* 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++.exe (GCC) 14.2.0'
make[1]: Entering directory '/d/temp/2025_09_29_01_50_00_31777/Rtmp84f9lY/R.INSTALL29be854b64f1f/EstMix/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcll_1d_baf.cpp -o calcll_1d_baf.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_1d_baf.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:201:
D:/RCompile/CRANpkg/lib/4.5/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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:692:
D:/RCompile/CRANpkg/lib/4.5/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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcll_baf.cpp -o calcll_baf.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_baf.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:201:
D:/RCompile/CRANpkg/lib/4.5/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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:692:
D:/RCompile/CRANpkg/lib/4.5/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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcll_cpp.cpp -o calcll_cpp.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_cpp.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:201:
D:/RCompile/CRANpkg/lib/4.5/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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:692:
D:/RCompile/CRANpkg/lib/4.5/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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcll_p1_cpp.cpp -o calcll_p1_cpp.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_p1_cpp.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:201:
D:/RCompile/CRANpkg/lib/4.5/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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:692:
D:/RCompile/CRANpkg/lib/4.5/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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcll_p3.cpp -o calcll_p3.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from calcll_p3.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:204:
D:/RCompile/CRANpkg/lib/4.5/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 D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:695:
D:/RCompile/CRANpkg/lib/4.5/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++ -std=gnu++17 -shared -s -static-libgcc -o EstMix.dll tmp.def RcppExports.o calcll_1d_baf.o calcll_baf.o calcll_cpp.o calcll_p1_cpp.o calcll_p3.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_09_29_01_50_00_31777/Rtmp84f9lY/R.INSTALL29be854b64f1f/EstMix/src'
make[1]: Entering directory '/d/temp/2025_09_29_01_50_00_31777/Rtmp84f9lY/R.INSTALL29be854b64f1f/EstMix/src'
make[1]: Leaving directory '/d/temp/2025_09_29_01_50_00_31777/Rtmp84f9lY/R.INSTALL29be854b64f1f/EstMix/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-EstMix/00new/EstMix/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'EstMix' as EstMix_1.0.1.zip
* DONE (EstMix)