* 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: ‘clang version 21.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/EstMix/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcll_1d_baf.cpp -o calcll_1d_baf.o
calcll_1d_baf.cpp:51:28: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
51 | lmax_baf = L_baf.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:56:22: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
56 | L(i,j) = L_tot.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:18:10: warning: variable 'Var' set but not used [-Wunused-but-set-variable]
18 | double Var;
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcll_baf.cpp -o calcll_baf.o
calcll_baf.cpp:55:28: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
55 | lmax_baf = L_baf.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:61:22: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
61 | L(i,j) = L_tot.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:18:10: warning: variable 'Var' set but not used [-Wunused-but-set-variable]
18 | double Var;
| ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcll_cpp.cpp -o calcll_cpp.o
calcll_cpp.cpp:54:28: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
54 | lmax_baf = L_baf.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:61:22: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
61 | L(i,j) = L_tot.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcll_p1_cpp.cpp -o calcll_p1_cpp.o
calcll_p1_cpp.cpp:57:28: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
57 | lmax_baf = L_baf.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated 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:66:22: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
66 | L(i,j) = L_tot.min(row,col);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:547:5: note: 'min' has been explicitly marked deprecated here
547 | [[deprecated("use .index_min() with ind2sub() instead")]] inline eT min(uword& row_of_min_val, uword& col_of_min_val) const;
| ^
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcll_p3.cpp -o calcll_p3.o
calcll_p3.cpp:62:32: warning: 'min' 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;
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Cube_bones.hpp:393:5: note: 'min' has been explicitly marked deprecated 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:64:26: warning: 'min' is deprecated: use .index_min() with ind2sub() instead [-Wdeprecated-declarations]
64 | L(i,j,k) = L_tot.min(row,col,slice);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/Cube_bones.hpp:393:5: note: 'min' has been explicitly marked deprecated 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;
| ^
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o EstMix.so RcppExports.o calcll_1d_baf.o calcll_baf.o calcll_cpp.o calcll_p1_cpp.o calcll_p3.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/EstMix/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/EstMix/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/EstMix/src'
installing to /data/gannet/ripley/R/packages/tests-clang/EstMix.Rcheck/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)