* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Racmacs’ ...
** package ‘Racmacs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpf80UkP/R.INSTALL3153217d6143aa/Racmacs/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Racmacs_wrappers.cpp -o Racmacs_wrappers.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Racmacs_wrappers_antigens.cpp -o Racmacs_wrappers_antigens.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Racmacs_wrappers_optimizations.cpp -o Racmacs_wrappers_optimizations.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Racmacs_wrappers_plotspec.cpp -o Racmacs_wrappers_plotspec.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Racmacs_wrappers_sera.cpp -o Racmacs_wrappers_sera.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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 -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_bootstrap.cpp -o ac_bootstrap.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_dimension_test.cpp -o ac_dimension_test.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_errorlines.cpp -o ac_errorlines.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_hemi_test.cpp -o ac_hemi_test.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_matching.cpp -o ac_matching.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_merge.cpp -o ac_merge.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_move_trapped_points.cpp -o ac_move_trapped_points.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_optim_map_stress.cpp -o ac_optim_map_stress.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_optimization.cpp -o ac_optimization.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_optimize_ag_reactivity.cpp -o ac_optimize_ag_reactivity.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_stress.cpp -o ac_stress.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_stress_blobs.cpp -o ac_stress_blobs.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_titers.cpp -o ac_titers.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ac_utils.cpp -o ac_utils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c acmap_map.cpp -o acmap_map.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c acmap_optimization.cpp -o acmap_optimization.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c acmap_point.cpp -o acmap_point.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c acmap_titers.cpp -o acmap_titers.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c json_assert.cpp -o json_assert.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c json_read_to_acmap.cpp -o json_read_to_acmap.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c json_write_from_acmap.cpp -o json_write_from_acmap.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c procrustes.cpp -o procrustes.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_error.cpp -o utils_error.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_euc_dist.cpp -o utils_euc_dist.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_geometry.cpp -o utils_geometry.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_interpolation.cpp -o utils_interpolation.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSTRICT_R_HEADERS -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/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEnsmallen/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rapidjsonr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_transformation.cpp -o utils_transformation.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Racmacs.so Racmacs_wrappers.o Racmacs_wrappers_antigens.o Racmacs_wrappers_optimizations.o Racmacs_wrappers_plotspec.o Racmacs_wrappers_sera.o RcppExports.o ac_bootstrap.o ac_dimension_test.o ac_errorlines.o ac_hemi_test.o ac_matching.o ac_merge.o ac_move_trapped_points.o ac_optim_map_stress.o ac_optimization.o ac_optimize_ag_reactivity.o ac_stress.o ac_stress_blobs.o ac_titers.o ac_utils.o acmap_map.o acmap_optimization.o acmap_point.o acmap_titers.o json_assert.o json_read_to_acmap.o json_write_from_acmap.o procrustes.o utils.o utils_error.o utils_euc_dist.o utils_geometry.o utils_interpolation.o utils_transformation.o -fopenmp -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/Rtmpf80UkP/R.INSTALL3153217d6143aa/Racmacs/src'
make[1]: Entering directory '/tmp/Rtmpf80UkP/R.INSTALL3153217d6143aa/Racmacs/src'
make[1]: Leaving directory '/tmp/Rtmpf80UkP/R.INSTALL3153217d6143aa/Racmacs/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Racmacs/00new/Racmacs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Racmacs’
finding HTML links ... done
RacMerge.options html
RacOptimizer.options html
RacViewer-shiny html
RacViewer html
RacViewer.options html
Racmacs-package html
acmap html
acmapAttributes html
addOptimization html
adjustedLogTiterTable html
adjustedTiterTable html
agAttributes html
agGroups html
agHomologousSr html
agLabIDs html
agReactivityAdjustments html
agSequences html
applyMapTransform html
applyPlotspec html
as.json html
blob html
blobsize html
bootstrapBlobs html
bootstrapMap html
checkHemisphering html
colBases html
deprecated_functions html
dilutionStepsize html
dimensionTestMap html
edit_agNames html
edit_srNames html
export_viewer html
getOptimization html
ggplot.acmap html
htmlAdjustedTiterTable html
htmlMergeReport html
htmlTiterTable html
keepBestOptimization html
keepOptimizations html
keepSingleOptimization html
layerNames html
listOptimizations html
logtiterTable html
logtiterTableLayers html
make.acmap html
map-table-distances html
mapBootstrapCoords html
mapCohesion html
mapComment html
mapDescription html
mapDimensions html
mapDistances html
mapGadget html
mapName html
mapRelaxed html
mapResiduals html
mapStress html
mapTransformation html
matchStrains html
mergeMaps html
mergeReport html
moveTrappedPoints html
optimizationProperties html
optimizeAgReactivity html
optimizeMap html
orderPoints html
plot.acmap html
pointStress html
procrustesData html
procrustesMap html
ptAnnotations html
ptBaseCoords html
ptBootstrapBlob html
ptBootstrapCoords html
ptClades html
ptCoords html
ptDrawingOrder html
ptLeverage html
ptOpacity html
ptStyles html
ptTriangulationBlob html
randomizeCoords html
read.acmap html
read.titerTable html
realignMap html
realignOptimizations html
recalculateStress html
reflectMap html
relaxMap html
relaxMapOneStep html
removeOptimizations html
removePoints html
rotateMap html
runGUI html
save.acmap html
save.coords html
save.titerTable html
setLegend html
sortOptimizations html
splitTiterLayers html
srAttributes html
srGroups html
srHomologousAgs html
srSequences html
standardizeStrainNames html
stressTable html
subsetCommonPoints html
subsetMap html
tableColbases html
tableDistances html
titerTable html
titerTableFlat html
titerTableLayers html
translateMap html
triangulationBlobs html
unstableMaps html
update_ferret_seraNames html
view html
view.acmap html
view.default 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
* creating tarball
packaged installation of ‘Racmacs’ as ‘Racmacs_1.2.9_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (Racmacs)