* installing *source* package ‘bamm’ ...
** this is package ‘bamm’ version ‘0.6.0’
** package ‘bamm’ 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[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/bamm/src'
g++ -std=gnu++17 -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    -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 -flto=10  -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/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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 -flto=10  -c randomize_pams.cpp -o randomize_pams.o
g++ -std=gnu++17 -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    -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 -flto=10  -c sdm_sim.cpp -o sdm_sim.o
sdm_sim.cpp: In function ‘arma::sp_mat safe_spmat_conversion(SEXP)’:
sdm_sim.cpp:50:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   50 |   for (int col = 0; col < n_cols; col++) {
      |                     ~~~~^~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o bamm.so RcppExports.o randomize_pams.o sdm_sim.o
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:27:7: warning: type ‘struct Mat’ violates the C++ One Definition Rule [-Wodr]
   27 | class Mat : public Base< eT, Mat<eT> >
      |       ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:27:7: note: a different type is defined in another translation unit
   27 | class Mat : public Base< eT, Mat<eT> >
      |       ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:34:16: note: the first difference of corresponding definitions is field ‘n_rows’
   34 |   const uword  n_rows;    //!< number of rows               (read-only)
      |                ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:34:16: note: a field of same name but different type is defined in another translation unit
   34 |   const uword  n_rows;    //!< number of rows               (read-only)
      |                ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Col_bones.hpp:25:7: warning: type ‘struct Col’ violates the C++ One Definition Rule [-Wodr]
   25 | class Col : public Mat<eT>
      |       ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Col_bones.hpp:25:7: note: a type with different bases is defined in another translation unit
   25 | class Col : public Mat<eT>
      |       ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:303:1: warning: type of ‘init_cold’ does not match original declaration [-Wlto-type-mismatch]
  303 | Mat<eT>::init_cold()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:303:1: note: ‘init_cold’ was previously declared here
  303 | Mat<eT>::init_cold()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:303:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: warning: type of ‘__dt_comp ’ does not match original declaration [-Wlto-type-mismatch]
   25 | Mat<eT>::~Mat()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: note: ‘__dt_comp ’ was previously declared here
   25 | Mat<eT>::~Mat()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: warning: type of ‘__dt_base ’ does not match original declaration [-Wlto-type-mismatch]
   25 | Mat<eT>::~Mat()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: note: ‘__dt_base ’ was previously declared here
   25 | Mat<eT>::~Mat()
      | ^
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:25:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/bamm/src'
installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/bamm-lib/00LOCK-bamm/00new/bamm/libs
** R
** 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 (bamm)
Time 3:13.26, 130.76 + 6.65