* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘treestats’ ...
** this is package ‘treestats’ version ‘1.70.8’
** package ‘treestats’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++-15 (Debian 15.2.0-16) 15.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmhebpK/R.INSTALL3d30776cb9aedd/treestats/src'
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c beta.cpp -o beta.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c brts.cpp -o brts.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c centralities.cpp -o centralities.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c colless.cpp -o colless.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c depth.cpp -o depth.o
In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33,
from /usr/include/c++/15/bits/allocator.h:46,
from /usr/include/c++/15/vector:65,
from depth.cpp:15:
In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = int]’,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = int]’ at /usr/include/c++/15/bits/alloc_traits.h:649:23,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:396:19,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:392:7,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:375:15,
inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:805:7,
inlined from ‘size_t ltab::stat::max_del_width()’ at ../inst/include/ltable.h:179:3,
inlined from ‘double calc_max_del_width_ltable_cpp(const Rcpp::NumericMatrix&)’ at depth.cpp:36:25:
/usr/include/c++/15/bits/new_allocator.h:172:66: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘<unknown>’ with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = int]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:387:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:405:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/15/bits/stl_vector.h:587:47,
inlined from ‘size_t ltab::stat::max_del_width()’ at ../inst/include/ltable.h:174:42,
inlined from ‘double calc_max_del_width_ltable_cpp(const Rcpp::NumericMatrix&)’ at depth.cpp:36:25:
/usr/include/c++/15/bits/new_allocator.h:151:73: note: returned from ‘void* operator new(std::size_t)’
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ladder.cpp -o ladder.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c laplacian.cpp -o laplacian.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mpd.cpp -o mpd.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c phylo.cpp -o phylo.o
g++-15 -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/nloptr/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c sackin.cpp -o sackin.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o treestats.so RcppExports.o beta.o brts.o centralities.o colless.o depth.o ladder.o laplacian.o mpd.o phylo.o sackin.o -fopenmp -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/RtmpmhebpK/R.INSTALL3d30776cb9aedd/treestats/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmhebpK/R.INSTALL3d30776cb9aedd/treestats/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmhebpK/R.INSTALL3d30776cb9aedd/treestats/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-treestats/00new/treestats/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘treestats’
finding HTML links ... done
ILnumber html
area_per_pair html
average_leaf_depth html
avg_ladder html
avg_vert_depth html
b1 html
b2 html
beta_statistic html
blum html
branching_times html
calc_all_stats html
calc_brts_stats html
calc_topology_stats html
cherries html
colless html
colless_corr html
colless_quad html
create_fully_balanced_tree html
create_fully_unbalanced_tree html
crown_age html
diameter html
double_cherries html
eigen_centrality html
entropy_j html
ew_colless html
four_prong html
gamma_statistic html
i_stat html
imbalance_steps html
j_one html
l_to_phylo html
laplacian_spectrum html
list_statistics html
ltable_to_newick html
make_unbalanced_tree html
max_betweenness html
max_closeness html
max_del_width html
max_depth html
max_ladder html
max_width html
mean_branch_length html
mean_branch_length_ext html
mean_branch_length_int html
mean_i html
mean_pair_dist html
minmax_adj html
minmax_laplace html
mntd html
mw_over_md html
nLTT html
nLTT_base html
number_of_lineages html
phylo_to_l html
phylogenetic_diversity html
pigot_rho html
pitchforks html
psv html
rebase_ltable html
rogers html
root_imbalance html
rquartet html
sackin html
sshape html
stairs html
stairs2 html
sym_nodes html
tot_coph html
tot_internal_path html
tot_path_length html
tree_height html
treeness html
treestats-package html
var_branch_length html
var_branch_length_ext html
var_branch_length_int html
var_leaf_depth html
var_pair_dist html
wiener 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 (treestats)