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:

....
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
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