I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/src -I/usr/local/Cellar/hdf5/1.8.14/include -I/Users/marco/IMP/build-fast/src/dependency/RMF/include -I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include -I/System/Library/Frameworks/Python.framework/Headers -I/Users/marco/IMP/src/swig -I/Users/marco/IMP/src/modules/rmf/dependency/RMF_source/swig -o /Users/marco/IMP/build-fast/lib/RMFPYTHON_wrap.cxx /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/swig/RMF.i /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments /Users/marco/IMP/src/modules/rmf/dependency/RMF_source/include/RMF/keys.h:41: Error: Macro 'RMF_DECLARE_KEY' expects 2 arguments ninja: build stopped: subcommand failed. In the mac I have the following versions of swig , clang , python and hdf5 SWIG Version 3.0.2 Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) Python 2.7.5 hdf5-1.8.14 I hope this message is enough to understand my problem. Best regards and thanks in advance for your help, Marco Di Stefano

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