Hi,
I did a checkout of the last release (r12796), but I still have the same compilation error: Errors building: build/src/IMP.algebra.py
Could it depend on the OS version?
> Linking Program modules/algebra/bin/benchmark_rotate > Building version check /project/devel/dbau/imp/imp-r12796/build/lib/IMP/algebra/_version_check.py > Generating swig interface build/swig/IMP_algebra.i from modules/algebra/pyext/swig.i-in > Install file: "modules/algebra/pyext/IMP_algebra_bounding_box.i" as "build/swig/IMP_algebra_bounding_box.i" > Install file: "modules/algebra/pyext/IMP_algebra_matrix2d.i" as "build/swig/IMP_algebra_matrix2d.i" > Install file: "modules/algebra/pyext/IMP_algebra_matrix3d.i" as "build/swig/IMP_algebra_matrix3d.i" > Install file: "modules/algebra/pyext/IMP_algebra_spherical_coords.i" as "build/swig/IMP_algebra_spherical_coords.i" > Install file: "modules/algebra/pyext/IMP_algebra_transformation2d.i" as "build/swig/IMP_algebra_transformation2d.i" > Install file: "modules/algebra/pyext/IMP_algebra_transformation3d.i" as "build/swig/IMP_algebra_transformation3d.i" > Install file: "modules/algebra/pyext/IMP_algebra_types.i" as "build/swig/IMP_algebra_types.i" > Install file: "modules/algebra/pyext/IMP_algebra_vector.i" as "build/swig/IMP_algebra_vector.i" > Install file: "build/swig/IMP_algebra.i" as "build/data/swig/IMP_algebra.i" > Running swig on file build/swig/IMP_algebra.i > /apps/SWIG/2.0.4/bin/swig -castmode -interface _IMP_algebra -DPySwigIterator=IMP_ALGEBRA_PySwigIterator -DSwigPyIterator=IMP_ALGEBRA_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /project/devel/dbau/imp/imp-r12796/build/src/IMP_algebra_wrap.cpp-in -oh /project/devel/dbau/imp/imp-r12796/build/src/IMP_algebra_wrap.h-in -Ibuild/swig -I/apps/IMP/include/ -I/apps/BOOST/1_48_0/include -I/apps/CGAL/3.9/include -I/project/devel/dbau/imp/imp-r12796/build/include -I/apps/SWIG/2.0.4/bin -DIMP_SWIG /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:243: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:244: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:245: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:246: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:247: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:248: Error: Template 'GridD' undefined. > /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:249: Error: Template 'GridD' undefined. > scons: *** Error 7 > Running swig on file build/swig/IMP_algebra.i > scons: *** [build/src/IMP.algebra.py] Error 7 > scons: building terminated because of errors. > > > IMP configuration: > boost ='yes' > boostlibs ='' > boostversion ='104800' > boostlibsuffix ='' > endian ='little' > boost_filesystem ='yes' > boost_filesystemlibs='boost_filesystem' > google_perftools_profile='no' > hdf5 ='no' > boost_thread ='yes' > boost_threadlibs ='boost_thread' > cgal ='no' > ann ='no' > gsl ='no' > fftw3 ='no' > boost_programoptions='no' > opencv21 ='no' > opencv22 ='no' > eigen3 ='no' > cholmod ='no' > build ='fast' > prefix ='/usr' > local ='True' > pythonpath ='/project/devel/dbau/imp/imp-r12796' > libpath ='/apps/BOOST/1_48_0/lib' > ldlibpath ='/project/devel/dbau/imp/imp-r12796' > swigpath ='/apps/SWIG/2.0.4/bin' > datapath ='/project/devel/dbau/imp/imp-r12796' > cxxcompiler ='g++' > cxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > pythoncxxflags ='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > bincxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > shliblinkflags =' -shared' > arliblinkflags ='' > binlinkflags ='' > pythonlinkflags =' -shared' > rpath ='True' > static ='False' > pythonsosuffix ='.so' > pkgconfig ='True' > path ="/apps/GCC/4.6.2/bin:/apps/PYTHON/2.7.2/bin:/apps/modules//wrappers/fortran:/apps/modules//wrappers/c++:/apps/modules//wrappers/c:/opt/mpi/mpibull2-1.3.9-18.s/bin:/opt/intel/Compiler/11.0/069/bin/intel64:/usr/kerberos/bin:/opt/cuda//bin:/usr/local/bin:/bin:/usr/bin:/home/devel/dbau/bin" > python ="/apps/PYTHON/2.7.2/bin/python" > > > Enabled dependencies: Boost.FileSystem, Boost.Thread, Boost > Disabled dependencies: HDF5, OpenCV21, CGAL, ANN, Boost.ProgramOptions, modeller, CHOLMOD, eigen3, google_perftools_profile, FFTW3, GSL, OpenCV22 > > Enabled modules: em, kernel, scratch, domino, misc, fivec, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, restrainer, example_system_local, base, atom, compatibility, pepdock, display > Disabled modules: rmf, RMF, cgal, multifit, gsl, modeller, em2d, isd > > Enabled applications: em_tools > Disabled applications: rmf_tools, pdb_tools, saxs_merge, saxs_tools, em3d_dock, rnapii, foxsdock, nup84, example_system, nmr_rtc, multifit_tools, em2d_dock, ligand_score, foxs > > Enabled systems: Groel > > Errors building: > build/src/IMP.algebra.py
On Feb 21, 2012, at 11:11 PM, Daniel Russel wrote:
> To fix the last problem, I would suggest removing all build and scons > files (if you are building out or source, do "rm -rf .scon* modules > build applications" if you are building in source, then just do "rm > -rf .scons* build" and you are probably OK. Scons gets easily > confused. > > On Tue, Feb 21, 2012 at 10:27 AM, Ben Webb ben@salilab.org wrote: >> On 02/21/2012 08:36 AM, Davide Baů wrote: >>> >>> On Feb 21, 2012, at 5:23 PM, Ben Webb wrote: >>>> >>>> Is there a reason this machine is years out of date? (The latest >>>> update for RHEL 5 is 5.7.) It seems entirely possible that a bug in >>>> one of the system headers was fixed in the interim. >>> >>> Actually I don't know. I will contact the informatics department to >>> ask if it is possible to update the system (unfortunately we can >>> just "use" the cluster.) >> >> >> You can point them to http://en.wikipedia.org/wiki/RHEL#Version_history >> 5.3 has been obsolete since 5.4 was released in September 2009. >> >>> I got a error on the algebra module: Errors building: >>> build/src/IMP.algebra.py. It's curious that there's a red box on the >>> algebra module on Mac while it compiled with no errors on my Mac. >> >> >> It's a different Mac (32-bit code is built on a 10.4 - Tiger - machine). >> Chances are your machine is more similar to our Snow Leopard 64-bit build >> machine. I've added more descriptive labels to this page, which should show >> up tomorrow. >> >> ... >>> >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:243: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:244: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:245: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:246: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:247: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:248: >>> Error: Template 'GridD' undefined. >>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:249: >> >> >> Odd. The SWIG file should be parsing algebra's GridD.h header, which defines >> that template. But Daniel did make some changes there recently - are you >> sure you don't have a mismatch of versions somewhere (perhaps an older >> version of GridD.h paired with a newer SWIG interface)? I'd suggest a fresh >> checkout to be sure. >> >> Ben >> -- >> ben@salilab.org http://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev