* installing *source* package ‘ripserr’ ...
** package ‘ripserr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ripserr/src'
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c cubical_2dim.cpp -o cubical_2dim.o
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c cubical_3dim.cpp -o cubical_3dim.o
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c cubical_4dim.cpp -o cubical_4dim.o
cubical_2dim.cpp: In member function 'void ComputePairs2::compute_pairs_main()':
cubical_2dim.cpp:528:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
528 | for (int i = 0; i < ctl_size; ++i)
| ~~^~~~~~~~~~
cubical_3dim.cpp: In constructor 'ColumnsToReduce3::ColumnsToReduce3(DenseCubicalGrids3*)':
cubical_3dim.cpp:394:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
394 | for (int y = ay; y > 0; --y)
| ^~~
cubical_3dim.cpp:401:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
401 | sort(columns_to_reduce.begin(), columns_to_reduce.end(), BirthdayIndex3Comparator());
| ^~~~
cubical_3dim.cpp: In member function 'void ComputePairs3::compute_pairs_main()':
cubical_3dim.cpp:804:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
804 | for(int i = 0; i < ctl_size; ++i) {
| ~~^~~~~~~~~~
cubical_4dim.cpp: In member function 'void ComputePairs4::compute_pairs_main()':
cubical_4dim.cpp:1045:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
1045 | for(int i = 0; i < ctl_size; ++i) {
| ~~^~~~~~~~~~
g++-14 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c ripser_short.cpp -o ripser_short.o
ripser_short.cpp: In member function 'void compressed_distance_matrix<Layout>::init_rows() [with compressed_matrix_layout Layout = LOWER_TRIANGULAR]':
ripser_short.cpp:302:32: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
302 | for (index_t_ripser i = 1; i < size(); ++i) {
| ~~^~~~~~~~
ripser_short.cpp: In member function 'void compressed_distance_matrix<Layout>::init_rows() [with compressed_matrix_layout Layout = UPPER_TRIANGULAR]':
ripser_short.cpp:310:32: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
310 | for (index_t_ripser i = 0; i < size() - 1; ++i) {
| ~~^~~~~~~~~~~~
ripser_short.cpp: In instantiation of 'Rcpp::NumericVector ripser_compute(const DistanceMatrix&, int, float, int) [with DistanceMatrix = compressed_distance_matrix<UPPER_TRIANGULAR>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
ripser_short.cpp:723:24: required from here
723 | return ripser_compute(dist, dim, thresh, p);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:709:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
709 | for (int i = 0; i < pers_hom.size(); i++){
| ~~^~~~~~~~~~~~~~~~~
ripser_short.cpp: In instantiation of 'Rcpp::NumericVector ripser_compute(const DistanceMatrix&, int, float, int) [with DistanceMatrix = compressed_distance_matrix<LOWER_TRIANGULAR>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
ripser_short.cpp:739:24: required from here
739 | return ripser_compute(dist, dim, thresh, p);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:709:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
709 | for (int i = 0; i < pers_hom.size(); i++){
| ~~^~~~~~~~~~~~~~~~~
ripser_short.cpp: In instantiation of 'void compute_pairs(std::vector<diameter_index_t>&, hash_map<long int, long int>&, index_t_ripser, index_t_ripser, value_t_ripser, coefficient_t_ripser, const std::vector<unsigned char>&, const DistanceMatrix&, const ComparatorCofaces&, const Comparator&, const binomial_coeff_table&, std::vector<std::vector<double> >&) [with DistanceMatrix = compressed_distance_matrix<UPPER_TRIANGULAR>; ComparatorCofaces = rips_filtration_comparator<const compressed_distance_matrix<UPPER_TRIANGULAR>&>; Comparator = rips_filtration_comparator<const compressed_distance_matrix<UPPER_TRIANGULAR>&>; index_t_ripser = long int; value_t_ripser = double; coefficient_t_ripser = unsigned char]':
ripser_short.cpp:699:20: required from 'Rcpp::NumericVector ripser_compute(const DistanceMatrix&, int, float, int) [with DistanceMatrix = compressed_distance_matrix<UPPER_TRIANGULAR>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
699 | compute_pairs(columns_to_reduce, pivot_column_index, dim, n, threshold, modulus, multiplicative_inverse, dist,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
700 | comp, comp_prev, binomial_coeff, pers_hom);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:723:24: required from here
723 | return ripser_compute(dist, dim, thresh, p);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:483:34: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'std::vector<diameter_index_t>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
483 | for (index_t_ripser i = 0; i < columns_to_reduce.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp: In instantiation of 'void compute_pairs(std::vector<diameter_index_t>&, hash_map<long int, long int>&, index_t_ripser, index_t_ripser, value_t_ripser, coefficient_t_ripser, const std::vector<unsigned char>&, const DistanceMatrix&, const ComparatorCofaces&, const Comparator&, const binomial_coeff_table&, std::vector<std::vector<double> >&) [with DistanceMatrix = compressed_distance_matrix<LOWER_TRIANGULAR>; ComparatorCofaces = rips_filtration_comparator<const compressed_distance_matrix<LOWER_TRIANGULAR>&>; Comparator = rips_filtration_comparator<const compressed_distance_matrix<LOWER_TRIANGULAR>&>; index_t_ripser = long int; value_t_ripser = double; coefficient_t_ripser = unsigned char]':
ripser_short.cpp:699:20: required from 'Rcpp::NumericVector ripser_compute(const DistanceMatrix&, int, float, int) [with DistanceMatrix = compressed_distance_matrix<LOWER_TRIANGULAR>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]'
699 | compute_pairs(columns_to_reduce, pivot_column_index, dim, n, threshold, modulus, multiplicative_inverse, dist,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
700 | comp, comp_prev, binomial_coeff, pers_hom);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:739:24: required from here
739 | return ripser_compute(dist, dim, thresh, p);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:483:34: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'std::vector<diameter_index_t>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
483 | for (index_t_ripser i = 0; i < columns_to_reduce.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++11 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o ripserr.so RcppExports.o cubical_2dim.o cubical_3dim.o cubical_4dim.o ripser_short.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ripserr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ripserr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ripserr/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ripserr.Rcheck/00LOCK-ripserr/00new/ripserr/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (ripserr)