* installing *source* package ‘mixAK’ ...
** package ‘mixAK’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/mixAK/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c 00mixAK_init.cpp -o 00mixAK_init.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c AK_BLAS.cpp -o AK_BLAS.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c AK_BSTAT.cpp -o AK_BSTAT.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c AK_LAPACK.cpp -o AK_LAPACK.o
AK_LAPACK.cpp:1002:17: warning: variable 'LTp' set but not used [-Wunused-but-set-variable]
1002 | static int i, LTp, p_p;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c AK_Utils.cpp -o AK_Utils.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_Dirichlet.cpp -o Dist_Dirichlet.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_Discrete.cpp -o Dist_Discrete.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_MVN.cpp -o Dist_MVN.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_MVT.cpp -o Dist_MVT.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_TMVN.cpp -o Dist_TMVN.o
Dist_TMVN.cpp:83:18: warning: variable 'zP' set but not used [-Wunused-but-set-variable]
83 | static double *zP, *z, *Gz;
| ^
Dist_TMVN.cpp:84:24: warning: variable 'alphaP' set but not used [-Wunused-but-set-variable]
84 | static const double *alphaP, *aP, *bP, *GzP;
| ^
Dist_TMVN.cpp:84:33: warning: variable 'aP' set but not used [-Wunused-but-set-variable]
84 | static const double *alphaP, *aP, *bP, *GzP;
| ^
Dist_TMVN.cpp:84:38: warning: variable 'bP' set but not used [-Wunused-but-set-variable]
84 | static const double *alphaP, *aP, *bP, *GzP;
| ^
Dist_TMVN.cpp:84:43: warning: variable 'GzP' set but not used [-Wunused-but-set-variable]
84 | static const double *alphaP, *aP, *bP, *GzP;
| ^
Dist_TMVN.cpp:85:21: warning: variable 'truncP' set but not used [-Wunused-but-set-variable]
85 | static const int *truncP;
| ^
6 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_TNorm.cpp -o Dist_TNorm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_TmixMVN.cpp -o Dist_TmixMVN.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_TmixNorm.cpp -o Dist_TmixNorm.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_Wishart.cpp -o Dist_Wishart.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_mixMVN.cpp -o Dist_mixMVN.o
Dist_mixMVN.cpp:213:13: warning: unused variable 'LTnx' [-Wunused-variable]
213 | const int LTnx = (*nx * (*nx + 1))/2;
| ^~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Dist_mixNorm.cpp -o Dist_mixNorm.o
Dist_mixNorm.cpp:91:7: warning: unused variable 'k' [-Wunused-variable]
91 | int k, j;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_Deviance.cpp -o GLMM_Deviance.o
GLMM_Deviance.cpp:86:24: warning: variable 'w_k' set but not used [-Wunused-but-set-variable]
86 | static const double *w_k, *df_k, *logw_k, *mu_k, *Li_k, *Q_k, *log_dets_k;
| ^
GLMM_Deviance.cpp:140:10: warning: unused variable 'U2_g' [-Wunused-variable]
140 | double U2_g[5];
| ^~~~
GLMM_Deviance.cpp:141:10: warning: unused variable 'H2_g' [-Wunused-variable]
141 | double H2_g[15];
| ^~~~
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_Deviance2.cpp -o GLMM_Deviance2.o
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_Deviance2Pr_obs.cpp -o GLMM_Deviance2Pr_obs.o
GLMM_Deviance2Pr_obs.cpp:34:17: warning: unused variable 'sum_w_L_ik' [-Wunused-variable]
34 | static double sum_w_L_ik;
| ^~~~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_MCMC.cpp -o GLMM_MCMC.o
GLMM_Deviance2.cpp:96:24: warning: variable 'w_k' set but not used [-Wunused-but-set-variable]
96 | static const double *w_k, *df_k, *logw_k, *mu_k, *Li_k, *Q_k, *log_dets_k;
| ^
GLMM_Deviance2.cpp:104:28: warning: unused variable 'bDb' [-Wunused-variable]
104 | static double log_det_R, bDb, loglik_ik, max_log_pi_ik;
| ^~~
GLMM_Deviance2.cpp:130:18: warning: unused variable 'bscaled_hatP' [-Wunused-variable]
130 | static double *bscaled_hatP;
| ^~~~~~~~~~~~
GLMM_Deviance2.cpp:160:10: warning: unused variable 'U2_g' [-Wunused-variable]
160 | double U2_g[5];
| ^~~~
GLMM_Deviance2.cpp:161:10: warning: unused variable 'H2_g' [-Wunused-variable]
161 | double H2_g[15];
| ^~~~
