Install log for 'ATNr'

* 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++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ATNr/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   -fopenmp  -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/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -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 Scaled.cpp -o Scaled.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   -fopenmp  -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 Scaled_loops.cpp -o Scaled_loops.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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:614,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from Scaled.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
   50 | pow
      | ^~~
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   -fopenmp  -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 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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:614,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from Unscaled.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
   50 | pow
      | ^~~
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   -fopenmp  -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 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++ -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   -fopenmp  -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 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 /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:614,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from Unscaled_nuts.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_powext.hpp:50:1: note: declared here
   50 | pow
      | ^~~
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   -fopenmp  -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 Unscaled_nuts_loops.cpp -o Unscaled_nuts_loops.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -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/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ATNr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ATNr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ATNr/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ATNr.Rcheck/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
** 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)