* installing *source* package ‘TukeyRegion’ ...
** package ‘TukeyRegion’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/TukeyRegion/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c TukeyRegionR.cpp -o TukeyRegionR.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.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();
| ^~~~
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c TukeyRegion.cpp -o TukeyRegion.o
1 warning generated.
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/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -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/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c qhAdapter.cpp -o qhAdapter.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c TConvexBody.cpp -o TConvexBody.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 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();
| ^~~~
/usr/local/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c TRegion.cpp -o TRegion.o
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/clang19/bin/clang++ -stdlib=libc++ -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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c TkRegions.cpp -o TkRegions.o
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/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/geom.c -o libqhull/geom.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();
| ^~~~
libqhull/geom.c:584:24: warning: variable 'flip' set but not used [-Wunused-but-set-variable]
584 | int i, j, k, pivoti, flip=0;
| ^
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();
| ^~~~
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/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/geom2.c -o libqhull/geom2.o
TRegion.cpp:308:8: warning: unused variable 'innerPointFound' [-Wunused-variable]
308 | bool innerPointFound = false;
| ^~~~~~~~~~~~~~~
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/global.c -o libqhull/global.o
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){
| ^~~~~~~~~~
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){
| ^~~~~~~~~~
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/io.c -o libqhull/io.o
3 warnings generated.
/usr/local/clang19/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/clang19/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/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/mem.c -o libqhull/mem.o
2 warnings generated.
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/merge.c -o libqhull/merge.o
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/poly.c -o libqhull/poly.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/poly.c:248:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable]
248 | 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/poly.c:564:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable]
564 | void **freelistp; /* used !qh_NOmem */
| ^
libqhull/merge.c:2086:10: warning: variable 'freelistp' set but not used [-Wunused-but-set-variable]
2086 | 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 */
| ^
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/poly2.c -o libqhull/poly2.o
4 warnings generated.
/usr/local/clang19/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/clang19/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 */
| ^
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/clang19/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/clang19/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/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/rboxlib.c -o libqhull/rboxlib.o
4 warnings generated.
/usr/local/clang19/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/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c libqhull/stat.c -o libqhull/stat.o
2 warnings generated.
/usr/local/clang19/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/clang19/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/clang19/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/clang19/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/clang19/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/clang19/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/clang19/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/clang19/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/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/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)