* installing *source* package ‘RxCEcolInf’ ... ** package ‘RxCEcolInf’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf/src' /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c RxCEcolInf_init.c -o RxCEcolInf_init.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c covariates.c -o covariates.o covariates.c:139:18: warning: unused variable 'tvec2_dimOMs' [-Wunused-variable] Matrix * const tvec2_dimOMs = rmatrix_new(1, p); ^ covariates.c:6:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ covariates.c:138:18: warning: unused variable 'tvec1_dimOMs' [-Wunused-variable] Matrix * const tvec1_dimOMs = rmatrix_new(1, p); ^ covariates.c:12:8: warning: unused variable 'acc_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ covariates.c:12:33: warning: unused variable 'vld_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ covariates.c:11:8: warning: unused variable 'acc_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ covariates.c:11:30: warning: unused variable 'vld_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ covariates.c:883:23: warning: unused variable 'current_ladder' [-Wunused-variable] index_t ladder_num, current_ladder; // Need to initialize ^ covariates.c:883:11: warning: unused variable 'ladder_num' [-Wunused-variable] index_t ladder_num, current_ladder; // Need to initialize ^ covariates.c:889:10: warning: unused variable 'log_p_theta_j_data_i' [-Wunused-variable] double log_p_theta_j_data_i = 0.0; ^ covariates.c:888:10: warning: unused variable 'log_p_theta_i_data_j' [-Wunused-variable] double log_p_theta_i_data_j = 0.0; ^ covariates.c:565:18: warning: unused variable 'tvec2_dimOMs' [-Wunused-variable] Matrix * const tvec2_dimOMs = rmatrix_new(1, p); ^ covariates.c:887:10: warning: unused variable 'log_p_theta_i_data_i' [-Wunused-variable] double log_p_theta_i_data_i = 0.0; ^ covariates.c:386:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ covariates.c:886:7: warning: unused variable 'rsign' [-Wunused-variable] int rsign=0; ^ covariates.c:564:18: warning: unused variable 'tvec1_dimOMs' [-Wunused-variable] Matrix * const tvec1_dimOMs = rmatrix_new(1, p); ^ covariates.c:885:22: warning: unused variable 'chain_j' [-Wunused-variable] index_t chain_i=0, chain_j=0; ^ covariates.c:885:11: warning: unused variable 'chain_i' [-Wunused-variable] index_t chain_i=0, chain_j=0; ^ covariates.c:891:10: warning: unused variable 're_log_mh_ratio' [-Wunused-variable] double re_log_mh_ratio = 0.0; ^ covariates.c:890:10: warning: unused variable 'log_p_theta_j_data_j' [-Wunused-variable] double log_p_theta_j_data_j = 0.0; ^ covariates.c:601:66: warning: variable 'kk' is uninitialized when used here [-Wuninitialized] error("Invalid dimension of NNs starting state (level %u)",kk+1); ^~ covariates.c:382:13: note: initialize the variable 'kk' to silence this warning index_t kk; ^ = 0 21 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c exitpoll.c -o exitpoll.o exitpoll.c:12:33: warning: unused variable 'vld_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ exitpoll.c:12:8: warning: unused variable 'acc_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ exitpoll.c:11:30: warning: unused variable 'vld_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ exitpoll.c:11:8: warning: unused variable 'acc_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ exitpoll.c:6:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ exitpoll.c:355:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ exitpoll.c:542:17: warning: unused variable 'tptr' [-Wunused-variable] SEXP checker, tptr; ^ exitpoll.c:351:11: warning: unused variable 'kk' [-Wunused-variable] index_t kk; ^ 8 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c gqjrssa.c -o gqjrssa.o gqjrssa.c:12:33: warning: unused variable 'vld_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ gqjrssa.c:12:8: