Dear all,
when compiling IMP 2.2.0 (on CentOS 5), `make` exits with the following errors:
imp-2.2.0 > make Scanning dependencies of target IMP-containers [ 0%] Built target IMP-containers Scanning dependencies of target IMP-version [ 0%] Computing version number [ 0%] Built target IMP-version Scanning dependencies of target IMP.base-version [ 0%] Building module version info [ 0%] Built target IMP.base-version Scanning dependencies of target IMP.base-all-header [ 0%] Built target IMP.base-all-header Scanning dependencies of target IMP.base-lib [ 0%] Building CXX object modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o [ 0%] Building CXX object modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_all.cpp.o /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/statistics.cpp: In function 'void IMP::base::show_timings(IMP::base::TextOutput)': /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/statistics.cpp:31: error: a function-definition is not allowed here before ':' token /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected primary-expression at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected `;' at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected primary-expression at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected `)' at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected statement at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected `}' at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp: At global scope: /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected `}' at end of input /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36: error: expected `}' at end of input make[2]: *** [modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_all.cpp.o] Error 1 make[1]: *** [modules/base/src/CMakeFiles/IMP.base-lib.dir/all] Error 2 make: *** [all] Error 2 imp-2.2.0 >
The previous `cmake` had run sccessfully (not all modules were found, though). You can find the complete `cmake` output at the end of this post.
Any idea how this problem can be tracked down?
Frank
---------------------------- cmake ----------------------------
imp-2.2.0 > /g/software/bin/cmake-3.0.0 ../imp-2.2.0 -DCMAKE_INSTALL_PREFIX=/g/software/linux/pack/imp-2.2.0 \ ? -DBoost_INCLUDE_DIR=/g/software/linux/pack/boost-1.46.0/include \ ? -DBoost_LIBRARY_DIRS=/g/software/linux/pack/boost-1.46.0/lib -- The C compiler identification is GNU 4.1.2 -- The CXX compiler identification is GNU 4.1.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Running check_common_problems -- Running clean_build_dir -- Running setup_cmake -- GCC version: 4.1.2 -- GCC version: 4.1.2 Traceback (most recent call last): File "<string>", line 1, in ? ImportError: No module named etree.ElementTree -- Python xml.etree not found, docs disabled. -- Python version is 2.4 -- Found PythonLibs: /usr/lib64/libpython2.4.so (found suitable exact version "2.4.3") -- Running setup -- Running setup_all -- Running making containers -- Running setup_module_alias for compatibility -- Setting up alias for module base as compatibility -- Running setup_module_alias for kernel -- Setting up alias for module kernel as -- Boost version: 1.46.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Performing Test IMP_COMPILER_HAS_AUTO -- Performing Test IMP_COMPILER_HAS_AUTO - Failed -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Success GPerfTools not found Log4CXX not found TCMalloc_HeapChecker not found TCMalloc_HeapProfiler not found -- Running generate paths.cpp Configuring module base ... yes -- Running setup_swig_wrappers base -- Running IMP.base making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/base.h Configuring module benchmark ... yes -- Running setup_swig_wrappers benchmark -- Running IMP.benchmark making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/benchmark.h -- CGAL not found. Set the CGAL_DIR cmake variable or environment variable to the directory containing CGALConfig.cmake. This is either the binary directory where CGAL was configured or PREFIX/lib/CGAL for an installation. Configuring module cgal ... CGAL not found Different data/build_info/sorted_modules -cgal Module IMP.cgal disabled Configuring module kmeans ... yes -- Running setup_swig_wrappers kmeans -- Running IMP.kmeans making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/kmeans.h Configuring module module_template ... yes -- Running setup_swig_wrappers module_template -- Running IMP.module_template making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/module_template.h -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES MPI_C_INCLUDE_PATH) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH) -- MPI not found Configuring module mpi ... MPI not found Different data/build_info/sorted_modules -mpi Module IMP.mpi disabled Configuring module test ... yes -- Running setup_swig_wrappers test -- Running IMP.test making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/test.h ANN not found Configuring module algebra ... yes -- Running setup_swig_wrappers algebra -- Running IMP.algebra making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/algebra.h Configuring module kernel ... yes -- Running setup_swig_wrappers kernel -- Running IMP.kernel making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/kernel.h Configuring module display ... yes -- Running setup_swig_wrappers display -- Running IMP.display making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/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 /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/gsl.h Configuring module parallel ... yes -- Running setup_swig_wrappers parallel -- Running IMP.parallel making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/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 /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/score_functor.h Configuring module statistics ... yes -- Running setup_swig_wrappers statistics -- Running IMP.statistics making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/statistics.h Configuring module core ... yes -- Running setup_swig_wrappers core -- Running IMP.core making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/core.h Configuring module container ... yes -- Running setup_swig_wrappers container -- Running IMP.container making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/container.h Configuring module modeller ... yes -- Running setup_swig_wrappers modeller -- Running IMP.modeller making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/modeller.h Configuring module symmetry ... yes -- Running setup_swig_wrappers symmetry -- Running IMP.symmetry making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/symmetry.h Configuring module atom ... yes -- Running setup_swig_wrappers atom -- Running IMP.atom making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/atom.h Configuring module scratch ... yes -- Running setup_swig_wrappers scratch -- Running IMP.scratch making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/scratch.h Configuring module em ... yes -- Running setup_swig_wrappers em -- Running IMP.em making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/em.h Configuring module kinematics ... yes -- Running setup_swig_wrappers kinematics -- Running IMP.kinematics making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/kinematics.h Configuring module misc ... yes -- Running setup_swig_wrappers misc -- Running IMP.misc making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/misc.h -- Performing Test RMF_environment -- Performing Test RMF_environment - Failed -- Building internal RMF -- Boost version: 1.46.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- iostreams -- Found HDF5: /g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/szlib-2.1/lib/libsz.so;/usr/lib64/libz.so;/usr/lib64/libm.so
-- Deprecated backends (and hdf5) are enabled -- GCC version: 4.1.2 -- GCC version: 4.1.2 -- Running Making RMF/HDF5.h -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/src/dependency/RMF/include/RMF/HDF5.h -- Running Making RMF.h -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/src/dependency/RMF/include/RMF.h -- Running setup_cmake.py -- Running Running setup_cmake.py -- Logging disabled -- Using VMD headers found in /g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/rmf/dependency/RMF_source/plugins/vmd/include -- Found SWIG: swig (found version "1.3.29") -- /usr/include/python2.4 Traceback (most recent call last): File "<string>", line 1, in ? ImportError: No module named etree.ElementTree -- Python xml.etree not found, docs disabled. -- RMF doc disabled Configuring module rmf ... yes -- Running setup_swig_wrappers rmf -- Running IMP.rmf making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/rmf.h Configuring module rotamer ... yes -- Running setup_swig_wrappers rotamer -- Running IMP.rotamer making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/rotamer.h Configuring module saxs ... yes -- Running setup_swig_wrappers saxs -- Running IMP.saxs making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/saxs.h -- Found HDF5 -- Found HDF5 Configuring module domino ... yes -- Running setup_swig_wrappers domino -- Running IMP.domino making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/domino.h Configuring module isd ... yes -- Running setup_swig_wrappers isd -- Running IMP.isd making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/isd.h -- Found FFTW3 -- Performing Test FFTW3_found -- Performing Test FFTW3_found - Success -- Found FFTW3 OpenCV21 not found OpenCV22 not found em2d is disabled Different data/build_info/sorted_modules -em2d Module IMP.em2d disabled ExampleDependency not found Configuring module example ... yes -- Running setup_swig_wrappers example -- Running IMP.example making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/example.h -- Found FFTW3 -- Found FFTW3 Configuring module multifit ... yes -- Running setup_swig_wrappers multifit -- Running IMP.multifit making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/multifit.h Configuring module pepdock ... yes -- Running setup_swig_wrappers pepdock -- Running IMP.pepdock making all header -- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/pepdock.h libTau not found Configuring module cnmultifit ... libTau not found Different data/build_info/sorted_modules -cnmultifit Module IMP.cnmultifit disabled -- Running setup_swig_dependencies 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 ... yes Configuring application ligand_score ... yes Configuring application multifit_tools ... yes 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: /g/software/linux/pack/imp-2.2.0/SRC/build imp-2.2.0 >