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[IMP-users] IMP 2.2.0 building: Syntax (?) errors when running `make`



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 >