* installing *source* package ‘RMCC’ ... ** package ‘RMCC’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RMCC/src' /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Algorithm.cpp -o Algorithm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CoordinateInterval.cpp -o CoordinateInterval.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DisjointRegions.cpp -o DisjointRegions.o In file included from Algorithm.cpp:26: In file included from ./IUnclassifiedPoints.h:18: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :3:2: note: expanded from here 3 | message("This header is deprecated. Use " "" " instead.") | ^ 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_; | ^ 3 warnings generated. In file included from DisjointRegions.cpp:24: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :325:2: note: expanded from here 325 | message("This header is deprecated. Use " "" " instead.") | ^ /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DuplicatePoints.cpp -o DuplicatePoints.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Geometry3D.cpp -o Geometry3D.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c GridBase.cpp -o GridBase.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c InterpolationRegion.cpp -o InterpolationRegion.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c LocaleUtilities.cpp -o LocaleUtilities.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PointVector.cpp -o PointVector.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c R_MCC.cpp -o R_MCC.o In file included from PointVector.cpp:17: In file included from ./PointVector.h:22: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :12:2: note: expanded from here 12 | message("This header is deprecated. Use " "" " instead.") | ^ /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RasterSurface.cpp -o RasterSurface.o 1 warning generated. In file included from R_MCC.cpp:5: In file included from ./PointVector.h:22: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :322:2: note: expanded from here 322 | message("This header is deprecated. Use " "" " instead.") | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RegularizedSpline.cpp -o RegularizedSpline.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c StackedPoints.cpp -o StackedPoints.o /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SurfaceInterpolation.cpp -o SurfaceInterpolation.o In file included from StackedPoints.cpp:19: In file included from ./IUnclassifiedPoints.h:18: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :394:2: note: expanded from here 394 | message("This header is deprecated. Use " "" " instead.") | ^ In file included from SurfaceInterpolation.cpp:21: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :325:2: note: expanded from here 325 | message("This header is deprecated. Use " "" " instead.") | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -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; | ^ 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c tpsdemo/spline.cpp -o tpsdemo/spline.o In file included from UnclassifiedPoints.cpp:19: In file included from ./UnclassifiedPoints.h:20: In file included from ./IUnclassifiedPoints.h:18: In file included from ./IPointVector.h:19: /data/gannet/ripley/R/test-clang/BH/include/boost/iterator.hpp:10:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] 10 | BOOST_HEADER_DEPRECATED("") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :158:2: note: expanded from here 158 | message("This header is deprecated. Use " "" " instead.") | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -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)