* installing *source* package ‘rgeoda’ ... ** package ‘rgeoda’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ 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)