* installing *source* package ‘TDAvec’ ...
** this is package ‘TDAvec’ version ‘0.1.41’
** package ‘TDAvec’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/TDAvec/src'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 AlgebraicFunctions.cpp -o AlgebraicFunctions.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 BettiCurve.cpp -o BettiCurve.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 ComplexPolynomial.cpp -o ComplexPolynomial.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 EulerCharacteristic.cpp -o EulerCharacteristic.o
ComplexPolynomial.cpp: In function ‘arma::mat computeComplexPolynomial(const arma::mat&, const int&, const int&, std::string)’:
ComplexPolynomial.cpp:50:16: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘const int’ [-Wsign-compare]
   50 |   if (x.n_elem < m) stop("m must be less than or equal to the number of points in the diagram!");
      |       ~~~~~~~~~^~~
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 Limits.cpp -o Limits.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 NormalizedLife.cpp -o NormalizedLife.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 PersistenceBlock.cpp -o PersistenceBlock.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 PersistenceImage.cpp -o PersistenceImage.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 PersistenceLandscape.cpp -o PersistenceLandscape.o
PersistenceLandscape.cpp: In function ‘arma::mat computePersistenceLandscape(const arma::mat&, const int&, const arma::vec&, const int&, const bool&, const std::string&, Rcpp::Nullable<double>)’:
PersistenceLandscape.cpp:36:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   36 |     for (int i=0; i<scaleSeq.n_elem; ++i){
      |                   ~^~~~~~~~~~~~~~~~
PersistenceLandscape.cpp:54:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   54 |     for (int i=0; i<scaleSeq.n_elem; ++i){
      |                   ~^~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 PersistenceSilhouette.cpp -o PersistenceSilhouette.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 PersistentEntropy.cpp -o PersistentEntropy.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 Stats.cpp -o Stats.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 TemplateFunction.cpp -o TemplateFunction.o
TemplateFunction.cpp: In function ‘Rcpp::NumericVector computeTemplateFunction(const arma::mat&, const int&, const double&, const int&, const double&)’:
TemplateFunction.cpp:60:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   60 |     for (int j = 0; j < center_l.n_elem; ++j) {
      |                     ~~^~~~~~~~~~~~~~~~~
TemplateFunction.cpp:71:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   71 |     for (int i = 0; i < center_x.n_elem; ++i) {
      |                     ~~^~~~~~~~~~~~~~~~~
TemplateFunction.cpp:72:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   72 |       for (int j = 0; j < center_l.n_elem; ++j) {
      |                       ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -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 TropicalCoordinates.cpp -o TropicalCoordinates.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:686,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from TemplateFunction.cpp:1:
In static member function ‘static eT arma::arrayops::accumulate(const eT*, arma::uword) [with eT = double]’,
    inlined from ‘static typename T1::elem_type arma::op_accu_mat::apply(const T1&) [with T1 = arma::mtOp<double, arma::eOp<arma::eOp<arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_minus_post>, arma::eop_abs>, arma::eop_scalar_times>, arma::eop_scalar_minus_pre>, arma::op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp:121:32,
    inlined from ‘auto arma::accu(const T1&, const typename enable_if<is_arma_type<T1>::value>::result*) [with T1 = mtOp<double, eOp<eOp<eOp<eOp<Col<double>, eop_scalar_minus_post>, eop_abs>, eop_scalar_times>, eop_scalar_minus_pre>, op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_accu.hpp:34:28,
    inlined from ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), typename T1::elem_type>::result arma::sum(const T1&) [with T1 = mtOp<double, eOp<eOp<eOp<eOp<Col<double>, eop_scalar_minus_post>, eop_abs>, eop_scalar_times>, eop_scalar_minus_pre>, op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_sum.hpp:31:14,
    inlined from ‘double tent_function_1D(const arma::vec&, const double&, const double&)’ at TemplateFunction.cpp:18:22:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/arrayops_meat.hpp:941:12: warning: ‘U.arma::quasi_unwrap<arma::mtOp<double, arma::eOp<arma::eOp<arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_minus_post>, arma::eop_abs>, arma::eop_scalar_times>, arma::eop_scalar_minus_pre>, arma::op_clamp> >::M.arma::Mat<double>::mem_local[0]’ may be used uninitialized [-Wmaybe-uninitialized]
  941 |       acc1 += (*src);
      |       ~~~~~^~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:802:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp: In function ‘double tent_function_1D(const arma::vec&, const double&, const double&)’:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp:119:28: note: ‘U’ declared here
  119 |     const quasi_unwrap<T1> U(X);
      |                            ^
In static member function ‘static eT arma::arrayops::accumulate(const eT*, arma::uword) [with eT = double]’,
    inlined from ‘static typename T1::elem_type arma::op_accu_mat::apply(const T1&) [with T1 = arma::mtOp<double, arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_times>, arma::eop_scalar_minus_pre>, arma::op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp:121:32,
    inlined from ‘auto arma::accu(const T1&, const typename enable_if<is_arma_type<T1>::value>::result*) [with T1 = mtOp<double, eOp<eOp<Col<double>, eop_scalar_times>, eop_scalar_minus_pre>, op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_accu.hpp:34:28,
    inlined from ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), typename T1::elem_type>::result arma::sum(const T1&) [with T1 = mtOp<double, eOp<eOp<Col<double>, eop_scalar_times>, eop_scalar_minus_pre>, op_clamp>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_sum.hpp:31:14,
    inlined from ‘double tent_function_2D(const arma::vec&, const arma::vec&, const double&, const double&, const double&)’ at TemplateFunction.cpp:12:22:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/arrayops_meat.hpp:941:12: warning: ‘U.arma::quasi_unwrap<arma::mtOp<double, arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_times>, arma::eop_scalar_minus_pre>, arma::op_clamp> >::M.arma::Mat<double>::mem_local[0]’ may be used uninitialized [-Wmaybe-uninitialized]
  941 |       acc1 += (*src);
      |       ~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp: In function ‘double tent_function_2D(const arma::vec&, const arma::vec&, const double&, const double&, const double&)’:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/op_accu_meat.hpp:119:28: note: ‘U’ declared here
  119 |     const quasi_unwrap<T1> U(X);
      |                            ^
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o TDAvec.so AlgebraicFunctions.o BettiCurve.o ComplexPolynomial.o EulerCharacteristic.o Limits.o NormalizedLife.o PersistenceBlock.o PersistenceImage.o PersistenceLandscape.o PersistenceSilhouette.o PersistentEntropy.o RcppExports.o Stats.o TemplateFunction.o TropicalCoordinates.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -fopenmp -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/TDAvec/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/TDAvec/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/TDAvec/src'
installing to /data/gannet/ripley/R/packages/tests-devel/TDAvec.Rcheck/00LOCK-TDAvec/00new/TDAvec/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 (TDAvec)