Install log for 'lidR'

* installing *source* package ‘lidR’ ...
** this is package ‘lidR’ version ‘4.2.2’
** package ‘lidR’ 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)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/lidR/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 C_Gatziolis2019.cpp -o C_Gatziolis2019.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 C_chm_prep.cpp -o C_chm_prep.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 C_dalponte2016.cpp -o C_dalponte2016.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 C_delaunay.cpp -o C_delaunay.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 LAS.cpp -o LAS.o
In file included from ../inst/include/SpatialIndex.h:6,
                 from LAS.cpp:4:
../inst/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> >&)’:
../inst/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)
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                              ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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)
      |                              ~~~~~~~~~~~^~~~~~~~~
LAS.cpp: In member function ‘void LAS::filter_local_maxima(Rcpp::NumericVector, double, bool)’:
LAS.cpp:413:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  413 |   for (int i = 0 ; i < npoints ; i++) { if (Z[i] < min_height) state[i] = NLM; }
      |                    ~~^~~~~~~~~
LAS.cpp:401:8: warning: unused variable ‘UKN’ [-Wunused-variable]
  401 |   char UKN = 0;
      |        ^~~
LAS.cpp:403:8: warning: unused variable ‘LMX’ [-Wunused-variable]
  403 |   char LMX = 2;
      |        ^~~
LAS.cpp: In member function ‘void LAS::filter_local_maxima(Rcpp::NumericVector)’:
LAS.cpp:489:10: warning: variable ‘orientation’ set but not used [-Wunused-but-set-variable]
  489 |   double orientation = 0;
      |          ^~~~~~~~~~~
LAS.cpp: In member function ‘SEXPREC* LAS::find_polygon_ids(Rcpp::List, bool)’:
LAS.cpp:666:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  666 |     for (size_t pid = 0; pid < X.size(); pid++)
      |                          ~~~~^~~~~~~~~~
LAS.cpp: In member function ‘void LAS::filter_isolated_voxel(double, unsigned int)’:
LAS.cpp:855:10: warning: unused variable ‘zmax’ [-Wunused-variable]
  855 |   double zmax = max(Z);
      |          ^~~~
LAS.cpp: In member function ‘Rcpp::DataFrame LAS::fast_eigen_decomposition(int, double, bool)’:
LAS.cpp:1710:22: warning: unused variable ‘found’ [-Wunused-variable]
 1710 |         const size_t found = tree.radiusSearch(p, rsq+EPSILON, matches);
      |                      ^~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 RcppFunction.cpp -o RcppFunction.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 UnitTests.cpp -o UnitTests.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 altrep.cpp -o altrep.o
In file included from ../inst/include/SpatialIndex.h:6,
                 from UnitTests.cpp:2:
../inst/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> >&)’:
../inst/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)
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                              ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 convaveman.cpp -o convaveman.o
In file included from ../inst/include/SpatialIndex.h:6,
                 from RcppFunction.cpp:471:
../inst/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> >&)’:
../inst/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)
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                              ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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) {
      |                            ~~~~~~~~~~~^~~~~~~~~
../inst/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> >&)’:
../inst/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  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 knn.cpp -o knn.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rnanoflann/include' -I/usr/local/include   -fopenmp -I../inst/include/ -DRCPP_NO_MODULES -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 openmputils.cpp -o openmputils.o
knn.cpp: In function ‘Rcpp::List cpp_knn(Rcpp::S4, int, int)’:
knn.cpp:59:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   59 |   for (unsigned int i = 0; i < npoints; i++)
      |                            ~~^~~~~~~~~
knn.cpp:70:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |     for (auto j = 1; j < indices.size(); j++)
      |                      ~~^~~~~~~~~~~~~~~~
knn.cpp: In function ‘Rcpp::List cpp_knnx(Rcpp::S4, Rcpp::S4, int, int)’:
knn.cpp:107:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  107 |   for (unsigned int i = 0 ; i < npoints ; i++)
      |                             ~~^~~~~~~~~
knn.cpp:118:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  118 |     for (auto j = 0; j < indices.size(); j++)
      |                      ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o lidR.so C_Gatziolis2019.o C_chm_prep.o C_dalponte2016.o C_delaunay.o LAS.o Progress.o RcppExports.o RcppFunction.o UnitTests.o altrep.o convaveman.o knn.o openmputils.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/lidR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/lidR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/lidR/src'
installing to /data/gannet/ripley/R/packages/tests-devel/lidR.Rcheck/00LOCK-lidR/00new/lidR/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 (lidR)