* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘GSE’ ...
** this is package ‘GSE’ version ‘4.2-3’
** package ‘GSE’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 21.1.6 (2)’
using C++ compiler: ‘Debian clang version 21.1.6 (2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpEhAQI4/R.INSTALL1443999833c52/GSE/src'
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c cov-em.cpp -o cov-em.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c emve.cpp -o emve.o
In file included from emve.cpp:4:
In file included from ./emve.h:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include/RcppCommon.h:30:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
   27 |     #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
      |             ^
1 warning generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c gse-rocke.cpp -o gse-rocke.o
gse-rocke.cpp:46:6: warning: unused variable 'print_step' [-Wunused-variable]
   46 |         int print_step = as<int>(Print_step);
      |             ^~~~~~~~~~
gse-rocke.cpp:131:6: warning: unused variable 'ximp_update' [-Wunused-variable]
  131 |         int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, gamma_tune_group, wgts_mem, wgtsp_mem, ximp_mem);
      |             ^~~~~~~~~~~
gse-rocke.cpp:162:6: warning: variable 'error_code' set but not used [-Wunused-but-set-variable]
  162 |         int error_code = *error_code_mem; // 0 = no error, 1 = non-positive scale, 2 = non-positive definite est scatter
      |             ^
gse-rocke.cpp:295:6: warning: unused variable 'n' [-Wunused-variable]
  295 |         int n = x.n_rows;
      |             ^
gse-rocke.cpp:416:12: warning: unused variable 'weight2' [-Wunused-variable]
  416 |                                 double weight2 = weight1 * (md / ppi);
      |                                        ^~~~~~~
5 warnings generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c gse.cpp -o gse.o
gse.cpp:41:9: warning: unused variable 'print_step' [-Wunused-variable]
   41 |     int print_step = as<int>(Print_step);
      |         ^~~~~~~~~~
gse.cpp:102:9: warning: unused variable 'ximp_update' [-Wunused-variable]
  102 |     int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, wgts_mem, wgtsp_mem, ximp_mem);
      |         ^~~~~~~~~~~
gse.cpp:132:9: warning: variable 'error_code' set but not used [-Wunused-but-set-variable]
  132 |     int error_code = *error_code_mem; // 0 = no error, 1 = non-positive scale, 2 = non-positive definite est scatter
      |         ^
gse.cpp:337:24: warning: unused variable 'weight2' [-Wunused-variable]
  337 |                 double weight2 = weight1 * (md / ppi);
      |                        ^~~~~~~
4 warnings generated.
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o GSE.so cov-em.o emve.o gse-rocke.o gse.o init.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpEhAQI4/R.INSTALL1443999833c52/GSE/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpEhAQI4/R.INSTALL1443999833c52/GSE/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpEhAQI4/R.INSTALL1443999833c52/GSE/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-GSE/00new/GSE/libs
** R
** data
** 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 (GSE)