* installing *source* package ‘GSE’ ...
** package ‘GSE’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.2’
using C++ compiler: ‘clang version 18.1.2’
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
/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
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 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.
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;
| ^
/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
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);
| ^~~~~~~
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);
| ^~~~~~~
5 warnings generated.
7 warnings generated.
8 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)