* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘DCLEAR’ ... ** package ‘DCLEAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfXkzLs/R.INSTALL16c8c41aeba586/DCLEAR/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'/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 DCLEAR.cpp -o DCLEAR.o DCLEAR.cpp: In function ‘arma::mat dist_w_ham(arma::mat, arma::vec)’: DCLEAR.cpp:14:13: warning: unused variable ‘n_InfoW’ [-Wunused-variable] 14 | const int n_InfoW = InfoW.size(); | ^~~~~~~ DCLEAR.cpp: In function ‘arma::mat dist_w_ham2(arma::mat, arma::vec)’: DCLEAR.cpp:50:11: warning: unused variable ‘d_c’ [-Wunused-variable] 50 | int d_c = 0; | ^~~ DCLEAR.cpp:38:13: warning: unused variable ‘n_InfoW’ [-Wunused-variable] 38 | const int n_InfoW = InfoW.size(); | ^~~~~~~ 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'/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 g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o DCLEAR.so DCLEAR.o RcppExports.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 '/home/hornik/tmp/scratch/RtmpfXkzLs/R.INSTALL16c8c41aeba586/DCLEAR/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfXkzLs/R.INSTALL16c8c41aeba586/DCLEAR/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfXkzLs/R.INSTALL16c8c41aeba586/DCLEAR/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-DCLEAR/00new/DCLEAR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘simulate’ in package ‘DCLEAR’ ** help *** installing help indices converting help for package ‘DCLEAR’ finding HTML links ... done DCLEAR html WH html WH_train html WH_train_fit html add_deletion html add_dropout html as_igraph-data.frame-method html as_igraph-phylo-method html as_igraph html as_lineage_tree-phyDat-phylo-lineage_tree_config-method html as_lineage_tree html as_phylo-igraph-method html as_phylo html dist_kmer_replacement_inference html dist_replacement-phyDat-kmer_summary-integer-method html dist_replacement-phyDat-missing-integer-method html dist_replacement html dist_weighted_hamming-phyDat-numeric-method html dist_weighted_hamming html downsample-igraph-method html downsample-lineage_tree-method html downsample html get_distance_prior html get_leaves-lineage_tree-method html get_leaves html get_node_names html get_replacement_probability html get_sequence html get_transition_probability html lineages html positional_mutation_prob html process_sequence-phyDat-method html process_sequence html prune-igraph-method html prune-lineage_tree-method html prune html random_tree html rbind-phyDat-method html sample_mutation_outcome html sample_mutation_site html sample_outcome_prob html score_simulation html sim_seqdata html simulate-lineage_tree_config-missing-method html simulate-lineage_tree_config-phyDat-method html simulate html simulate_core html substr_kmer-kmer_summary-method html substr_kmer html subtract-lineage_tree-lineage_tree-method html subtract html subtree-lineage_tree-method html subtree-phylo-method html subtree html summarize_kmer-phyDat-method html summarize_kmer html summarize_kmer_core 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 (DCLEAR)