* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PLNmodels’ ...
** package ‘PLNmodels’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpLcXdne/R.INSTALL3c477b382823b8/PLNmodels/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c nlopt_wrapper.cpp -o nlopt_wrapper.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_diag_cov.cpp -o optim_diag_cov.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_fixed_cov.cpp -o optim_fixed_cov.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_full_cov.cpp -o optim_full_cov.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_genet_cov.cpp -o optim_genet_cov.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_rank_cov.cpp -o optim_rank_cov.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c optim_spherical.cpp -o optim_spherical.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c packing.cpp -o packing.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PLNmodels.so RcppExports.o nlopt_wrapper.o optim_diag_cov.o optim_fixed_cov.o optim_full_cov.o optim_genet_cov.o optim_rank_cov.o optim_spherical.o packing.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLcXdne/R.INSTALL3c477b382823b8/PLNmodels/src'
make[1]: Entering directory '/tmp/RtmpLcXdne/R.INSTALL3c477b382823b8/PLNmodels/src'
make[1]: Leaving directory '/tmp/RtmpLcXdne/R.INSTALL3c477b382823b8/PLNmodels/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PLNmodels/00new/PLNmodels/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'sqrt' 
Note: wrong number of arguments to 'sqrt' 
** help
*** installing help indices
  converting help for package ‘PLNmodels’
    finding HTML links ... done
    PLN                                     html  
    PLNLDA                                  html  
    PLNLDA_param                            html  
    PLNLDAfit                               html  
    finding level-2 HTML links ... done

    PLNLDAfit_diagonal                      html  
    PLNPCA                                  html  
    PLNPCA_param                            html  
    PLNPCAfamily                            html  
    PLNPCAfit                               html  
    PLN_param                               html  
    PLNfamily                               html  
    PLNfit                                  html  
    PLNfit_diagonal                         html  
    PLNfit_fixedcov                         html  
    PLNfit_spherical                        html  
    PLNmixture                              html  
    PLNmixture_param                        html  
    PLNmixturefamily                        html  
    PLNmixturefit                           html  
    PLNmodels-package                       html  
    PLNnetwork                              html  
    PLNnetwork_param                        html  
    PLNnetworkfamily                        html  
    PLNnetworkfit                           html  
    barents                                 html  
    coef.PLNLDAfit                          html  
    coef.PLNfit                             html  
    coef.PLNmixturefit                      html  
    coefficient_path                        html  
    compute_PLN_starting_point              html  
    compute_offset                          html  
    extract_probs                           html  
    fitted.PLNfit                           html  
    fitted.PLNmixturefit                    html  
    getBestModel                            html  
    getModel                                html  
    mollusk                                 html  
    oaks                                    html  
    pipe                                    html  
    plot.PLNLDAfit                          html  
    plot.PLNPCAfamily                       html  
    plot.PLNPCAfit                          html  
    plot.PLNfamily                          html  
    plot.PLNmixturefamily                   html  
    plot.PLNmixturefit                      html  
    plot.PLNnetworkfamily                   html  
    plot.PLNnetworkfit                      html  
    predict.PLNLDAfit                       html  
    predict.PLNfit                          html  
    predict.PLNmixturefit                   html  
    predict_cond                            html  
    prepare_data                            html  
    rPLN                                    html  
    sigma.PLNfit                            html  
    sigma.PLNmixturefit                     html  
    stability_selection                     html  
    standard_error                          html  
    trichoptera                             html  
    vcov.PLNfit                             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 (PLNmodels)