* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘scistreer’ ...
** this is package ‘scistreer’ version ‘1.2.0’
** package ‘scistreer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-5) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpP9PkSl/R.INSTALL23b5b93dfb8f47/scistreer/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   71 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
      |                                                                                                                                                         ^
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c scistreer.cpp -o scistreer.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
                 from scistreer.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
   71 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
      |                                                                                                                                                         ^
scistreer.cpp: In function ‘std::vector<std::vector<int, std::allocator<int> > > allChildrenCPP(arma::Mat<int>)’:
scistreer.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
   22 |     for(int i = 0; i<parent.size(); i++) {
      |                    ~^~~~~~~~~~~~~~
scistreer.cpp: In function ‘arma::Mat<int> reorder_rows(arma::Mat<int>, arma::Col<int>)’:
scistreer.cpp:52:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   52 |     for (int i = 0; i < y.n_elem; ++i) {
      |                     ~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o scistreer.so RcppExports.o scistreer.o -lpthread -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/RtmpP9PkSl/R.INSTALL23b5b93dfb8f47/scistreer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpP9PkSl/R.INSTALL23b5b93dfb8f47/scistreer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpP9PkSl/R.INSTALL23b5b93dfb8f47/scistreer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-scistreer/00new/scistreer/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘scistreer’
    finding HTML links ... done
    P_example                               html  
    P_small                                 html  
    annotate_tree                           html  
    get_mut_graph                           html  
    gtree_small                             html  
    label_edges                             html  
    ladderize                               html  
    mut_nodes_small                         html  
    mut_to_tree                             html  
    perform_nni                             html  
    plot_phylo_heatmap                      html  
    run_scistree                            html  
    score_tree                              html  
    to_phylo                                html  
    transfer_links                          html  
    tree_small                              html  
    tree_upgma                              html  
** building package indices
** 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 (scistreer)