* installing *source* package ‘RcppTskit’ ...
** this is package ‘RcppTskit’ version ‘0.2.0’
** package ‘RcppTskit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++20
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++20
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/RcppTskit/src'
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/convert.c -o tskit/convert.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/core.c -o tskit/core.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/genotypes.c -o tskit/genotypes.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/haplotype_matching.c -o tskit/haplotype_matching.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/kastore.c -o tskit/kastore.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/stats.c -o tskit/stats.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/tables.c -o tskit/tables.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -fpic -c tskit/trees.c -o tskit/trees.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tests_c.c -o tests_c.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppTskit.cpp -o RcppTskit.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c tests.cpp -o tests.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/data/gannet/ripley/R/R-devel/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include   -DNDEBUG -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o RcppTskit.so tskit/convert.o tskit/core.o tskit/genotypes.o tskit/haplotype_matching.o tskit/kastore.o tskit/stats.o tskit/tables.o tskit/trees.o tests_c.o RcppTskit.o tests.o RcppExports.o -Wl,-soname,RcppTskit.so
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/RcppTskit/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/RcppTskit/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/RcppTskit/src'
installing to /data/gannet/ripley/R/packages/tests-devel/RcppTskit.Rcheck/00LOCK-RcppTskit/00new/RcppTskit/libs
** R
** 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 (RcppTskit)