Maybe it has nothing to do with your problem, but I remarked sometimes the latest svn version does not compile. In these cases, I go back to the latest imp version I could compile (either with "svn update -r…" or more drastically with a full src reinstall "svn co -r"). For me, the v7943 compiled successfully on various linux machines as well as on my macbook. you should also want to use the -k option to scons in order to prevent it to crash and stop when one module cannot compile.
Hope this helps
--Ben
Le 21 janv. 2011 à 15:26, Robert Brynmor Fenwick a écrit :
> > 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
Dr. Benjamin SCHWARZ Biocomputing group Email : schwarz@igbmc.fr Voice : +33 (0)3 68 85 47 30 FAX : +33 (0)3 68 85 47 18
Structural Biology & Genomics Dept. - IGBMC 1 rue Laurent Fries BP 10142 F - 67404 Illkirch CEDEX