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_NMixRelabel.cpp -o GLMM_NMixRelabel.o
GLMM_MCMC.cpp:96:13: warning: unused variable 'DEBUG' [-Wunused-variable]
96 | const int DEBUG = 0;
| ^~~~~
GLMM_MCMC.cpp:253:17: warning: unused variable 'h_df' [-Wunused-variable]
253 | const double *h_df = g_df + 1;
| ^~~~
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_PED.cpp -o GLMM_PED.o
GLMM_NMixRelabel.cpp:346:1: warning: '/*' within block comment [-Wcomment]
346 | /***** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *****/
| ^
GLMM_PED.cpp:123:7: warning: unused variable 'LT_max_p_fi' [-Wunused-variable]
123 | int LT_max_p_fi = (max_p_fi * (max_p_fi + 1)) / 2;
| ^~~~~~~~~~~
GLMM_PED.cpp:355:7: warning: unused variable 'max_N_s' [-Wunused-variable]
355 | int max_N_s = AK_Basic::maxArray(N_s, R);
| ^~~~~~~
GLMM_PED.cpp:512:12: warning: unused variable 'eta_zsrespP' [-Wunused-variable]
512 | double **eta_zsrespP = R_Calloc(R, double*);
| ^~~~~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_copy_shift_eta_meanY_Zresp.cpp -o GLMM_copy_shift_eta_meanY_Zresp.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_create_SZitZiS.cpp -o GLMM_create_SZitZiS.o
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_create_SZitZiS_4longitDA.cpp -o GLMM_create_SZitZiS_4longitDA.o
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_create_XtX.cpp -o GLMM_create_XtX.o
GLMM_create_SZitZiS_4longitDA.cpp:34:41: warning: unused variable 'SZitZiSP' [-Wunused-variable]
34 | double *SZitZiS_c_is, *SZitZiS_d_is, *SZitZiSP, *SZitZiS_prev;
| ^~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_create_ZS.cpp -o GLMM_create_ZS.o
GLMM_create_ZS.cpp:33:26: warning: unused variable 'scaleP2' [-Wunused-variable]
33 | const double *scaleP, *scaleP2;
| ^~~~~~~
GLMM_create_ZS.cpp:42:7: warning: unused variable 'iZS' [-Wunused-variable]
42 | int iZS = 0;
| ^~~
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_create_ZiS.cpp -o GLMM_create_ZiS.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_dY_meanY.cpp -o GLMM_dY_meanY.o
GLMM_dY_meanY.cpp:36:17: warning: variable 'Y_cP' set but not used [-Wunused-but-set-variable]
36 | const double *Y_cP = Y_c;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_eta_fixed_random2eta_meanY.cpp -o GLMM_eta_fixed_random2eta_meanY.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_fitted_Bernoulli_Logit.cpp -o GLMM_fitted_Bernoulli_Logit.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_fitted_Poisson_Log.cpp -o GLMM_fitted_Poisson_Log.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_linear_predictors.cpp -o GLMM_linear_predictors.o
GLMM_linear_predictors.cpp:495:14: warning: variable 'cumq_riP' set but not used [-Wunused-but-set-variable]
495 | const int *cumq_riP = cumq_ri;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_longitDA.cpp -o GLMM_longitDA.o
GLMM_longitDA.cpp:63:13: warning: unused variable 'DEBUG' [-Wunused-variable]
63 | const int DEBUG = 0;
| ^~~~~
GLMM_longitDA.cpp:66:14: warning: unused variable 'm' [-Wunused-variable]
66 | int s, cl, m, i, j, k;
| ^
GLMM_longitDA.cpp:66:20: warning: unused variable 'j' [-Wunused-variable]
66 | int s, cl, m, i, j, k;
| ^
GLMM_longitDA.cpp:70:13: warning: unused variable 'R_I' [-Wunused-variable]
70 | const int R_I = R * *I;
| ^~~
GLMM_longitDA.cpp:162:7: warning: unused variable 'backs' [-Wunused-variable]
162 | int backs = 1;
| ^~~~~
GLMM_longitDA.cpp:172:14: warning: variable 'p_fi_cl' set but not used [-Wunused-but-set-variable]
172 | const int *p_fi_cl = p_fi;
| ^
6 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_longitDA2.cpp -o GLMM_longitDA2.o
GLMM_longitDA2.cpp:435:22: warning: '&&' within '||' [-Wlogical-op-parentheses]
435 | if (*nonSilent && !(iter_lC % *info) || iter_lC == *keepMCMC_cl){
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ~~
GLMM_longitDA2.cpp:435:22: note: place parentheses around the '&&' expression to silence this warning
435 | if (*nonSilent && !(iter_lC % *info) || iter_lC == *keepMCMC_cl){
| ^
| ( )
GLMM_longitDA2.cpp:85:14: warning: unused variable 'm' [-Wunused-variable]
85 | int s, cl, m, i, j, k;
| ^
GLMM_longitDA2.cpp:290:7: warning: unused variable 'backs' [-Wunused-variable]
