* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘treestats’ ...
** this is package ‘treestats’ version ‘1.71.13’
** package ‘treestats’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmplx0efk/R.INSTALL705a52864965c/treestats/src'
g++-16 -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++-16 -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
In file included from beta.cpp:20:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from ../inst/include/branching_times.h:17,
from brts.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from centralities.cpp:20:
../inst/include/centralities.h: In member function ‘void LRSizes::compute(const edge&, const std::vector<double>&, bool)’:
../inst/include/centralities.h:35:18: warning: comparison of integer expressions of different signedness: ‘const std::array<long unsigned int, 2>::value_type’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
35 | if (i[0] < root_no) root_no = i[0];
../inst/include/centralities.h:36:18: warning: comparison of integer expressions of different signedness: ‘const std::array<long unsigned int, 2>::value_type’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
36 | if (i[0] > max_node_no) max_node_no = i[0];
../inst/include/centralities.h: In function ‘double diameter(const edge&, const std::vector<double>&, bool)’:
../inst/include/centralities.h:281:14: warning: comparison of integer expressions of different signedness: ‘const std::array<long unsigned int, 2>::value_type’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
281 | if (i[0] > max_num_nodes) max_num_nodes = i[0];
../inst/include/centralities.h:286:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::array<long unsigned int, 2> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
286 | for (int i = 0; i < e.size(); i++) {
| ~~^~~~~~~~~~
In file included from centralities.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from colless.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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 depth.cpp:19:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
In file included from depth.cpp:20:
../inst/include/depth.h: In instantiation of ‘double depth::depth_tree<NODE>::calc_b2() [with NODE = depth::node_poly]’:
../inst/include/depth.h:440:10: required from here
440 | double calc_b2() override {
| ^~~~~~~
../inst/include/depth.h:445:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
445 | for (size_t i = 0; i < root_no; ++i) {
| ~~^~~~~~~~~
../inst/include/depth.h: In instantiation of ‘double depth::depth_tree<NODE>::calc_b2() [with NODE = depth::node_binary]’:
../inst/include/depth.h:440:10: required from here
440 | double calc_b2() override {
| ^~~~~~~
../inst/include/depth.h:445:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
445 | for (size_t i = 0; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from ladder.cpp:19:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from laplacian.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from mpd.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
In file included from mpd.cpp:22:
../inst/include/mpd.h: In member function ‘std::vector<std::vector<double> > mpd_tree::phylo_path_tree::calculate_inv_path_length()’:
../inst/include/mpd.h:173:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
173 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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
In file included from phylo.cpp:21:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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 rspectra_helpers.cpp -o rspectra_helpers.o
g++-16 -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
In file included from sackin.cpp:20:
../inst/include/util.h: In function ‘bool is_binary(const std::vector<int, std::allocator<int> >&)’:
../inst/include/util.h:121:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
121 | for (size_t i = 1; i < root_no; ++i) {
| ~~^~~~~~~~~
In file included from sackin.cpp:23:
../inst/include/depth.h: In instantiation of ‘double depth::depth_tree<NODE>::calc_b2() [with NODE = depth::node_poly]’:
../inst/include/depth.h:440:10: required from here
440 | double calc_b2() override {
| ^~~~~~~
../inst/include/depth.h:445:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
445 | for (size_t i = 0; i < root_no; ++i) {
| ~~^~~~~~~~~
../inst/include/depth.h: In instantiation of ‘double depth::depth_tree<NODE>::calc_b2() [with NODE = depth::node_binary]’:
../inst/include/depth.h:440:10: required from here
440 | double calc_b2() override {
| ^~~~~~~
../inst/include/depth.h:445:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
445 | for (size_t i = 0; i < root_no; ++i) {
| ~~^~~~~~~~~
g++-16 -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 rspectra_helpers.o sackin.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmplx0efk/R.INSTALL705a52864965c/treestats/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmplx0efk/R.INSTALL705a52864965c/treestats/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmplx0efk/R.INSTALL705a52864965c/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
check_binary 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
inv_branch_dist 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)