* 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++-14 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-14 -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++-14 (Debian 14.2.0-16) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprpQebJ/R.INSTALL39a5f4229171a7/aphylo/src'
g++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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++-14 -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 '/home/hornik/tmp/scratch/RtmprpQebJ/R.INSTALL39a5f4229171a7/aphylo/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprpQebJ/R.INSTALL39a5f4229171a7/aphylo/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprpQebJ/R.INSTALL39a5f4229171a7/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  
    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)