* installing *source* package ‘SBIOS’ ...
** this is package ‘SBIOS’ version ‘1.0’
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.7 (10)’
using C++17
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c RcppExports.cpp -o RcppExports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c SBIOS0.cpp -o SBIOS0.o
SBIOS0.cpp:173:11: warning: unused variable 'pr' [-Wunused-variable]
  173 |       int pr = Q.n_rows;
      |           ^~
SBIOS0.cpp:152:10: warning: unused variable 'save_eta_count' [-Wunused-variable]
  152 |   double save_eta_count = 0;
      |          ^~~~~~~~~~~~~~
2 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c SBIOS_help_fun.cpp -o SBIOS_help_fun.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c SBIOSimp.cpp -o SBIOSimp.o
SBIOSimp.cpp:355:10: warning: variable 'sigma_Y2_diff' set but not used [-Wunused-but-set-variable]
  355 |   double sigma_Y2_diff=0;
      |          ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c method2_final_zero_imp_allSGLD.cpp -o method2_final_zero_imp_allSGLD.o
method2_final_zero_imp_allSGLD.cpp:188:11: warning: unused variable 'pr' [-Wunused-variable]
  188 |       int pr = Q.n_rows;
      |           ^~
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigstatsr/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RSpectra/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c method2_gs_noMem.cpp -o method2_gs_noMem.o
method2_gs_noMem.cpp:184:11: warning: unused variable 'Lr' [-Wunused-variable]
  184 |       int Lr = D.n_elem;
      |           ^~
method2_gs_noMem.cpp:185:11: warning: unused variable 'pr' [-Wunused-variable]
  185 |       int pr = Q.n_rows;
      |           ^~
method2_gs_noMem.cpp:323:12: warning: unused variable 'b_Y' [-Wunused-variable]
  323 |     double b_Y=0; // for sigma_Y2 update
      |            ^~~
3 warnings generated.
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SBIOS.so RcppExports.o SBIOS0.o SBIOS_help_fun.o SBIOSimp.o method2_final_zero_imp_allSGLD.o method2_gs_noMem.o -llapack -L/home/hornik/tmp/R/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN_pretest/SBIOS.Rcheck/00LOCK-SBIOS/00new/SBIOS/libs
** R
** 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 (SBIOS)