warning: unused variable 'acc_NNs_multinom_matrix' [-Wunused-variable] SEXP acc_NNs_multinom_matrix, vld_NNs_multinom_matrix; ^ gqjrssa.c:11:30: warning: unused variable 'vld_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ gqjrssa.c:11:8: warning: unused variable 'acc_NNs_multinom_vec' [-Wunused-variable] SEXP acc_NNs_multinom_vec, vld_NNs_multinom_vec; ^ gqjrssa.c:6:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ gqjrssa.c:961:11: warning: unused variable 'ladder_num' [-Wunused-variable] index_t ladder_num, current_ladder; // Need to initialize ^ gqjrssa.c:337:10: warning: variable 'm12_log_SIGMA_det_cu' set but not used [-Wunused-but-set-variable] double m12_log_SIGMA_det_cu; ^ 7 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsMH.c -o jimsMH.o jimsMH.c:404:10: warning: variable 'tmp_kk' set but not used [-Wunused-but-set-variable] double tmp_kk, mm_prop, mm_curr, tmp_val; ^ jimsMH.c:404:36: warning: unused variable 'tmp_val' [-Wunused-variable] double tmp_kk, mm_prop, mm_curr, tmp_val; ^ 2 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsimatrix.c -o jimsimatrix.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimslprob.c -o jimslprob.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsmatrix.c -o jimsmatrix.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsmatrix_p.c -o jimsmatrix_p.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsmatrixinterface.c -o jimsmatrixinterface.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsmisc.c -o jimsmisc.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c jimsrandom.c -o jimsrandom.o jimsrandom.c:1399:23: warning: unused variable 'll' [-Wunused-variable] index_t ii, jj, kk, ll; ^ jimsrandom.c:1869:16: warning: unused variable 'numrows_pt_m1' [-Wunused-variable] const index_t numrows_pt_m1 = (numrows_pt-1); ^ jimsrandom.c:1967:31: warning: unused variable 'log_MH_ratio' [-Wunused-variable] double tmp_u, tmp_c, alpha, log_MH_ratio; ^ jimsrandom.c:1967:24: warning: unused variable 'alpha' [-Wunused-variable] double tmp_u, tmp_c, alpha, log_MH_ratio; ^ jimsrandom.c:2251:16: warning: unused variable 'nr_KKtots' [-Wunused-variable] const index_t nr_KKtots = numrows(KKtots); ^ jimsrandom.c:2253:9: warning: variable 'NN_prec_row_tot' set but not used [-Wunused-but-set-variable] double NN_prec_row_tot, NN_prec_col_tot; ^ 6 warnings generated. /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DUSE_FC_LEN_T -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c nchg.c -o nchg.o nchg.c:251:63: warning: if statement has empty body [-Wempty-body] if ( (f<=lepsilon) || (r<=sixfifths) );// SHOULD THIS LINE BE LIKE THIS??? ^ nchg.c:251:63: note: put the semicolon on a separate line to silence this warning nchg.c:293:38: warning: variable 'downcounter' set but not used [-Wunused-but-set-variable] int exactcheck = 0, upcounter = 0, downcounter = 0; ^ nchg.c:293:23: warning: variable 'upcounter' set but not used [-Wunused-but-set-variable] int exactcheck = 0, upcounter = 0, downcounter = 0; ^ nchg.c:424:24: warning: variable 'upcounter' set but not used [-Wunused-but-set-variable] int exactcheck = 0, upcounter = 0, downcounter = 0; ^ nchg.c:424:39: warning: variable 'downcounter' set but not used [-Wunused-but-set-variable] int exactcheck = 0, upcounter = 0, downcounter = 0; ^ 5 warnings generated. /usr/local/clang15/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang15/lib -L/usr/local/lib64 -o RxCEcolInf.so RxCEcolInf_init.o covariates.o exitpoll.o gqjrssa.o jimsMH.o jimsimatrix.o jimslprob.o jimsmatrix.o jimsmatrix_p.o jimsmatrixinterface.o jimsmisc.o jimsrandom.o nchg.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf/src' installing to /data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00LOCK-RxCEcolInf/00new/RxCEcolInf/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 (RxCEcolInf)