Install log for 'PLNmodels'

* installing *source* package ‘PLNmodels’ ...
** this is package ‘PLNmodels’ version ‘1.2.2’
** package ‘PLNmodels’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/PLNmodels/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c lambertW.cpp -o lambertW.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c nlopt_wrapper.cpp -o nlopt_wrapper.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_diag_cov.cpp -o optim_diag_cov.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_fixed_cov.cpp -o optim_fixed_cov.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_full_cov.cpp -o optim_full_cov.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_genet_cov.cpp -o optim_genet_cov.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_rank_cov.cpp -o optim_rank_cov.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_spherical.cpp -o optim_spherical.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c optim_zi-pln.cpp -o optim_zi-pln.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c packing.cpp -o packing.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/nloptr/include' -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/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   -c utils-R.cpp -o utils-R.o
In file included from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo:437,
                 from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51,
                 from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
                 from packing.h:7,
                 from packing.cpp:1:
In static member function ‘static void arma::memory::release(eT*) [with eT = const double]’,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:32:20,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:25:1,
    inlined from ‘arma::Col<double>::~Col()’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Col_bones.hpp:25:7,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:37:48:
/data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/memory.hpp:125:14: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  125 |     std::free( (void *)(mem) );
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/16/x86_64-redhat-linux/bits/c++allocator.h:33,
                 from /usr/include/c++/16/bits/allocator.h:46,
                 from /usr/include/c++/16/bits/alloc_traits.h:39,
                 from /usr/include/c++/16/ext/alloc_traits.h:36,
                 from /usr/include/c++/16/bits/hashtable_policy.h:40,
                 from /usr/include/c++/16/bits/hashtable.h:37,
                 from /usr/include/c++/16/bits/unordered_map.h:33,
                 from /usr/include/c++/16/unordered_map:43,
                 from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:39,
                 from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:67,
                 from /data/localhost/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
                 from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
In member function ‘constexpr _Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
    inlined from ‘constexpr _Tp* std::allocator< <template-parameter-1-1> >::allocate(std::size_t) [with _Tp = double]’ at /usr/include/c++/16/bits/allocator.h:206:40,
    inlined from ‘static constexpr _Tp* std::allocator_traits<std::allocator<_Up> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
    inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
    inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:27:59:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: returned from ‘void* operator new(std::size_t)’
  162 |           return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
      |                                                                           ^
In static member function ‘static void arma::memory::release(eT*) [with eT = const double]’,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:32:20,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:25:1,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:45:26:
/data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/memory.hpp:125:14: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  125 |     std::free( (void *)(mem) );
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function ‘constexpr _Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
    inlined from ‘constexpr _Tp* std::allocator< <template-parameter-1-1> >::allocate(std::size_t) [with _Tp = double]’ at /usr/include/c++/16/bits/allocator.h:206:40,
    inlined from ‘static constexpr _Tp* std::allocator_traits<std::allocator<_Up> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
    inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
    inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:27:59:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: returned from ‘void* operator new(std::size_t)’
  162 |           return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
      |                                                                           ^
In static member function ‘static void arma::memory::release(eT*) [with eT = const double]’,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:32:20,
    inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:25:1,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:47:48:
/data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/memory.hpp:125:14: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  125 |     std::free( (void *)(mem) );
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~
In member function ‘constexpr _Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
    inlined from ‘constexpr _Tp* std::allocator< <template-parameter-1-1> >::allocate(std::size_t) [with _Tp = double]’ at /usr/include/c++/16/bits/allocator.h:206:40,
    inlined from ‘static constexpr _Tp* std::allocator_traits<std::allocator<_Up> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /usr/include/c++/16/bits/alloc_traits.h:638:28,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:389:33,
    inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:407:44,
    inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:341:26,
    inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/16/bits/stl_vector.h:577:47,
    inlined from ‘bool cpp_test_packing()’ at packing.cpp:27:59:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: returned from ‘void* operator new(std::size_t)’
  162 |           return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
      |                                                                           ^
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o PLNmodels.so RcppExports.o lambertW.o nlopt_wrapper.o optim_diag_cov.o optim_fixed_cov.o optim_full_cov.o optim_genet_cov.o optim_rank_cov.o optim_spherical.o optim_zi-pln.o packing.o utils-R.o -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/PLNmodels/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/PLNmodels/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/PLNmodels/src'
installing to /data/localhost/ripley/R/packages/tests-devel/PLNmodels.Rcheck/00LOCK-PLNmodels/00new/PLNmodels/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'sqrt' 
Note: wrong number of arguments to 'sqrt' 
** 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 (PLNmodels)