* installing *source* package ‘rgeoda’ ...
** package ‘rgeoda’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.2’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rgeoda/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/libgeoda.cpp -o libgeoda/libgeoda.o
In file included from libgeoda/libgeoda.cpp:14:
In file included from libgeoda/./shape/centroid.h:14:
In file included from libgeoda/./shape/ttmath/ttmath.h:58:
In file included from libgeoda/./shape/ttmath/ttmathbig.h:46:
In file included from libgeoda/./shape/ttmath/ttmathint.h:48:
libgeoda/./shape/ttmath/ttmathuint.h:1350:10: warning: variable 'c' set but not used [-Wunused-but-set-variable]
1350 | uint i, c, xc, yc;
| ^
libgeoda/libgeoda.cpp:204:9: warning: variable 'shppointtotal' set but not used [-Wunused-but-set-variable]
204 | int shppointtotal = 0, shppoint = 0;
| ^
libgeoda/libgeoda.cpp:269:9: warning: variable 'shppointtotal' set but not used [-Wunused-but-set-variable]
269 | int shppointtotal = 0, shppoint = 0, shpringtotal = 0, shpring = 0;
| ^
libgeoda/libgeoda.cpp:269:42: warning: variable 'shpringtotal' set but not used [-Wunused-but-set-variable]
269 | int shppointtotal = 0, shppoint = 0, shpringtotal = 0, shpring = 0;
| ^
libgeoda/libgeoda.cpp:269:60: warning: variable 'shpring' set but not used [-Wunused-but-set-variable]
269 | int shppointtotal = 0, shppoint = 0, shpringtotal = 0, shpring = 0;
| ^
5 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/gda_sa.cpp -o libgeoda/gda_sa.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/gda_data.cpp -o libgeoda/gda_data.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/gda_weights.cpp -o libgeoda/gda_weights.o
libgeoda/gda_weights.cpp:204:9: warning: variable 'line_cnt' set but not used [-Wunused-but-set-variable]
204 | int line_cnt = 0;
| ^
libgeoda/gda_weights.cpp:448:6: warning: variable 'line_num' set but not used [-Wunused-but-set-variable]
448 | int line_num = 1;
| ^
libgeoda/gda_weights.cpp:502:9: warning: variable 'swmType' set but not used [-Wunused-but-set-variable]
502 | int swmType = 0; // old
| ^
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/gda_clustering.cpp -o libgeoda/gda_clustering.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/GenGeomAlgs.cpp -o libgeoda/GenGeomAlgs.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/GenUtils.cpp -o libgeoda/GenUtils.o
libgeoda/GenUtils.cpp:122:12: warning: variable 'SP' set but not used [-Wunused-but-set-variable]
122 | double SP=0, SE=0;
| ^
libgeoda/GenUtils.cpp:122:18: warning: variable 'SE' set but not used [-Wunused-but-set-variable]
122 | double SP=0, SE=0;
| ^
libgeoda/GenUtils.cpp:2047:9: warning: variable 'max_gvf_ind' set but not used [-Wunused-but-set-variable]
2047 | int max_gvf_ind = 0;
| ^
3 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/SpatialIndAlgs.cpp -o libgeoda/SpatialIndAlgs.o
libgeoda/SpatialIndAlgs.cpp:120:7: warning: variable 'qcnt' set but not used [-Wunused-but-set-variable]
120 | int qcnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:104:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
104 | int cnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:132:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
132 | int cnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:340:9: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
340 | int cnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:728:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
728 | int cnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:833:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
833 | int cnt=0;
| ^
libgeoda/SpatialIndAlgs.cpp:1001:6: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
1001 | int cnt=0;
| ^
7 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/pg/geoms.cpp -o libgeoda/pg/geoms.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/pg/utils.cpp -o libgeoda/pg/utils.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/shapelib/dbfopen.cpp -o libgeoda/shapelib/dbfopen.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/shapelib/safileio.cpp -o libgeoda/shapelib/safileio.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/shapelib/shpopen.cpp -o libgeoda/shapelib/shpopen.o
libgeoda/shapelib/shpopen.cpp:988:21: warning: variable 'nCurrentRecordOffset' set but not used [-Wunused-but-set-variable]
988 | unsigned int nCurrentRecordOffset = 0;
