* 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 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5KhjBJ/R.INSTALL339c102da82d61/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/Rtmp5KhjBJ/R.INSTALL339c102da82d61/DCLEAR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5KhjBJ/R.INSTALL339c102da82d61/DCLEAR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5KhjBJ/R.INSTALL339c102da82d61/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)