Checking configuration ------------------------------ Getting Dependencies -------------------------------------  Checkouting micrograph_cleaner_em ... Already up to date.  Checkouting CTPL ...  git checkout master Already on 'master' Your branch is up to date with 'origin/master'. Already up to date. Getting sources -------------------------------------  Checkouting xmippCore ... Already up to date.  Checkouting xmippViz ... Already up to date.  Checkouting scipion-em-xmipp ... Already up to date.  Checkouting xmipp ... Building Dependencies ------------------------------------- Compiling -------------------------------------------  scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `lib/libXmippCore.so' is up to date. scons: `lib/xmippCore.so' is up to date. scons: done building targets.  scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... g++ -o libraries/data/filters.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/data/filters.cpp g++ -o libraries/data/sampling.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/data/sampling.cpp g++ -o libraries/data/steerable.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/data/steerable.cpp g++ -o libraries/dimred/pca.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/dimred/pca.cpp g++ -o libraries/dimred/probabilisticPCA.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/dimred/probabilisticPCA.cpp g++ -o libraries/dimred/spe.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/dimred/spe.cpp g++ -o libraries/dimred/transform_dimred.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/dimred/transform_dimred.cpp g++ -o libraries/interface/docfile.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/interface/docfile.cpp libraries/data/sampling.cpp: In member function 'void Sampling::removeRedundantPoints(int, int)': libraries/data/sampling.cpp:978:40: error: no matching function for call to 'Euler_angles2matrix(int, int, int, Matrix2D&)' Euler_angles2matrix(0, 90, 0, A); ^ libraries/data/sampling.cpp:978:40: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:978:40: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0, 90, 0, A); ^ libraries/data/sampling.cpp:1009:49: error: no matching function for call to 'Euler_angles2matrix(int, double, int, Matrix2D&)' Euler_angles2matrix(0,31.7174745559,0, A); ^ libraries/data/sampling.cpp:1009:49: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:1009:49: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0,31.7174745559,0, A); ^ libraries/data/sampling.cpp:1040:50: error: no matching function for call to 'Euler_angles2matrix(int, double, int, Matrix2D&)' Euler_angles2matrix(0,-31.7174745559,0, A); ^ libraries/data/sampling.cpp:1040:50: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:1040:50: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0,-31.7174745559,0, A); ^ libraries/data/sampling.cpp:1110:40: error: no matching function for call to 'Euler_angles2matrix(int, int, int, Matrix2D&)' Euler_angles2matrix(0, 90, 0, A); ^ libraries/data/sampling.cpp:1110:40: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:1110:40: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0, 90, 0, A); ^ libraries/data/sampling.cpp:1143:49: error: no matching function for call to 'Euler_angles2matrix(int, double, int, Matrix2D&)' Euler_angles2matrix(0,31.7174745559,0, A); ^ libraries/data/sampling.cpp:1143:49: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:1143:49: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0,31.7174745559,0, A); ^ libraries/data/sampling.cpp:1181:50: error: no matching function for call to 'Euler_angles2matrix(int, double, int, Matrix2D&)' Euler_angles2matrix(0,-31.7174745559,0, A); ^ libraries/data/sampling.cpp:1181:50: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/symmetries.h:36, from libraries/data/sampling.h:35, from libraries/data/sampling.cpp:25: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/sampling.cpp:1181:50: note: deduced conflicting types for parameter 'T' ('int' and 'double') Euler_angles2matrix(0,-31.7174745559,0, A); ^ libraries/data/filters.cpp: In function 'Matrix2D centerImage(MultidimArray&, CorrelationAux&, RotationalCorrelationAux&, int, bool)': libraries/data/filters.cpp:3345:36: error: no matching function for call to 'rotation2DMatrix(int, Matrix2D&)' rotation2DMatrix(-90, R); ^ libraries/data/filters.cpp:3345:36: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image_base.h:31:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image.h:34, from libraries/data/filters.h:32, from libraries/data/filters.cpp:26: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:97:6: note: template void rotation2DMatrix(T, Matrix2D&, bool) void rotation2DMatrix(T ang, Matrix2D &m, bool homogeneous=true); ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:97:6: note: template argument deduction/substitution failed: libraries/data/filters.cpp:3345:36: note: deduced conflicting types for parameter 'T' ('int' and 'double') rotation2DMatrix(-90, R); ^ libraries/data/steerable.cpp: In member function 'void MissingWedge::removeWedge(MultidimArray&) const': libraries/data/steerable.cpp:37:46: error: no matching function for call to 'Euler_angles2matrix(const double&, const double&, int, Matrix2D&)' Euler_angles2matrix(rotPos,tiltPos,0,Epos); ^ libraries/data/steerable.cpp:37:46: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image_base.h:31, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image.h:34, from libraries/data/filters.h:32, from libraries/data/steerable.cpp:30: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/steerable.cpp:37:46: note: deduced conflicting types for parameter 'T' ('double' and 'int') Euler_angles2matrix(rotPos,tiltPos,0,Epos); ^ libraries/data/steerable.cpp:38:46: error: no matching function for call to 'Euler_angles2matrix(const double&, const double&, int, Matrix2D&)' Euler_angles2matrix(rotNeg,tiltNeg,0,Eneg); ^ libraries/data/steerable.cpp:38:46: note: candidate is: In file included from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/transformations.h:38:0, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image_base.h:31, from /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/xmipp_image.h:34, from libraries/data/filters.h:32, from libraries/data/steerable.cpp:30: /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template void Euler_angles2matrix(T, T, T, Matrix2D&, bool) void Euler_angles2matrix(T a, T b, T g, Matrix2D& A, ^ /home/guest/xmipp-bundle/xmipp/src/xmippCore/core/geometry.h:574:6: note: template argument deduction/substitution failed: libraries/data/steerable.cpp:38:46: note: deduced conflicting types for parameter 'T' ('double' and 'int') Euler_angles2matrix(rotNeg,tiltNeg,0,Eneg); ^ g++ -o libraries/interface/frm.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/scipion/software/include -fPIC -I/home/guest/scipion/software/include/python2.7 -I/home/guest/scipion/software/lib/python2.7/site-packages -I/home/guest/scipion/software/lib/python2.7/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/interface/frm.cpp scons: *** [libraries/data/steerable.os] Error 1 scons: *** [libraries/data/sampling.os] Error 1 scons: *** [libraries/data/filters.os] Error 1 scons: building terminated because of errors.  Some error occurred during the compilation of 'xmipp'.