* installing *source* package ‘TukeyRegion’ ... ** package ‘TukeyRegion’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TukeyRegion/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 TukeyRegionR.cpp -o TukeyRegionR.o In file included from TukeyRegionR.cpp:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 TukeyRegion.cpp -o TukeyRegion.o In file included from TukeyRegion.cpp:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ In file included from TukeyRegion.cpp:6: In file included from ./TukeyRegion.h:23: ./common.h:26:12: warning: unused function 'compareAsc' [-Wunused-function] 26 | static int compareAsc(IndexRec x, IndexRec y){ | ^~~~~~~~~~ 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 common.cpp -o common.o In file included from common.cpp:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ common.cpp:960:15: warning: variable 'pointsAbove' set but not used [-Wunused-but-set-variable] 960 | int pointsAbove = 0;int pointsBelow = 0; | ^ common.cpp:1178:15: warning: variable 'pointsAbove' set but not used [-Wunused-but-set-variable] 1178 | int pointsAbove = 0;int pointsBelow = 0; | ^ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 qhAdapter.cpp -o qhAdapter.o In file included from qhAdapter.cpp:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ qhAdapter.cpp:32:22: warning: unused variable 'vertexp' [-Wunused-variable] 32 | vertexT *vertex, **vertexp; | ^~~~~~~ In file included from qhAdapter.cpp:6: In file included from ./TukeyRegion.h:23: ./common.h:26:12: warning: unused function 'compareAsc' [-Wunused-function] 26 | static int compareAsc(IndexRec x, IndexRec y){ | ^~~~~~~~~~ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 TConvexBody.cpp -o TConvexBody.o In file included from TConvexBody.cpp:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ TConvexBody.cpp:184:24: warning: unused variable 'vertexp' [-Wunused-variable] 184 | vertexT *vertex, **vertexp; | ^~~~~~~ TConvexBody.cpp:846:8: warning: unused variable 'exists' [-Wunused-variable] 846 | bool exists = true; | ^~~~~~ In file included from TConvexBody.cpp:6: In file included from ./TukeyRegion.h:23: ./common.h:26:12: warning: unused function 'compareAsc' [-Wunused-function] 26 | static int compareAsc(IndexRec x, IndexRec y){ | ^~~~~~~~~~ 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 TRegion.cpp -o TRegion.o In file included from TRegion.cpp:6: In file included from ./TRegion.h:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ TRegion.cpp:308:8: warning: unused variable 'innerPointFound' [-Wunused-variable] 308 | bool innerPointFound = false; | ^~~~~~~~~~~~~~~ In file included from TRegion.cpp:6: In file included from ./TRegion.h:6: In file included from ./TukeyRegion.h:23: ./common.h:26:12: warning: unused function 'compareAsc' [-Wunused-function] 26 | static int compareAsc(IndexRec x, IndexRec y){ | ^~~~~~~~~~ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 TkRegions.cpp -o TkRegions.o In file included from TkRegions.cpp:6: In file included from ./TkRegions.h:6: In file included from ./TukeyRegion.h:24: ./hypermatrix.h:37:6: warning: unused variable 'size' [-Wunused-variable] 37 | int size = index.size(); | ^~~~ In file included from TkRegions.cpp:6: In file included from ./TkRegions.h:6: In file included from ./TukeyRegion.h:23: ./common.h:26:12: warning: unused function 'compareAsc' [-Wunused-function] 26 | static int compareAsc(IndexRec x, IndexRec y){ | ^~~~~~~~~~ 2 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/geom.c -o libqhull/geom.o libqhull/geom.c:584:24: warning: variable 'flip' set but not used [-Wunused-but-set-variable] 584 | int i, j, k, pivoti, flip=0; | ^ libqhull/geom.c:897:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 897 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/geom.c:935:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 935 | void **freelistp; /* used !qh_NOmem */ | ^ 3 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/geom2.c -o libqhull/geom2.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/global.c -o libqhull/global.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/io.c -o libqhull/io.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/libqhull.c -o libqhull/libqhull.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/mem.c -o libqhull/mem.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/merge.c -o libqhull/merge.o libqhull/merge.c:219:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 219 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/merge.c:322:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 322 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/merge.c:1840:17: warning: variable 'total' set but not used [-Wunused-but-set-variable] 1840 | int cycles=0, total=0, facets, nummerge; | ^ libqhull/merge.c:2086:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 2086 | void **freelistp; /* used !qh_NOmem */ | ^ 4 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/poly.c -o libqhull/poly.o libqhull/poly.c:248:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 248 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/poly.c:564:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 564 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/poly.c:981:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 981 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/poly.c:1014:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 1014 | void **freelistp; /* used !qh_NOmem */ | ^ 4 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/poly2.c -o libqhull/poly2.o libqhull/poly2.c:72:37: warning: variable 'notgood' set but not used [-Wunused-but-set-variable] 72 | int numpart= 0, facet_i, facet_n, notgood= 0, notverified= 0; | ^ libqhull/poly2.c:1076:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 1076 | void **freelistp; /* used !qh_NOmem */ | ^ 2 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/qset.c -o libqhull/qset.o libqhull/qset.c:717:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 717 | void **freelistp; /* used !qh_NOmem */ | ^ libqhull/qset.c:927:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable] 927 | void **freelistp; /* used !qh_NOmem */ | ^ 2 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/random.c -o libqhull/random.o libqhull/random.c:84:7: warning: misleading indentation; statement is not part of the previous 'else' [-Wmisleading-indentation] 84 | strcat(command, s); | ^ libqhull/random.c:82:6: note: previous statement is here 82 | }else | ^ 1 warning generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/rboxlib.c -o libqhull/rboxlib.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/stat.c -o libqhull/stat.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/user.c -o libqhull/user.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/usermem.c -o libqhull/usermem.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/userprintf.c -o libqhull/userprintf.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"libqhull" -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 -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/userprintf_rbox.c -o libqhull/userprintf_rbox.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 TukeyRegion.so TukeyRegionR.o RcppExports.o TukeyRegion.o common.o qhAdapter.o TConvexBody.o TRegion.o TkRegions.o libqhull/geom.o libqhull/geom2.o libqhull/global.o libqhull/io.o libqhull/libqhull.o libqhull/mem.o libqhull/merge.o libqhull/poly.o libqhull/poly2.o libqhull/qset.o libqhull/random.o libqhull/rboxlib.o libqhull/stat.o libqhull/user.o libqhull/usermem.o libqhull/userprintf.o libqhull/userprintf_rbox.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/TukeyRegion/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TukeyRegion/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/TukeyRegion/src' installing to /data/gannet/ripley/R/packages/tests-clang/TukeyRegion.Rcheck/00LOCK-TukeyRegion/00new/TukeyRegion/libs ** R ** 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 (TukeyRegion)