* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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 g++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking for macOS... not found as on Linux
checking for OpenMP... found
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpLgqIuw/R.INSTALLa3caa205bcd11/aphylo/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c aphylo_pruner.cpp -o aphylo_pruner.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c auc.cpp -o auc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.cpp -o misc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c predict.cpp -o predict.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c prediction_score_rand.cpp -o prediction_score_rand.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c sim_phylo.cpp -o sim_phylo.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o aphylo.so RcppExports.o aphylo_pruner.o auc.o misc.o predict.o prediction_score_rand.o sim_phylo.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLgqIuw/R.INSTALLa3caa205bcd11/aphylo/src'
make[1]: Entering directory '/tmp/RtmpLgqIuw/R.INSTALLa3caa205bcd11/aphylo/src'
make[1]: Leaving directory '/tmp/RtmpLgqIuw/R.INSTALLa3caa205bcd11/aphylo/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
converting help for package ‘aphylo’
finding HTML links ... done
LogLike html
accuracy_sifter html
ape-methods html
aphylo-class html
finding level-2 HTML links ... done
aphylo-index html
aphylo-info html
aphylo-methods html
aphylo-model html
aphylo-package html
aphylo_cv html
aphylo_estimates html
aphylo_from_data_frame html
aphylo_mcmc html
aphylo_mle html
as.phylo html
auc html
balance_ann html
bprior html
fakeexperiment html
faketree html
imputate_duplications html
list_offspring html
mislabel html
multiAphylo html
new_aphylo_pruner html
panther-tree html
plot.aphylo_prediction_score html
plot_logLik html
plot_multivariate html
posterior-probabilities html
prediction_score html
raphylo html
rdrop_annotations html
read_nhx html
read_pli html
sim_fun_on_tree html
sim_tree html
states html
write_pli html
*** 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)