My guess is that you checked things in between my checking in patches last night and found IMP in an inconsistent state. Do you still get this behavior on the head version? eg "svn co http://svn.salilab.org/imp/trunk imp" Thanks. Daniel
On Jan 21, 2011, at 6:26 AM, Robert Brynmor Fenwick wrote:
> > Hi, > > I've just checked out this: > > svn co http://svn.salilab.org/imp/branches/stable imp > .... > Checked out revision 8381. > > and tried to compile it, I am using the same compiler that compiles the imp 1.0 version so I don't think it is a compiler problem > > Install file: "modules/cgal/include/internal/knn.h" as "build/include/IMP/cgal/internal/knn.h" > g++ -o modules/cgal/src/internal/knn.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/knn.cpp > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, unsigned int, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, double, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, unsigned int, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, double, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, unsigned int, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' > modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, double, double, IMP::Ints&) const': > modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' > Install file: "modules/cgal/include/internal/polygons.h" as "build/include/IMP/cgal/internal/polygons.h" > g++ -o modules/cgal/src/internal/polygons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polygons.cpp > Install file: "modules/cgal/include/internal/polyhedrons.h" as "build/include/IMP/cgal/internal/polyhedrons.h" > Install file: "modules/algebra/include/Plane3D.h" as "build/include/IMP/algebra/Plane3D.h" > g++ -o modules/cgal/src/internal/polyhedrons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polyhedrons.cpp > modules/cgal/src/internal/polyhedrons.cpp: In function 'std::vector<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > >, std::allocator<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > > > > IMP::cgal::internal::<unnamed>::get_facets(CGAL::Nef_polyhedron_3<K, typename CGAL::Default_items<Kernel>::Items, bool>&)': > modules/cgal/src/internal/polyhedrons.cpp:99: internal compiler error: Bus error > Please submit a full bug report, > with preprocessed source if appropriate. > See URL:http://developer.apple.com/bugreporter for instructions. > scons: *** [modules/cgal/src/internal/polyhedrons.os] Error 1 > scons: building terminated because of errors. > > > Enabled dependencies: python, NetCDF, FFTW3, CGAL, Boost.FileSystem, Boost.ProgramOptions > Disabled/unfound optional dependencies: ANN, ExampleLib, GSL, OpenCV, Bullet, OpenMM > > Enabled modules: kernel, cgal, algebra, core, container, atom, display, domino, em, example, misc, saxs, helper, statistics, restrainer, domino2, multifit, benchmark > Disabled modules: gsl, modeller, em2d, bullet, openmm > Errors building: > modules/cgal/src/internal/polyhedrons.os > > -- > R. Bryn Fenwick > robert.fenwick@irbbarcelona.org > Post-doctoral fellow > Chemistry and Molecular Pharmacology Programme > Institute for Research in Biomedicine (IRB Barcelona) > Parc Científic de Barcelona > Baldiri Reixac 10, 08028 Barcelona, SPAIN > Tel. (+34) 9340 20460 > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users