* installing *source* package ‘spanner’ ...
** this is package ‘spanner’ version ‘1.0.2’
** package ‘spanner’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spanner/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 Progress.cpp -o Progress.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 algorithms.cpp -o algorithms.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 code.cpp -o code.o
algorithms.cpp: In function ‘std::vector<double> irlsCylinder(std::vector<std::vector<double> >&, std::vector<double>, double, unsigned int)’:
algorithms.cpp:411:10: warning: unused variable ‘success’ [-Wunused-variable]
  411 |     bool success = optim::nm(init,nmCylinderDist,&las);
      |          ^~~~~~~
In file included from /data/gannet/ripley/R/test-dev/lidR/include/SpatialIndex.h:6,
                 from code.cpp:9:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:166:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  166 |   while (pts.size() < k && pts.size() < npoints)
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:193:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  193 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius) {
      |                              ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:223:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  223 |   while (pts.size() < k && pts.size() < npoints) {
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:248:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  248 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius)
      |                              ~~~~~~~~~~~^~~~~~~~~
code.cpp: In function ‘Rcpp::List C_eigen_in_sphere(Rcpp::S4, double, int)’:
code.cpp:74:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   74 |   for(unsigned int i = 0 ; i < n ; i++)
      |                            ~~^~~
code.cpp:266:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  266 |       for (unsigned int j = 0; j < k; ++j) {
      |                                ~~^~~
code.cpp:300:18: warning: unused variable ‘a’ [-Wunused-variable]
  300 |           double a = h(0);
      |                  ^
code.cpp:368:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  368 |     for (unsigned int j = 0; j < k; ++j) {
      |                              ~~^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 methods.cpp -o methods.o
In file included from utils.h:25,
                 from algorithms.h:27,
                 from methods.h:25,
                 from methods.cpp:22:
In copy constructor ‘HoughCenters::HoughCenters(const HoughCenters&)’,
    inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = HoughCenters; _Args = {const HoughCenters&}; _Tp = HoughCenters]’ at /usr/include/c++/15/bits/new_allocator.h:191:4,
    inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = HoughCenters; _Args = {const HoughCenters&}; _Tp = HoughCenters]’ at /usr/include/c++/15/bits/alloc_traits.h:674:17,
    inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = HoughCenters; _Alloc = std::allocator<HoughCenters>]’ at /usr/include/c++/15/bits/stl_vector.h:1421:30,
    inlined from ‘std::vector<HoughCenters> getCenters(Raster*, double, double, unsigned int)’ at methods.cpp:142:28:
classes.h:179:7: warning: ‘g_cen.HoughCenters::main_circle’ may be used uninitialized [-Wmaybe-uninitialized]
  179 | class HoughCenters{
      |       ^~~~~~~~~~~~
methods.cpp: In function ‘std::vector<HoughCenters> getCenters(Raster*, double, double, unsigned int)’:
methods.cpp:135:22: note: ‘g_cen’ declared here
  135 |         HoughCenters g_cen;
      |                      ^~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 pcv.cpp -o pcv.o
In file included from /data/gannet/ripley/R/test-dev/lidR/include/SpatialIndex.h:6,
                 from pcv.h:33,
                 from pcv.cpp:18:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:166:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  166 |   while (pts.size() < k && pts.size() < npoints)
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:193:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  193 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius) {
      |                              ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:223:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  223 |   while (pts.size() < k && pts.size() < npoints) {
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:248:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  248 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius)
      |                              ~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 r_interface.cpp -o r_interface.o
In file included from /data/gannet/ripley/R/test-dev/lidR/include/SpatialIndex.h:6,
                 from pcv.h:33,
                 from r_interface.cpp:23:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:166:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  166 |   while (pts.size() < k && pts.size() < npoints)
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:193:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  193 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius) {
      |                              ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:223:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  223 |   while (pts.size() < k && pts.size() < npoints) {
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:248:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  248 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius)
      |                              ~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 ssao.cpp -o ssao.o
In file included from /data/gannet/ripley/R/test-dev/lidR/include/SpatialIndex.h:6,
                 from ssao.h:29,
                 from ssao.cpp:18:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:166:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  166 |   while (pts.size() < k && pts.size() < npoints)
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXY&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:193:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  193 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius) {
      |                              ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:223:39: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  223 |   while (pts.size() < k && pts.size() < npoints) {
      |                            ~~~~~~~~~~~^~~~~~~~~
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h: In member function ‘void lidR::SparsePartition3D::knn(const lidR::PointXYZ&, unsigned int, double, std::vector<lidR::Point3D<double, double, double, unsigned int> >&)’:
/data/gannet/ripley/R/test-dev/lidR/include/lidR/SparsePartition.h:248:41: warning: comparison of integer expressions of different signedness: ‘std::vector<lidR::Point3D<double, double, double, unsigned int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  248 |     while (pts.size() < k && pts.size() < npoints && radius <= maxradius)
      |                              ~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I'/data/gannet/ripley/R/test-dev/lidR/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/BH/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 utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o spanner.so Progress.o RcppExports.o algorithms.o code.o methods.o pcv.o r_interface.o ssao.o utils.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spanner/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spanner/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spanner/src'
installing to /data/gannet/ripley/R/packages/tests-devel/spanner.Rcheck/00LOCK-spanner/00new/spanner/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (spanner)