* 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 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOBtZCM/R.INSTALL21c4de51c4852a/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
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
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) {
      |                     ~~^~~~~~~~~~
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOBtZCM/R.INSTALL21c4de51c4852a/scistreer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOBtZCM/R.INSTALL21c4de51c4852a/scistreer/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOBtZCM/R.INSTALL21c4de51c4852a/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)