* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PhylogeneticEM’ ...
** package ‘PhylogeneticEM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpIvHprz/R.INSTALL949f37a4db1de/PhylogeneticEM/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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
gcc-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c upward_downward.cpp -o upward_downward.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PhylogeneticEM.so RcppExports.o init.o upward_downward.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/RtmpIvHprz/R.INSTALL949f37a4db1de/PhylogeneticEM/src'
make[1]: Entering directory '/tmp/RtmpIvHprz/R.INSTALL949f37a4db1de/PhylogeneticEM/src'
make[1]: Leaving directory '/tmp/RtmpIvHprz/R.INSTALL949f37a4db1de/PhylogeneticEM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PhylogeneticEM/00new/PhylogeneticEM/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 ‘PhylogeneticEM’
finding HTML links ... done
PhyloEM html
finding level-2 HTML links ... done
add_complementary html
allocate_regimes_from_shifts html
allocate_shifts_from_regimes html
allocate_subset_node.simulate html
check.selection.strength html
check_data html
check_dimensions html
check_parsimony html
check_parsimony_clusters html
check_range_alpha html
clusters_from_shifts html
compute_E.simple html
compute_actualization_matrix_ultrametric
html
compute_betas_from_shifts html
compute_diff_exp.BM html
compute_dist_phy html
compute_expectations.BM html
compute_expectations.scOU html
compute_fixed_moments html
compute_gauss_lasso html
compute_log_likelihood.simple html
compute_mahalanobis_distance.simple html
compute_mean_variance.simple html
compute_residuals.simple html
compute_shifts_from_betas html
compute_state_filter html
compute_stationary_variance html
compute_sum_var_diff html
compute_times_ca html
compute_tree_correlations_matrix.BM html
compute_tree_correlations_matrix.scOU html
compute_var_M.BM html
compute_var_diff.BM html
compute_variance_block_diagonal.BM html
compute_variance_block_diagonal.OU html
compute_variance_covariance.BM html
compute_variance_covariance.OU html
compute_variance_covariance.OU.nonsym html
compute_variance_covariance.scOU html
correspondenceEdges html
enlight html
enumerate_parsimony html
enumerate_tips_under_edges html
equivalent_shifts html
equivalent_shifts_edges html
equivalent_shifts_values html
estimate.alpha html
estimateEM html
extract html
extract.enumerate_parsimony html
extract.equivalent_shifts html
extract.parsimonyCost html
extract.parsimonyNumber html
extract.partitionsNumber html
extract.simul_process html
extract_variance_covariance html
find_grid_alpha html
find_independent_regression_vectors.glmnet_multivariate
html
find_rotation html
find_shift_values html
format_output html
get_criterion html
get_variance_node html
go_back_to_original_process html
imputed_traits html
incidence.matrix html
incidence.matrix.full html
incidence_matrix_actualization_factors
html
init.EM.lasso html
init.allocate_regimes_from_shifts html
init.alpha.gamma.estimation html
init.compute_betas_from_shifts html
init.enumerate_parsimony html
init.incidence.matrix html
init.incidence.matrix.full html
init.parsimonyCost html
init.parsimonyNumber html
init.simulate.BM html
init.simulate.OU html
init.simulate.StateAndExp html
is.in.ranges html
lasso_regression_K_fixed.glmnet_multivariate
html
log_likelihood html
matrix_of_possibles html
merge_complementary_vectors html
merge_params_independent html
merge_rotations html
model_selection html
monkeys html
node_optimal_values html
params_BM html
params_OU html
params_process.PhyloEM html
params_process html
params_process.character html
parsimonyCost html
parsimonyNumber html
partitionsNumber html
penalty_BaraudGiraudHuet_likelihood html
penalty_BirgeMassart_shape1 html
penalty_BirgeMassart_shape2 html
penalty_pBIC html
plot.PhyloEM html
plot.enumerate_parsimony html
plot.equivalent_shifts html
plot.params_process html
plot_criterion html
prod_index html
qr_solve_exact html
recursionDown html
residuals.PhyloEM html
sample_edges_intervals html
sample_shifts_edges html
scale_params html
segmentation.BM html
segmentation.OU.specialCase.lasso html
segmentation.OU.specialCase.same_shifts
html
shifts.list_to_matrix html
shifts.list_to_vector html
shifts.matrix_to_list html
shifts.vector_to_list html
shifts_to_simmap html
simul_process html
simulate_internal html
split_params_independent html
sum_partitions html
sum_partitions.cardFixed html
sum_prod.comb html
sum_simplex html
test.root.state html
transform_branch_length html
transform_shifts_values html
update.allocate_regimes_from_shifts html
update.compute_betas_from_shifts html
update.enumerate_parsimony html
update.incidence.matrix html
update.incidence.matrix.full html
update.parsimonyCost html
update.parsimonyNumber html
update.partitionsNumber.gen html
wrapper_E_step html
** 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 (PhylogeneticEM)