* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘sorcering’ ...
** this is package ‘sorcering’ version ‘1.2.0’
** package ‘sorcering’ 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/Rtmp8swlwW/R.INSTALL179c9c561bc3d3/sorcering/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 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c sorcering.cpp -o sorcering.o
sorcering.cpp: In function ‘Rcpp::List sorcering(Rcpp::Nullable<Rcpp::Matrix<14>&>, const Rcpp::String&, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<SEXPREC**>, Rcpp::Nullable<SEXPREC**>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<SEXPREC**>, Rcpp::Nullable<Rcpp::Matrix<14>&>, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<SEXPREC**>, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, int, Rcpp::Nullable<Rcpp::Matrix<14>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, bool, bool, bool, bool, bool, bool, bool, const Rcpp::NumericVector&, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, bool, Rcpp::Nullable<Rcpp::Vector<13>&>, int, int, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, Rcpp::Nullable<Rcpp::Vector<19>&>, bool, const Rcpp::String&, bool, int, Rcpp::List)’:
sorcering.cpp:1198:57: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
1198 | if (RothC_dpmrpm_arma.n_elem<(list_length) && model.get_cstring()==rothc && RothC_dpmrpm_arma.n_elem>1) c3c +=("Fewer RothC_dpmrpm arguments than sites!");
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
sorcering.cpp:2294:96: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eGlue<arma::subview_elem1<double, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find> >, arma::subview_elem1<double, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find> >, arma::eglue_div>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
2294 | CNbio = arma::conv_to<double>::from( C0_arma.elem(find(pt_arma==2,1))/N0_arma.elem(find(pt_arma==2,1)) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:496,
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 sorcering.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
| ^~~~~~~~~~~~~~~
sorcering.cpp:2329:99: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::eGlue<arma::subview_elem1<double, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find> >, arma::subview_elem1<double, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find> >, arma::eglue_div>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
2329 | double CNres = arma::conv_to<double>::from( C0_arma.elem(find(pt_arma==3,1)) / N0_arma.elem(find(pt_arma==3,1)) );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
| ^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o sorcering.so RcppExports.o sorcering.o -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/Rtmp8swlwW/R.INSTALL179c9c561bc3d3/sorcering/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8swlwW/R.INSTALL179c9c561bc3d3/sorcering/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8swlwW/R.INSTALL179c9c561bc3d3/sorcering/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-sorcering/00new/sorcering/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 ‘sorcering’
finding HTML links ... done
RothC_C0_ex html
RothC_Cin_ex html
RothC_Cin_ex_sl html
RothC_Cin_ex_sl_spin html
RothC_N0_ex html
RothC_Nin_ex html
RothC_Nin_ex_sl html
RothC_Nin_ex_sl_spin html
RothC_env_in_ex html
RothC_site_ex html
RothC_xi_ex html
Yasso_C0_ex_sl html
Yasso_Cin_ex_wood_u_sl html
Yasso_N0_ex_sl html
Yasso_Nin_ex_wood_u_sl html
fget_A_RothC html
meas_data_ex html
sorcering 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 (sorcering)