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/PointsToContigWeights.cpp -o libgeoda/weights/PointsToContigWeights.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/PolysToContigWeights.cpp -o libgeoda/weights/PolysToContigWeights.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/GalWeight.cpp -o libgeoda/weights/GalWeight.o
libgeoda/weights/GalWeight.cpp:120:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
120 | std::sort(undef_obj_positions.begin(),
| ^
libgeoda/weights/GalWeight.cpp:116:5: note: previous statement is here
116 | if (undef_obj_positions.empty())
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/GwtWeight.cpp -o libgeoda/weights/GwtWeight.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/GeodaWeight.cpp -o libgeoda/weights/GeodaWeight.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/weights/VoronoiUtils.cpp -o libgeoda/weights/VoronoiUtils.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/BatchLISA.cpp -o libgeoda/sa/BatchLISA.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/BatchLocalMoran.cpp -o libgeoda/sa/BatchLocalMoran.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/LISA.cpp -o libgeoda/sa/LISA.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/MultiGeary.cpp -o libgeoda/sa/MultiGeary.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/MultiJoinCount.cpp -o libgeoda/sa/MultiJoinCount.o
libgeoda/sa/MultiJoinCount.cpp:237:9: warning: variable 'validNeighbors' set but not used [-Wunused-but-set-variable]
237 | int validNeighbors = 0;
| ^
libgeoda/sa/MultiJoinCount.cpp:255:9: warning: variable 'validNeighbors' set but not used [-Wunused-but-set-variable]
255 | int validNeighbors = 0;
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/UniG.cpp -o libgeoda/sa/UniG.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/UniGeary.cpp -o libgeoda/sa/UniGeary.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/UniGstar.cpp -o libgeoda/sa/UniGstar.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/UniJoinCount.cpp -o libgeoda/sa/UniJoinCount.o
libgeoda/sa/UniJoinCount.cpp:237:9: warning: variable 'validNeighbors' set but not used [-Wunused-but-set-variable]
237 | int validNeighbors = 0;
| ^
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/UniLocalMoran.cpp -o libgeoda/sa/UniLocalMoran.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/sa/BiLocalMoran.cpp -o libgeoda/sa/BiLocalMoran.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/fastcluster.cpp -o libgeoda/clustering/fastcluster.o
In file included from libgeoda/clustering/fastcluster.cpp:8:
libgeoda/clustering/fastcluster.h:912:35: warning: bitwise negation of a boolean expression; did you mean logical negation? [-Wbool-operation]
912 | NTF += (Xb(i,k) & ~Xb(j,k)) ;
| ^~~~~~~~
| !
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/redcap.cpp -o libgeoda/clustering/redcap.o
libgeoda/clustering/redcap.cpp:392:9: warning: variable 'evaluated' set but not used [-Wunused-but-set-variable]
392 | int evaluated = 0;
| ^
libgeoda/clustering/redcap.cpp:529:25: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
529 | int cnt1=0, cnt2=0, cnt=0;
| ^
libgeoda/clustering/redcap.cpp:723:12: warning: variable 'sum_length' set but not used [-Wunused-but-set-variable]
723 | double sum_length=0;
| ^
libgeoda/clustering/redcap.cpp:990:9: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
990 | int cnt = 0;
| ^
libgeoda/clustering/redcap.cpp:1272:9: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
1272 | int cnt = 0;
| ^
5 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/redcap_wrapper.cpp -o libgeoda/clustering/redcap_wrapper.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/azp.cpp -o libgeoda/clustering/azp.o
libgeoda/clustering/azp.cpp:1448:9: warning: variable 'totalMoves' set but not used [-Wunused-but-set-variable]
1448 | int totalMoves = 0;
| ^
libgeoda/clustering/azp.cpp:1449:9: warning: variable 'acceptedMoves' set but not used [-Wunused-but-set-variable]
1449 | int acceptedMoves = 0;
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/maxp_wrapper.cpp -o libgeoda/clustering/maxp_wrapper.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/azp_wrapper.cpp -o libgeoda/clustering/azp_wrapper.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/schc_wrapper.cpp -o libgeoda/clustering/schc_wrapper.o
In file included from libgeoda/clustering/schc_wrapper.cpp:10:
libgeoda/clustering/fastcluster.h:912:35: warning: bitwise negation of a boolean expression; did you mean logical negation? [-Wbool-operation]
912 | NTF += (Xb(i,k) & ~Xb(j,k)) ;
| ^~~~~~~~
| !
