* installing *source* package ‘GSE’ ... ** package ‘GSE’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GSE/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cov-em.cpp -o cov-em.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c emve.cpp -o emve.o In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from cov-em.h:4, from cov-em.cpp:1: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from emve.h:4, from emve.cpp:4: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c gse-rocke.cpp -o gse-rocke.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c gse.cpp -o gse.o In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from gse-rocke.h:4, from gse-rocke.cpp:1: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo:26, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29, from gse.h:4, from gse.cpp:1: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ 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){ | ~~~^~~~ emve.cpp:153:16: warning: variable 'max_cand_scale' set but not used [-Wunused-but-set-variable] 153 | double max_cand_scale; | ^~~~~~~~~~~~~~ emve.cpp:154:16: warning: variable 'min_cand_scale' set but not used [-Wunused-but-set-variable] 154 | double min_cand_scale; | ^~~~~~~~~~~~~~ gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.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(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); | ^~~~~~~ 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(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); | ^~~~~~~ g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o GSE.so cov-em.o emve.o gse-rocke.o gse.o init.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GSE/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GSE/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GSE/src' installing to /data/gannet/ripley/R/packages/tests-devel/GSE.Rcheck/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)