* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/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: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
make[1]: Entering directory '/tmp/RtmpJnSjji/R.INSTALL1cef9e6d5195ff/GSE/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 cov-em.cpp -o cov-em.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 emve.cpp -o emve.o
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from emve.h:5,
from emve.cpp:4:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#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’
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"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emve.cpp: In function ‘arma::cube emve_resamp(arma::mat, arma::umat, arma::vec, int, int, arma::vec, arma::mat, int, arma::uvec, arma::umat, arma::uvec, arma::umat, arma::umat, arma::uvec, int, int, int, arma::uvec, arma::vec, arma::vec, int)’:
emve.cpp:193:20: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
193 | if( rk == p){
| ~~~^~~~
emve.cpp:216:24: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
216 | if( rk == p){
| ~~~^~~~
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 gse-rocke.cpp -o gse-rocke.o
gse-rocke.cpp: In function ‘SEXPREC* GSE_Rocke(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
gse-rocke.cpp:46:13: warning: unused variable ‘print_step’ [-Wunused-variable]
46 | int print_step = as<int>(Print_step);
| ^~~~~~~~~~
gse-rocke.cpp:131:13: 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: In function ‘arma::mat iterS(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double*, double*, double*, int*)’:
gse-rocke.cpp:263:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
263 | for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
| ~~~^~~
gse-rocke.cpp:162:13: 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: In function ‘arma::mat gradient(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double, int, double)’:
gse-rocke.cpp:295:13: warning: unused variable ‘n’ [-Wunused-variable]
295 | int n = x.n_rows;
| ^
gse-rocke.cpp: In function ‘int update(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double*, double*, double*)’:
gse-rocke.cpp:426:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
426 | for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
| ~~~^~~
gse-rocke.cpp:416:40: warning: unused variable ‘weight2’ [-Wunused-variable]
416 | double weight2 = weight1 * (md / ppi);
| ^~~~~~~
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 gse.cpp -o gse.o
gse.cpp: In function ‘SEXPREC* GSE_Rcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
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: In function ‘arma::mat iterS(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, double*, double*, double*, int*)’:
gse.cpp:233:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
233 | for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
| ~~~^~~
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: In function ‘int update(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, double*, double*, double*)’:
gse.cpp:347:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
347 | for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
| ~~~^~~
gse.cpp:337:24: warning: unused variable ‘weight2’ [-Wunused-variable]
337 | double weight2 = weight1 * (md / ppi);
| ^~~~~~~
gcc-15 -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 -Wstrict-prototypes -pedantic -mtune=native -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'.
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/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-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/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 '/tmp/RtmpJnSjji/R.INSTALL1cef9e6d5195ff/GSE/src'
make[1]: Entering directory '/tmp/RtmpJnSjji/R.INSTALL1cef9e6d5195ff/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 '/tmp/RtmpJnSjji/R.INSTALL1cef9e6d5195ff/GSE/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/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)