* installing *source* package ‘RMCC’ ...
** this is package ‘RMCC’ version ‘0.1.2’
** package ‘RMCC’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.7’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RMCC/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Algorithm.cpp -o Algorithm.o
In file included from Algorithm.cpp:21:
./Algorithm.h:37:12: warning: private field 'writeNongroundPts_' is not used [-Wunused-private-field]
37 | bool writeNongroundPts_;
| ^
./Algorithm.h:38:12: warning: private field 'writeRasterSurfaces_' is not used [-Wunused-private-field]
38 | bool writeRasterSurfaces_;
| ^
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c CoordinateInterval.cpp -o CoordinateInterval.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c DisjointRegions.cpp -o DisjointRegions.o
In file included from DisjointRegions.cpp:21:
In file included from ./DisjointRegions.h:20:
In file included from ./Grid.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/multi_array.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/base.hpp:25:
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/storage_order.hpp:51:18: warning: 'assign' is deprecated: please use `fill` instead [-Wdeprecated-declarations]
51 | ascending_.assign(true);
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/multi_array_ref.hpp:113:18: note: in instantiation of member function 'boost::general_storage_order<2>::general_storage_order' requested here
113 | base_(base), storage_(c_storage_order()) {
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/multi_array_ref.hpp:463:5: note: in instantiation of member function 'boost::const_multi_array_ref<mcc::InterpolationRegion, 2, mcc::InterpolationRegion *>::const_multi_array_ref' requested here
463 | super_type(base,ranges) { }
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array.hpp:202:5: note: in instantiation of member function 'boost::multi_array_ref<mcc::InterpolationRegion, 2>::multi_array_ref' requested here
202 | super_type((T*)initial_base_,ranges),
| ^
./Grid.h:73:7: note: in instantiation of member function 'boost::multi_array<mcc::InterpolationRegion, 2>::multi_array' requested here
73 | values_(boost::extents[rows][columns]),
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator.h:153:24: note: in instantiation of member function 'mcc::Grid<mcc::InterpolationRegion>::Grid' requested here
153 | ::new ((void*)__p) _Up(std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/allocator_traits.h:296:9: note: in instantiation of function template specialization 'std::allocator<mcc::Grid<mcc::InterpolationRegion>>::construct<mcc::Grid<mcc::InterpolationRegion>, int &, int &, mcc::XYCoordinates, double, double>' requested here
296 | __a.construct(__p, std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:162:33: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<mcc::Grid<mcc::InterpolationRegion>>>::construct<mcc::Grid<mcc::InterpolationRegion>, int &, int &, mcc::XYCoordinates, double, double, 0>' requested here
162 | allocator_traits<_TpAlloc>::construct(__tmp, __get_elem(), std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:736:51: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<mcc::Grid<mcc::InterpolationRegion>, std::allocator<mcc::Grid<mcc::InterpolationRegion>>>::__shared_ptr_emplace<int &, int &, mcc::XYCoordinates, double, double, std::allocator<mcc::Grid<mcc::InterpolationRegion>>, 0>' requested here
736 | ::new ((void*)std::addressof(*__guard.__get())) _ControlBlock(__a, std::forward<_Args>(__args)...);
| ^
/usr/local/clang21/bin/../include/c++/v1/__memory/shared_ptr.h:744:15: note: in instantiation of function template specialization 'std::allocate_shared<mcc::Grid<mcc::InterpolationRegion>, std::allocator<mcc::Grid<mcc::InterpolationRegion>>, int &, int &, mcc::XYCoordinates, double, double, 0>' requested here
744 | return std::allocate_shared<_Tp>(allocator<__remove_cv_t<_Tp> >(), std::forward<_Args>(__args)...);
| ^
DisjointRegions.cpp:233:21: note: in instantiation of function template specialization 'std::make_shared<mcc::Grid<mcc::InterpolationRegion>, int &, int &, mcc::XYCoordinates, double, double, 0>' requested here
233 | regions_ = std::make_shared< Grid<InterpolationRegion> >(nRows, nColumns, raster.lowerLeft(),
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/array.hpp:193:9: note: 'assign' has been explicitly marked deprecated here
193 | BOOST_DEPRECATED( "please use `fill` instead" )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/config/compiler/clang.hpp:346:46: note: expanded from macro 'BOOST_DEPRECATED'
346 | #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg)))
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c DuplicatePoints.cpp -o DuplicatePoints.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Geometry3D.cpp -o Geometry3D.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c GridBase.cpp -o GridBase.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c InterpolationRegion.cpp -o InterpolationRegion.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c LocaleUtilities.cpp -o LocaleUtilities.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c PointVector.cpp -o PointVector.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c R_MCC.cpp -o R_MCC.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RasterSurface.cpp -o RasterSurface.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
In file included from RasterSurface.cpp:19:
In file included from ./RasterSurface.h:19:
In file included from ./Grid.h:18:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/multi_array.hpp:29:
In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/base.hpp:25:
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/storage_order.hpp:51:18: warning: 'assign' is deprecated: please use `fill` instead [-Wdeprecated-declarations]
51 | ascending_.assign(true);
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/multi_array_ref.hpp:113:18: note: in instantiation of member function 'boost::general_storage_order<2>::general_storage_order' requested here
113 | base_(base), storage_(c_storage_order()) {
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array/multi_array_ref.hpp:463:5: note: in instantiation of member function 'boost::const_multi_array_ref<double, 2, double *>::const_multi_array_ref' requested here
463 | super_type(base,ranges) { }
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/multi_array.hpp:202:5: note: in instantiation of member function 'boost::multi_array_ref<double, 2>::multi_array_ref' requested here
202 | super_type((T*)initial_base_,ranges),
| ^
RasterSurface.cpp:66:39: note: in instantiation of member function 'boost::multi_array<double, 2>::multi_array' requested here
66 | boost::multi_array<Coordinate, 2> averages(boost::extents[kernelSize][columns()]);
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/array.hpp:193:9: note: 'assign' has been explicitly marked deprecated here
193 | BOOST_DEPRECATED( "please use `fill` instead" )
| ^
/data/gannet/ripley/R/test-clang/BH/include/boost/config/compiler/clang.hpp:346:46: note: expanded from macro 'BOOST_DEPRECATED'
346 | #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg)))
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RegularizedSpline.cpp -o RegularizedSpline.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c StackedPoints.cpp -o StackedPoints.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c SurfaceInterpolation.cpp -o SurfaceInterpolation.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c UnclassifiedPoints.cpp -o UnclassifiedPoints.o
SurfaceInterpolation.cpp:109:9: warning: variable 'nSplinesComputed' set but not used [-Wunused-but-set-variable]
109 | int nSplinesComputed = 0;
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c tpsdemo/spline.cpp -o tpsdemo/spline.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o RMCC.so ./Algorithm.o ./CoordinateInterval.o ./DisjointRegions.o ./DuplicatePoints.o ./Geometry3D.o ./GridBase.o ./InterpolationRegion.o ./LocaleUtilities.o ./PointVector.o ./R_MCC.o ./RasterSurface.o ./RcppExports.o ./RegularizedSpline.o ./StackedPoints.o ./SurfaceInterpolation.o ./UnclassifiedPoints.o tpsdemo/spline.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RMCC/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RMCC/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RMCC/src'
installing to /data/gannet/ripley/R/packages/tests-clang/RMCC.Rcheck/00LOCK-RMCC/00new/RMCC/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RMCC)