search

salilab / imp

The Integrative Modeling Platform
https://integrativemodeling.org
GNU General Public License v3.0
74 stars 30 forks source link

compilation issues #540

Closed Pellarin closed 11 years ago

Pellarin commented 11 years ago

some file missing in the latest committed version

/Users/riccardopellarin/imp-021013/imp-fast/src/test_swig/wrap.cpp:152:10: fatal error: 'Python.h' file not found
#include <Python.h>
         ^
[ 32%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/parsing/ResolvingDecoder.cc.o
1 error generated.
make[2]: *** [modules/base/pyext/CMakeFiles/IMP.base-python.dir/__/__/__/src/base_swig/wrap.cpp.o] Error 1
make[1]: *** [modules/base/pyext/CMakeFiles/IMP.base-python.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 33%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/parsing/Symbol.cc.o
1 error generated.
make[2]: *** [modules/benchmark/pyext/CMakeFiles/IMP.benchmark-python.dir/__/__/__/src/benchmark_swig/wrap.cpp.o] Error 1
make[1]: *** [modules/benchmark/pyext/CMakeFiles/IMP.benchmark-python.dir/all] Error 2
[ 33%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/parsing/ValidatingCodec.cc.o
1 error generated.
make[2]: *** [modules/kmeans/pyext/CMakeFiles/IMP.kmeans-python.dir/__/__/__/src/kmeans_swig/wrap.cpp.o] Error 1
make[1]: *** [modules/kmeans/pyext/CMakeFiles/IMP.kmeans-python.dir/all] Error 2
[ 33%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Resolver.cc.o
1 error generated.
make[2]: *** [modules/mpi/pyext/CMakeFiles/IMP.mpi-python.dir/__/__/__/src/mpi_swig/wrap.cpp.o] Error 1
make[1]: *** [modules/mpi/pyext/CMakeFiles/IMP.mpi-python.dir/all] Error 2
[ 34%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/ResolverSchema.cc.o
[ 34%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Schema.cc.o
[ 34%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Stream.cc.o
[ 34%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Types.cc.o
[ 35%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Validator.cc.o
[ 35%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/ValidSchema.cc.o
[ 35%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/AvroCpp/impl/Zigzag.cc.o
[ 36%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/All.json.cpp.o
[ 36%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/File.json.cpp.o
[ 36%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/Frame.json.cpp.o
[ 37%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/Nodes.json.cpp.o
[ 37%] Building CXX object src/dependency/RMF/src/CMakeFiles/RMF-lib.dir/backend/avro/Data.json.cpp.o
Linking CXX shared library ../../../../lib/libRMF.dylib
[ 37%] Built target RMF-lib
1 error generated.
make[2]: *** [modules/test/pyext/CMakeFiles/IMP.test-python.dir/__/__/__/src/test_swig/wrap.cpp.o] Error 1
make[1]: *** [modules/test/pyext/CMakeFiles/IMP.test-python.dir/all] Error 2
Linking CXX shared library ../../../lib/libimp_cgal.dylib
[ 37%] Built target IMP.cgal-lib
make: *** [all] Error 2
benmwebb commented 11 years ago

It looks to me like cmake couldn't find Python on your system. Did it?

Pellarin commented 11 years ago

Not really:

