* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘EstMix’ ...
** this is package ‘EstMix’ version ‘1.0.1’
** package ‘EstMix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’
make[1]: Entering directory '/tmp/RtmpjcKHAM/R.INSTALL1aa4287d633993/EstMix/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-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++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcll_1d_baf.cpp -o calcll_1d_baf.o
calcll_1d_baf.cpp: In function ‘Rcpp::List calcll_1d_baf(double, double, double, double, arma::mat, arma::mat, double, int, int)’:
calcll_1d_baf.cpp:51:31: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
51 | lmax_baf = L_baf.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:201,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_1d_baf.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:71: note: declared here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^~~
calcll_1d_baf.cpp:56:25: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
56 | L(i,j) = L_tot.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:692:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7871:1: note: declared here
7871 | Mat<eT>::min(uword& row_of_min_val, uword& col_of_min_val) const
| ^~~~~~~
calcll_1d_baf.cpp:18:10: warning: variable ‘Var’ set but not used [-Wunused-but-set-variable]
18 | double Var;
| ^~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcll_baf.cpp -o calcll_baf.o
calcll_baf.cpp: In function ‘Rcpp::List calcll_baf(double, double, double, double, arma::mat, arma::mat, double, int, int)’:
calcll_baf.cpp:55:31: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
55 | lmax_baf = L_baf.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:201,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_baf.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:71: note: declared here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^~~
calcll_baf.cpp:61:25: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
61 | L(i,j) = L_tot.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:692:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7871:1: note: declared here
7871 | Mat<eT>::min(uword& row_of_min_val, uword& col_of_min_val) const
| ^~~~~~~
calcll_baf.cpp:18:10: warning: variable ‘Var’ set but not used [-Wunused-but-set-variable]
18 | double Var;
| ^~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcll_cpp.cpp -o calcll_cpp.o
calcll_cpp.cpp: In function ‘Rcpp::List calcll_cpp(arma::vec&, arma::vec&, arma::mat, arma::mat, double, double, double, int, int)’:
calcll_cpp.cpp:54:31: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
54 | lmax_baf = L_baf.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:201,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_cpp.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:71: note: declared here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^~~
calcll_cpp.cpp:61:25: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
61 | L(i,j) = L_tot.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:692:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7871:1: note: declared here
7871 | Mat<eT>::min(uword& row_of_min_val, uword& col_of_min_val) const
| ^~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcll_p1_cpp.cpp -o calcll_p1_cpp.o
calcll_p1_cpp.cpp: In function ‘Rcpp::List calcll_p1_cpp(arma::vec&, arma::vec&, arma::mat, arma::mat, double, double, double, int, int)’:
calcll_p1_cpp.cpp:57:31: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
57 | lmax_baf = L_baf.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:201,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_p1_cpp.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:71: note: declared here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^~~
calcll_p1_cpp.cpp:66:25: warning: ‘eT arma::Mat<eT>::min(arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
66 | L(i,j) = L_tot.min(row,col);
| ~~~~~~~~~^~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:692:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7871:1: note: declared here
7871 | Mat<eT>::min(uword& row_of_min_val, uword& col_of_min_val) const
| ^~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcll_p3.cpp -o calcll_p3.o
calcll_p3.cpp: In function ‘arma::cube calcll_p3(arma::vec&, arma::vec&, double, double, double, int, int)’:
calcll_p3.cpp:62:35: warning: ‘eT arma::Cube<eT>::min(arma::uword&, arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
62 | lmax_baf = L_baf.min(row,col,slice);L_tot(r1,r2,r3) += lmax_baf;
| ~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:204,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_p3.cpp:1:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Cube_bones.hpp:393:71: note: declared here
393 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val, uword& slice_of_min_val) const;
| ^~~
calcll_p3.cpp:64:29: warning: ‘eT arma::Cube<eT>::min(arma::uword&, arma::uword&, arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
64 | L(i,j,k) = L_tot.min(row,col,slice);
| ~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:695:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/Cube_meat.hpp:4529:1: note: declared here
4529 | Cube<eT>::min(uword& row_of_min_val, uword& col_of_min_val, uword& slice_of_min_val) const
| ^~~~~~~~
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o EstMix.so RcppExports.o calcll_1d_baf.o calcll_baf.o calcll_cpp.o calcll_p1_cpp.o calcll_p3.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpjcKHAM/R.INSTALL1aa4287d633993/EstMix/src'
make[1]: Entering directory '/tmp/RtmpjcKHAM/R.INSTALL1aa4287d633993/EstMix/src'
make[1]: Leaving directory '/tmp/RtmpjcKHAM/R.INSTALL1aa4287d633993/EstMix/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-EstMix/00new/EstMix/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (EstMix)