* 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:3:2: note: expanded from here
3 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:325:2: note: expanded from here
325 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:12:2: note: expanded from here
12 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:322:2: note: expanded from here
322 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:394:2: note: expanded from here
394 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:325:2: note: expanded from here
325 | message("This header is deprecated. Use " "<iterator>" " 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 <iterator> instead. [-W#pragma-messages]
10 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^
/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)))
| ^
<scratch space>:158:2: note: expanded from here
158 | message("This header is deprecated. Use " "<iterator>" " 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)