* installing *source* package ‘TDAstats’ ...
** package ‘TDAstats’ 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/TDAstats/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 ripser_short.cpp -o ripser_short.o
ripser_short.cpp: In function 'bool is_prime(coefficient_t_ripser)':
ripser_short.cpp:50:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
50 | for (coefficient_t_ripser p = 3, q = n / p, r = n % p; p <= q; p += 2, q = n / p, r = n % p)
| ^~~
ripser_short.cpp:52:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
52 | return true;
| ^~~~~~
ripser_short.cpp: In member function 'value_t_ripser rips_filtration_comparator<DistanceMatrix>::diameter(index_t_ripser) const':
ripser_short.cpp:165:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
165 | for (index_t_ripser i = 0; i <= dim; ++i)
| ^~~
ripser_short.cpp:167:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
167 | return diam;
| ^~~~~~
ripser_short.cpp: In member function 'void compressed_distance_matrix<Layout>::init_rows() [with compressed_matrix_layout Layout = LOWER_TRIANGULAR]':
ripser_short.cpp:255:32: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
255 | 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:263:32: warning: comparison of integer expressions of different signedness: 'index_t_ripser' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
263 | for (index_t_ripser i = 0; i < size() - 1; ++i) {
| ~~^~~~~~~~~~~~
ripser_short.cpp: In function 'compressed_lower_distance_matrix getLowerDistMatrix(Rcpp::NumericMatrix)':
ripser_short.cpp:557:17: warning: unused variable 'numCols' [-Wunused-variable]
557 | numCols = inputMat.ncol();
| ^~~~~~~
ripser_short.cpp: In function 'Rcpp::NumericVector ripser_cpp(Rcpp::NumericMatrix, int, float, int)':
ripser_short.cpp:671:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
671 | for (int i = 0; i < pers_hom.size(); i++)
| ~~^~~~~~~~~~~~~~~~~
ripser_short.cpp:671:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
671 | for (int i = 0; i < pers_hom.size(); i++)
| ^~~
ripser_short.cpp:677:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
677 | return ans;
| ^~~~~~
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<short int>&, 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<compressed_distance_matrix<LOWER_TRIANGULAR> >; Comparator = rips_filtration_comparator<compressed_distance_matrix<LOWER_TRIANGULAR> >; index_t_ripser = long int; value_t_ripser = double; coefficient_t_ripser = short int]':
ripser_short.cpp:661:18: required from here
661 | compute_pairs(columns_to_reduce, pivot_column_index, dim, n, threshold, modulus, multiplicative_inverse, dist,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
662 | comp, comp_prev, binomial_coeff, pers_hom);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ripser_short.cpp:436:32: 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]
436 | 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 TDAstats.so RcppExports.o ripser_short.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/TDAstats/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/TDAstats/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/TDAstats/src'
installing to /data/gannet/ripley/R/packages/tests-devel/TDAstats.Rcheck/00LOCK-TDAstats/00new/TDAstats/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (TDAstats)