* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ATNr’ ...
** this is package ‘ATNr’ version ‘1.1.1’
** package ‘ATNr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOHNjwZ/R.INSTALL3b175150c95a62/ATNr/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Scaled.cpp -o Scaled.o
Scaled.cpp: In member function ‘arma::vec Scaled::ODE(arma::vec, double)’:
Scaled.cpp:166:20: warning: ‘arma::Mat<typename T1::elem_type> arma::pow(const subview_each1<parent, mode>&, const Base<typename parent::elem_type, T2>&) [with parent = Mat<double>; unsigned int mode = 1; T2 = Op<Col<double>, op_htrans>; typename T1::elem_type = double; typename parent::elem_type = double]’ is deprecated: refactor your code to use pow() in conjunction with repmat() [-Wdeprecated-declarations]
166 | pow_bioms = pow(pow_bioms.each_row(), q.t());
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:614,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from Scaled.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
50 | pow
| ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Scaled_loops.cpp -o Scaled_loops.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Unscaled.cpp -o Unscaled.o
Unscaled.cpp: In member function ‘arma::vec Unscaled::ODE(arma::vec, double)’:
Unscaled.cpp:145:20: warning: ‘arma::Mat<typename T1::elem_type> arma::pow(const subview_each1<parent, mode>&, const Base<typename parent::elem_type, T2>&) [with parent = Mat<double>; unsigned int mode = 1; T2 = Op<Col<double>, op_htrans>; typename T1::elem_type = double; typename parent::elem_type = double]’ is deprecated: refactor your code to use pow() in conjunction with repmat() [-Wdeprecated-declarations]
145 | pow_bioms = pow(pow_bioms.each_row(), q.t());
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:614,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from Unscaled.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
50 | pow
| ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Unscaled_loops.cpp -o Unscaled_loops.o
Unscaled_loops.cpp: In constructor ‘Unscaled_loops::Unscaled_loops(int, int)’:
Unscaled_loops.cpp:101:29: warning: unused variable ‘cons’ [-Wunused-variable]
101 | IntegerVector::iterator cons;
| ^~~~
Unscaled_loops.cpp:102:29: warning: unused variable ‘cons2’ [-Wunused-variable]
102 | IntegerVector::iterator cons2;
| ^~~~~
Unscaled_loops.cpp:103:29: warning: unused variable ‘res’ [-Wunused-variable]
103 | IntegerVector::iterator res;
| ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Unscaled_nuts.cpp -o Unscaled_nuts.o
Unscaled_nuts.cpp: In member function ‘arma::vec Unscaled_nuts::ODE(arma::vec, double)’:
Unscaled_nuts.cpp:195:20: warning: ‘arma::Mat<typename T1::elem_type> arma::pow(const subview_each1<parent, mode>&, const Base<typename parent::elem_type, T2>&) [with parent = Mat<double>; unsigned int mode = 1; T2 = Op<Col<double>, op_htrans>; typename T1::elem_type = double; typename parent::elem_type = double]’ is deprecated: refactor your code to use pow() in conjunction with repmat() [-Wdeprecated-declarations]
195 | pow_bioms = pow(pow_bioms.each_row(), q.t());
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:614,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from Unscaled_nuts.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
50 | pow
| ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Unscaled_nuts_loops.cpp -o Unscaled_nuts_loops.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ATNr.so RcppExports.o Scaled.o Scaled_loops.o Unscaled.o Unscaled_loops.o Unscaled_nuts.o Unscaled_nuts_loops.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOHNjwZ/R.INSTALL3b175150c95a62/ATNr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOHNjwZ/R.INSTALL3b175150c95a62/ATNr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOHNjwZ/R.INSTALL3b175150c95a62/ATNr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ATNr/00new/ATNr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ATNr’
finding HTML links ... done
Scaled html
Scaled_loops html
TroLev html
Unscaled html
Unscaled_loops html
Unscaled_nuts html
Unscaled_nuts_loops html
create_Lmatrix html
create_matrix_parameter html
create_model_Scaled html
create_model_Unscaled html
create_model_Unscaled_nuts html
create_niche_model html
dot-filter_extinct html
dot-remove_Scaled html
dot-remove_Unscaled html
dot-remove_Unscaled_nuts html
initialise_default_Scaled html
initialise_default_Unscaled html
initialise_default_Unscaled_nuts html
is_connected html
jacobian html
lsoda_wrapper html
plot_odeweb html
remove_species html
run_checks html
schneider html
sort_input html
** 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 (ATNr)