* installing *source* package ‘aphylo’ ...
** package ‘aphylo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/local/clang18/bin/clang++ -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... /usr/local/clang18/bin/clang++ -std=gnu++17 -E
checking for macOS... not found as on Linux
checking for OpenMP... R was not built as a library
missing
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘clang version 18.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/aphylo/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/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'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c aphylo_pruner.cpp -o aphylo_pruner.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c auc.cpp -o auc.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c misc.cpp -o misc.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c predict.cpp -o predict.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c prediction_score_rand.cpp -o prediction_score_rand.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -I../inst/include/   -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c sim_phylo.cpp -o sim_phylo.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 aphylo.so RcppExports.o aphylo_pruner.o auc.o misc.o predict.o prediction_score_rand.o sim_phylo.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/aphylo/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/aphylo/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/aphylo/src'
installing to /data/gannet/ripley/R/packages/tests-clang/aphylo.Rcheck/00LOCK-aphylo/00new/aphylo/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (aphylo)