* installing *source* package ‘GSE’ ... ** package ‘GSE’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/GSE/src' /usr/local/clang18/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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cov-em.cpp -o cov-em.o In file included from cov-em.cpp:1: In file included from ./cov-em.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c emve.cpp -o emve.o /usr/local/clang18/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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c gse-rocke.cpp -o gse-rocke.o In file included from emve.cpp:4: In file included from ./emve.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from gse-rocke.cpp:1: In file included from ./gse-rocke.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c gse.cpp -o gse.o In file included from gse.cpp:1: In file included from ./gse.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ 3 warnings generated. /usr/local/clang18/bin/clang -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/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o 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; | ^ gse-rocke.cpp:46:6: warning: unused variable 'print_step' [-Wunused-variable] 46 | int print_step = as(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); | ^~~~~~~ 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: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); | ^~~~~~~ 5 warnings generated. 8 warnings generated. 7 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o GSE.so cov-em.o emve.o gse-rocke.o gse.o init.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/GSE/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/GSE/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/GSE/src' installing to /data/gannet/ripley/R/packages/tests-clang/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)