Install log for 'geometry'

* installing *source* package ‘geometry’ ...
** this is package ‘geometry’ version ‘0.5.2’
** package ‘geometry’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 21.1.4’
using C++ compiler: ‘clang version 21.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/geometry/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c QuadTree.cpp -o QuadTree.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rconvhulln.c -o Rconvhulln.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rdelaunayn.c -o Rdelaunayn.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rgeometry.c -o Rgeometry.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rhalfspacen.c -o Rhalfspacen.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rinhulln.c -o Rinhulln.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c Rtsearch.cpp -o Rtsearch.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rtsearch_orig.c -o Rtsearch_orig.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Rtsearchn.c -o Rtsearchn.o
Rtsearchn.c:61:7: warning: variable 'nf' set but not used [-Wunused-but-set-variable]
   61 |   int nf = 0;                   /* Number of facets */
      |       ^
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c geom2_r.c -o geom2_r.o
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c geom_r.c -o geom_r.o
geom_r.c:623:24: warning: variable 'flip' set but not used [-Wunused-but-set-variable]
  623 |   int i, j, k, pivoti, flip=0;
      |                        ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c geometry_init.c -o geometry_init.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c global_r.c -o global_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c io_r.c -o io_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c libqhull_r.c -o libqhull_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c mem_r.c -o mem_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c merge_r.c -o merge_r.o
merge_r.c:2907:17: warning: variable 'total' set but not used [-Wunused-but-set-variable]
 2907 |   int cycles=0, total=0, facets, nummerge, numdegen= 0;
      |                 ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c poly2_r.c -o poly2_r.o
poly2_r.c:103:37: warning: variable 'notgood' set but not used [-Wunused-but-set-variable]
  103 |   int numpart= 0, facet_i, facet_n, notgood= 0, notverified= 0;
      |                                     ^
1 warning generated.
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c poly_r.c -o poly_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c qset_r.c -o qset_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c random_r.c -o random_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c rboxlib_r.c -o rboxlib_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c stat_r.c -o stat_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c user_r.c -o user_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c usermem_r.c -o usermem_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c userprintf_r.c -o userprintf_r.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppProgress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include   -include Rgeometry.h -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c userprintf_rbox_r.c -o userprintf_rbox_r.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o geometry.so QuadTree.o Rconvhulln.o RcppExports.o Rdelaunayn.o Rgeometry.o Rhalfspacen.o Rinhulln.o Rtsearch.o Rtsearch_orig.o Rtsearchn.o geom2_r.o geom_r.o geometry_init.o global_r.o io_r.o libqhull_r.o mem_r.o merge_r.o poly2_r.o poly_r.o qset_r.o random_r.o rboxlib_r.o stat_r.o user_r.o usermem_r.o userprintf_r.o userprintf_rbox_r.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/geometry/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/geometry/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/geometry/src'
installing to /data/gannet/ripley/R/packages/tests-clang/geometry.Rcheck/00LOCK-geometry/00new/geometry/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (geometry)