* 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++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/treestats/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c centralities.cpp -o centralities.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c colless.cpp -o colless.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c depth.cpp -o depth.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ladder.cpp -o ladder.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) {
| ~~^~~~~~~~~
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) {
| ~~^~~~~~~~~
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 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) {
| ~~^~~~~~~~~
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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c laplacian.cpp -o laplacian.o
In file included from /usr/include/c++/16/x86_64-redhat-linux/bits/c++allocator.h:33,
from /usr/include/c++/16/bits/allocator.h:46,
from /usr/include/c++/16/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++/16/bits/alloc_traits.h:689:23,
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++/16/bits/stl_vector.h:398:19,
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++/16/bits/stl_vector.h:394:7,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/16/bits/stl_vector.h:378:15,
inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/16/bits/stl_vector.h:795:7,
inlined from ‘size_t ltab::stat::max_del_width()’ at ../inst/include/ltable.h:220:3,
inlined from ‘double calc_max_del_width_ltable_cpp(const Rcpp::NumericMatrix&)’ at depth.cpp:41:25:
/usr/include/c++/16/bits/new_allocator.h:183:66: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘<unknown>’ with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
183 | _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++/16/bits/alloc_traits.h:638:28,
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++/16/bits/stl_vector.h:389:33,
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++/16/bits/stl_vector.h:407:44,
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++/16/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++/16/bits/stl_vector.h:577:47,
inlined from ‘size_t ltab::stat::max_del_width()’ at ../inst/include/ltable.h:215:42,
inlined from ‘double calc_max_del_width_ltable_cpp(const Rcpp::NumericMatrix&)’ at depth.cpp:41:25:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: returned from ‘void* operator new(std::size_t)’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mpd.cpp -o mpd.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c phylo.cpp -o phylo.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) {
| ~~^~~~~~~~~
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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rspectra_helpers.cpp -o rspectra_helpers.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++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I/usr/local/include -I../inst/include -I. -DARMA_USE_CURRENT -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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++ -std=gnu++17 -shared -L/usr/local/lib64 -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/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/treestats/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/treestats/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/treestats/src'
installing to /data/localhost/ripley/R/packages/tests-devel/treestats.Rcheck/00LOCK-treestats/00new/treestats/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)