-- Running check_common_problems
-- Running clean_build_dir
-- Running setup_cmake
-- /Users/riccardopellarin/imp-021013/imp-fast
-- Python version is 2.7
-- Running setup
--     Different data/build_info/disabled
    -em2d
    Different data/build_info/sorted_modules
    +gsl
    +domino
    +em2d
    +example
    +multifit
    +pepdock
    +cnmultifit
    Different data/build_info/applications
    +EMageFit
    +cnmultifit_tools
    +multifit_tools
    +saxs_merge
-- Running setup_containers
-- Running setup_all
-- 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: 1.51.0
-- Found the following Boost libraries:
--   system
--   filesystem
--   thread
--   program_options
-- Running generate paths.cpp
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module base ... yes
-- Running setup_swig_wrappers base
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module benchmark ... yes
-- Running setup_swig_wrappers benchmark
-- Build type: Release
-- USING CXXFLAGS = '-w -O3 -DNDEBUG'
-- USING EXEFLAGS = '  '
-- Targetting Unix Makefiles
-- Using /usr/bin/c++ compiler.
-- DARWIN_VERSION=12
-- Mac Leopard detected
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module cgal ... yes
-- Running setup_swig_wrappers cgal
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module kmeans ... yes
-- Running setup_swig_wrappers kmeans
-- MPI found
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module mpi ... yes
-- Running setup_swig_wrappers mpi
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module test ... yes
-- Running setup_swig_wrappers test
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module algebra ... yes
-- Running setup_swig_wrappers algebra
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module kernel ... yes
-- Running setup_swig_wrappers kernel
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module display ... yes
-- Running setup_swig_wrappers display
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module gsl ... GSL not found
    Different data/build_info/sorted_modules
    -gsl
Module IMP.gsl disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module parallel ... yes
-- Running setup_swig_wrappers parallel
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module score_functor ... yes
-- Running setup_swig_wrappers score_functor
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module statistics ... yes
-- Running setup_swig_wrappers statistics
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module system ... yes
-- Running setup_swig_wrappers system
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module core ... yes
-- Running setup_swig_wrappers core
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module container ... yes
-- Running setup_swig_wrappers container
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module modeller ... yes
-- Running setup_swig_wrappers modeller
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module symmetry ... yes
-- Running setup_swig_wrappers symmetry
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module atom ... yes
-- Running setup_swig_wrappers atom
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module scratch ... yes
-- Running setup_swig_wrappers scratch
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module em ... yes
-- Running setup_swig_wrappers em
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module kinematics ... yes
-- Running setup_swig_wrappers kinematics
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module misc ... yes
-- Running setup_swig_wrappers misc
-- RMF already setup
-- Building internal RMF
-- Running setup_cmake.py
-- checking for module 'log4cxx'
--   package 'log4cxx' not found
-- Logging disabled
-- Boost version: 1.51.0
-- Found the following Boost libraries:
--   system
--   filesystem
--   thread
--   program_options
-- Found HDF5: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libhdf5.dylib;debug;/usr/local/Cellar/hdf5/1.8.9/lib/libhdf5.dylib;debug;/usr/local/lib/libsz.dylib;debug;/usr/lib/libz.dylib;debug;/usr/lib/libm.dylib;optimized;/usr/local/Cellar/hdf5/1.8.9/lib/libhdf5.dylib;optimized;/usr/local/lib/libsz.dylib;optimized;/usr/lib/libz.dylib;optimized;/usr/lib/libm.dylib  
-- Compilation of VMD plugin disabled. Defined VMDPLUGIN_INCLUDE_DIR to point to the include path for the header.
-- /usr/local/Cellar/python/2.7.4/Frameworks/Python.framework/Versions/2.7/include/python2.7
-- benchmark_rmf
-- benchmark_size
-- Could NOT find Doxygen (missing:  DOXYGEN_EXECUTABLE) 
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module rmf ... yes
-- Running setup_swig_wrappers rmf
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module rotamer ... yes
-- Running setup_swig_wrappers rotamer
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module saxs ... yes
-- Running setup_swig_wrappers saxs
-- /Users/riccardopellarin/imp-021013/imp-fast
domino is disabled
    Different data/build_info/sorted_modules
    -domino
Module IMP.domino disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module isd ... yes
-- Running setup_swig_wrappers isd
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module restrainer ... yes
-- Running setup_swig_wrappers restrainer
-- /Users/riccardopellarin/imp-021013/imp-fast
em2d is disabled
    Different data/build_info/sorted_modules
    -em2d
Module IMP.em2d disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module example ... IMP.domino not found
    Different data/build_info/sorted_modules
    -example
Module IMP.example disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module multifit ... IMP.domino not found
    Different data/build_info/sorted_modules
    -multifit
Module IMP.multifit disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module pepdock ... IMP.domino not found
    Different data/build_info/sorted_modules
    -pepdock
Module IMP.pepdock disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring module cnmultifit ... libTau not found
    Different data/build_info/sorted_modules
    -cnmultifit
Module IMP.cnmultifit disabled
-- Running setup_swig_dependencies
-- Creating thread pool with 4
    Different src/rmf_swig.deps
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/physics_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/sequence_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/shape_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/external_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/feature_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/alias_decorators.h
    +/Users/riccardopellarin/imp-021013/imp-fast/src/dependency/RMF/include/RMF/publication_decorators.h
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application EMageFit ... no
    Different data/build_info/applications
    -EMageFit
Application EMageFit disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application cnmultifit_tools ... no
    Different data/build_info/applications
    -cnmultifit_tools
Application cnmultifit_tools disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application em_tools ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application example_app ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application foxs ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application integrative_docking ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application ligand_score ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application multifit_tools ... no
    Different data/build_info/applications
    -multifit_tools
Application multifit_tools disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application pdb_tools ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application rmf_tools ... yes
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application saxs_merge ... no
    Different data/build_info/applications
    -saxs_merge
Application saxs_merge disabled
-- /Users/riccardopellarin/imp-021013/imp-fast
Configuring application saxs_tools ... yes
-- Running setup_imppy
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/riccardopellarin/imp-021013/imp-fast
drussel commented 11 years ago

This looks like the same sort of issue with non-system python we keep having. If you don't have a good reason to have a homebrew copy of python installed, I'd just uninstall it and rerun cmake (perhaps after deleting CMakeCache.txt).

On a side note, to make the push for using ninja again, if you are using ninja, then error messages like the first one include the compilation command so we get to see the include paths used. They also don't have all the useless lines after the error message that don't tell us anything.

Pellarin commented 11 years ago

Yes, you're right. It's a homebrew python issue. Mac OS X native python works fine.