* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* 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: ‘Debian clang version 21.1.8 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnMqtZP/R.INSTALL328cde17214839/RMCC/src'
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -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.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c CoordinateInterval.cpp -o CoordinateInterval.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array.hpp:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array/base.hpp:25:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array/storage_order.hpp:51:18: warning: 'assign' is deprecated: please use `fill` instead [-Wdeprecated-declarations]
51 | ascending_.assign(true);
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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()) {
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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) { }
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/stl_construct.h:133:38: note: in instantiation of member function 'mcc::Grid<mcc::InterpolationRegion>::Grid' requested here
133 | ::new(static_cast<void*>(__p)) _Tp(std::forward<_Args>(__args)...);
| ^
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/alloc_traits.h:805:9: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
805 | { std::_Construct(__p, std::forward<_Args>(__args)...); }
| ^
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/shared_ptr_base.h:970:6: note: in instantiation of function template specialization 'std::_Sp_counted_ptr_inplace<mcc::Grid<mcc::InterpolationRegion>, std::allocator<void>, __gnu_cxx::_S_atomic>::_Sp_counted_ptr_inplace<int &, int &, mcc::XYCoordinates, double, double>' requested here
970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...);
| ^
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/shared_ptr_base.h:1719:14: note: in instantiation of function template specialization 'std::__shared_count<>::__shared_count<mcc::Grid<mcc::InterpolationRegion>, std::allocator<void>, int &, int &, mcc::XYCoordinates, double, double>' requested here
1719 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...)
| ^
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/shared_ptr.h:463:4: note: in instantiation of function template specialization 'std::__shared_ptr<mcc::Grid<mcc::InterpolationRegion>>::__shared_ptr<std::allocator<void>, int &, int &, mcc::XYCoordinates, double, double>' requested here
463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...)
| ^
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/shared_ptr.h:1007:14: note: in instantiation of function template specialization 'std::shared_ptr<mcc::Grid<mcc::InterpolationRegion>>::shared_ptr<std::allocator<void>, int &, int &, mcc::XYCoordinates, double, double>' requested here
1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a},
| ^
DisjointRegions.cpp:233:21: note: in instantiation of function template specialization 'std::make_shared<mcc::Grid<mcc::InterpolationRegion>, int &, int &, mcc::XYCoordinates, double, double>' requested here
233 | regions_ = std::make_shared< Grid<InterpolationRegion> >(nRows, nColumns, raster.lowerLeft(),
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/array.hpp:193:9: note: 'assign' has been explicitly marked deprecated here
193 | BOOST_DEPRECATED( "please use `fill` instead" )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c DuplicatePoints.cpp -o DuplicatePoints.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c Geometry3D.cpp -o Geometry3D.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c GridBase.cpp -o GridBase.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c InterpolationRegion.cpp -o InterpolationRegion.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c LocaleUtilities.cpp -o LocaleUtilities.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c PointVector.cpp -o PointVector.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c R_MCC.cpp -o R_MCC.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RasterSurface.cpp -o RasterSurface.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 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array.hpp:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array/base.hpp:25:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/multi_array/storage_order.hpp:51:18: warning: 'assign' is deprecated: please use `fill` instead [-Wdeprecated-declarations]
51 | ascending_.assign(true);
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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()) {
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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) { }
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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()]);
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include/boost/array.hpp:193:9: note: 'assign' has been explicitly marked deprecated here
193 | BOOST_DEPRECATED( "please use `fill` instead" )
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RegularizedSpline.cpp -o RegularizedSpline.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c StackedPoints.cpp -o StackedPoints.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c SurfaceInterpolation.cpp -o SurfaceInterpolation.o
SurfaceInterpolation.cpp:109:9: warning: variable 'nSplinesComputed' set but not used [-Wunused-but-set-variable]
109 | int nSplinesComputed = 0;
| ^
1 warning generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c UnclassifiedPoints.cpp -o UnclassifiedPoints.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c tpsdemo/spline.cpp -o tpsdemo/spline.o
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnMqtZP/R.INSTALL328cde17214839/RMCC/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnMqtZP/R.INSTALL328cde17214839/RMCC/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnMqtZP/R.INSTALL328cde17214839/RMCC/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)