Install log for 'PLNmodels'

* installing *source* package ‘PLNmodels’ ...
** this is package ‘PLNmodels’ version ‘1.3.0’
** 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 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_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_zipln_mstep.cpp -o optim_zipln_mstep.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
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:49:48:
/data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/memory.hpp:125:14: warning: ‘void free(void*)’ called on pointer ‘*(double**)((char*)&packed + offsetof(std::vector<double, std::allocator<double> >,std::vector<double, std::allocator<double> >::<unnamed>.std::_Vector_base<double, std::allocator<double> >::_M_impl.std::_Vector_base<double, std::allocator<double> >::_Vector_impl::<unnamed>.std::allocator<double>::<unnamed>))’ with nonzero offset [320, 34359738680] [-Wfree-nonheap-object]
  125 |     std::free( (void *)(mem) );
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~
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
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 wrappers_builtin_optim_pln.cpp -o wrappers_builtin_optim_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 wrappers_builtin_optim_plnpca.cpp -o wrappers_builtin_optim_plnpca.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 wrappers_builtin_optim_zipln.cpp -o wrappers_builtin_optim_zipln.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 wrappers_nlopt_optim_pln.cpp -o wrappers_nlopt_optim_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 wrappers_nlopt_optim_plnpca.cpp -o wrappers_nlopt_optim_plnpca.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 wrappers_nlopt_optim_zipln.cpp -o wrappers_nlopt_optim_zipln.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o PLNmodels.so RcppExports.o nlopt_wrapper.o optim_genet_cov.o optim_zipln_mstep.o packing.o utils-R.o wrappers_builtin_optim_pln.o wrappers_builtin_optim_plnpca.o wrappers_builtin_optim_zipln.o wrappers_nlopt_optim_pln.o wrappers_nlopt_optim_plnpca.o wrappers_nlopt_optim_zipln.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)