1 warning generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/cluster.cpp -o libgeoda/clustering/cluster.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/joincount_ratio.cpp -o libgeoda/clustering/joincount_ratio.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/make_spatial.cpp -o libgeoda/clustering/make_spatial.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/clustering/spatial_validation.cpp -o libgeoda/clustering/spatial_validation.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/ANN.cpp -o libgeoda/knn/ANN.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/perf.cpp -o libgeoda/knn/perf.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_util.cpp -o libgeoda/knn/kd_util.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_tree.cpp -o libgeoda/knn/kd_tree.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_split.cpp -o libgeoda/knn/kd_split.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_search.cpp -o libgeoda/knn/kd_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_pr_search.cpp -o libgeoda/knn/kd_pr_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_fix_rad_search.cpp -o libgeoda/knn/kd_fix_rad_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/kd_dump.cpp -o libgeoda/knn/kd_dump.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/brute.cpp -o libgeoda/knn/brute.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/bd_tree.cpp -o libgeoda/knn/bd_tree.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/bd_search.cpp -o libgeoda/knn/bd_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/bd_pr_search.cpp -o libgeoda/knn/bd_pr_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 libgeoda/knn/bd_fix_rad_search.cpp -o libgeoda/knn/bd_fix_rad_search.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 rcpp_rgeoda.cpp -o rcpp_rgeoda.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 rcpp_weights.cpp -o rcpp_weights.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 rcpp_utils.cpp -o rcpp_utils.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 rcpp_lisa.cpp -o rcpp_lisa.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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 rcpp_clustering.cpp -o rcpp_clustering.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I./libgeoda -D__USE_PTHREAD__ -D__RGEODA__ -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++17 -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 rgeoda.so ./libgeoda/libgeoda.o ./libgeoda/gda_sa.o ./libgeoda/gda_data.o ./libgeoda/gda_weights.o ./libgeoda/gda_clustering.o ./libgeoda/GenGeomAlgs.o ./libgeoda/GenUtils.o ./libgeoda/SpatialIndAlgs.o ./libgeoda/pg/geoms.o ./libgeoda/pg/utils.o ./libgeoda/shapelib/dbfopen.o ./libgeoda/shapelib/safileio.o ./libgeoda/shapelib/shpopen.o ./libgeoda/weights/PointsToContigWeights.o ./libgeoda/weights/PolysToContigWeights.o ./libgeoda/weights/GalWeight.o ./libgeoda/weights/GwtWeight.o ./libgeoda/weights/GeodaWeight.o ./libgeoda/weights/VoronoiUtils.o ./libgeoda/sa/BatchLISA.o ./libgeoda/sa/BatchLocalMoran.o ./libgeoda/sa/LISA.o ./libgeoda/sa/MultiGeary.o ./libgeoda/sa/MultiJoinCount.o ./libgeoda/sa/UniG.o ./libgeoda/sa/UniGeary.o ./libgeoda/sa/UniGstar.o ./libgeoda/sa/UniJoinCount.o ./libgeoda/sa/UniLocalMoran.o ./libgeoda/sa/BiLocalMoran.o ./libgeoda/clustering/fastcluster.o ./libgeoda/clustering/redcap.o ./libgeoda/clustering/redcap_wrapper.o ./libgeoda/clustering/azp.o ./libgeoda/clustering/maxp_wrapper.o ./libgeoda/clustering/azp_wrapper.o ./libgeoda/clustering/schc_wrapper.o ./libgeoda/clustering/cluster.o ./libgeoda/clustering/joincount_ratio.o ./libgeoda/clustering/make_spatial.o ./libgeoda/clustering/spatial_validation.o ./libgeoda/knn/ANN.o ./libgeoda/knn/perf.o ./libgeoda/knn/kd_util.o ./libgeoda/knn/kd_tree.o ./libgeoda/knn/kd_split.o ./libgeoda/knn/kd_search.o ./libgeoda/knn/kd_pr_search.o ./libgeoda/knn/kd_fix_rad_search.o ./libgeoda/knn/kd_dump.o ./libgeoda/knn/brute.o ./libgeoda/knn/bd_tree.o ./libgeoda/knn/bd_search.o ./libgeoda/knn/bd_pr_search.o ./libgeoda/knn/bd_fix_rad_search.o rcpp_rgeoda.o rcpp_weights.o rcpp_utils.o rcpp_lisa.o rcpp_clustering.o RcppExports.o -pthread
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rgeoda/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rgeoda/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rgeoda/src'
installing to /data/gannet/ripley/R/packages/tests-clang/rgeoda.Rcheck/00LOCK-rgeoda/00new/rgeoda/libs
** R
** 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 (rgeoda)