* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘topolow’ ...
** this is package ‘topolow’ version ‘2.1.0’
** package ‘topolow’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXuje7j/R.INSTALL39804f49b54c6e/topolow/src'
g++-16 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c optimization.cpp -o optimization.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o topolow.so RcppExports.o optimization.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXuje7j/R.INSTALL39804f49b54c6e/topolow/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXuje7j/R.INSTALL39804f49b54c6e/topolow/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXuje7j/R.INSTALL39804f49b54c6e/topolow/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-topolow/00new/topolow/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 ‘topolow’
finding HTML links ... done
Euclidify html
adaptive_MC_sampling html
analyze_network_structure html
calculate_diagnostics html
calculate_prediction_interval html
calculate_weighted_marginals html
check_gaussian_convergence html
check_matrix_connectivity html
clean_data html
color_palettes html
compute_kernel_velocity html
coordinates_to_matrix html
create_base_theme html
create_cv_folds html
create_diagnostic_plots html
create_diagnostic_report html
create_topolow_map html
denv_data html
detect_outliers_mad html
error_calculator_comparison html
euclidean_embedding html
example_positions html
extract_numeric_values html
generate_kde_samples html
get_grid html
ggsave_white_bg html
h3n2_data html
hiv_titers html
hiv_viruses html
initial_parameter_optimization html
likelihood_function html
list_to_matrix html
log_transform_parameters html
make_interactive html
new_aesthetic_config html
new_annotation_config html
new_dim_reduction_config html
new_layout_config html
parameter_sensitivity_analysis html
plot.parameter_sensitivity html
plot.profile_likelihood html
plot.topolow_convergence html
plot.topolow_diagnostics html
plot_3d_mapping html
plot_cluster_mapping html
plot_cv_errors html
plot_embedding_quality html
plot_euclidify_diagnostics html
plot_ll_improvement html
plot_mcmc_diagnostics html
plot_network_structure html
plot_parameter_search html
plot_performance_trace html
plot_temporal_mapping html
prepare_clade_membership html
print.parameter_sensitivity html
print.profile_likelihood html
print.topolow html
print.topolow_convergence html
print.topolow_diagnostics html
process_antigenic_data html
profile_likelihood html
profile_likelihood_result html
prune_sparse_matrix html
reduce_dimensions html
run_adaptive_sampling html
sanity_check_subsample html
save_plot html
scale_to_original_distances html
scatterplot_fitted_vs_true html
subsample_dissimilarity_matrix html
summary.topolow html
symmetric_to_nonsymmetric_matrix html
table_to_matrix html
titers_list_to_matrix html
topolow-package html
validate_topolow_df html
vectorized_process_distance_matrix html
weighted_kde 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 (topolow)