290 | int backs = 1;
| ^~~~~
GLMM_longitDA2.cpp:325:14: warning: variable 'p_fi_cl' set but not used [-Wunused-but-set-variable]
325 | const int *p_fi_cl = p_fi;
| ^
4 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_longitPred_nmix_gauss.cpp -o GLMM_longitPred_nmix_gauss.o
GLMM_longitPred_nmix_gauss.cpp:82:31: warning: unused variable 'eta_randomP' [-Wunused-variable]
82 | static double *eta_fixedP, *eta_randomP, *eta_zsP;
| ^~~~~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_newData.cpp -o GLMM_newData.o
GLMM_newData.cpp:47:15: warning: unused variable 'fname' [-Wunused-variable]
47 | const char *fname = "GLMM::newData";
| ^~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_scale_ZitZi.cpp -o GLMM_scale_ZitZi.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_updateFixEf.cpp -o GLMM_updateFixEf.o
GLMM_updateFixEf.cpp:72:40: warning: unused variable 'dworkP' [-Wunused-variable]
72 | static double *mu_fullP, *Li_fullP, *dworkP, *beta_propP;
| ^~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_updateHyperVars_eps.cpp -o GLMM_updateHyperVars_eps.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_updateRanEf.cpp -o GLMM_updateRanEf.o
GLMM_updateRanEf.cpp:498:5: warning: '/*' within block comment [-Wcomment]
498 | /*** +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ***/
| ^
GLMM_updateRanEf.cpp:76:32: warning: unused variable 'row' [-Wunused-variable]
76 | static int s, i, j, k, itmp, row, col;
| ^~~
GLMM_updateRanEf.cpp:76:37: warning: unused variable 'col' [-Wunused-variable]
76 | static int s, i, j, k, itmp, row, col;
| ^~~
GLMM_updateRanEf.cpp:82:88: warning: unused variable 'Li_full_backupP' [-Wunused-variable]
82 | static double *bP, *bscaledP, *bscaled_i, *b_i, *eta_random_propP, *mean_Y_d_propP, *Li_full_backupP, *Li_fullP;
| ^~~~~~~~~~~~~~~
GLMM_updateRanEf.cpp:82:106: warning: unused variable 'Li_fullP' [-Wunused-variable]
82 | static double *bP, *bscaledP, *bscaled_i, *b_i, *eta_random_propP, *mean_Y_d_propP, *Li_full_backupP, *Li_fullP;
| ^~~~~~~~
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_updateRanEf_QR.cpp -o GLMM_updateRanEf_QR.o
GLMM_updateRanEf_QR.cpp:73:20: warning: unused variable 'j' [-Wunused-variable]
73 | static int s, i, j, k, l;
| ^
GLMM_updateRanEf_QR.cpp:73:23: warning: unused variable 'k' [-Wunused-variable]
73 | static int s, i, j, k, l;
| ^
GLMM_updateRanEf_QR.cpp:73:26: warning: unused variable 'l' [-Wunused-variable]
73 | static int s, i, j, k, l;
| ^
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c GLMM_updateVars_eps.cpp -o GLMM_updateVars_eps.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c LogLik_Bernoulli_Logit.cpp -o LogLik_Bernoulli_Logit.o
LogLik_Bernoulli_Logit.cpp:610:24: warning: variable 'etaP' set but not used [-Wunused-but-set-variable]
610 | static const double *etaP, *offsetP, *piP, *scaleP, *xP, *SxxSP;
| ^
LogLik_Bernoulli_Logit.cpp:610:31: warning: variable 'offsetP' set but not used [-Wunused-but-set-variable]
610 | static const double *etaP, *offsetP, *piP, *scaleP, *xP, *SxxSP;
| ^
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c LogLik_Gauss_Identity.cpp -o LogLik_Gauss_Identity.o
LogLik_Gauss_Identity.cpp:32:48: warning: unused variable 'log_y_factorP' [-Wunused-variable]
32 | static const double *offsetP, *xP, *thetaP, *log_y_factorP;
| ^~~~~~~~~~~~~
LogLik_Gauss_Identity.cpp:106:48: warning: unused variable 'log_y_factorP' [-Wunused-variable]
106 | static const double *offsetP, *xP, *thetaP, *log_y_factorP;
| ^~~~~~~~~~~~~
LogLik_Gauss_Identity.cpp:188:48: warning: unused variable 'log_y_factorP' [-Wunused-variable]
188 | static const double *offsetP, *xP, *thetaP, *log_y_factorP;
| ^~~~~~~~~~~~~
LogLik_Gauss_Identity.cpp:460:20: warning: unused variable 'k' [-Wunused-variable]
460 | static int i, j, k;
| ^
4 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c LogLik_Poisson_Log.cpp -o LogLik_Poisson_Log.o
LogLik_Poisson_Log.cpp:295:17: warning: unused variable 'eta_now' [-Wunused-variable]
295 | static double eta_now, ll_now;
| ^~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c MCMC_Moments_NormalApprox.cpp -o MCMC_Moments_NormalApprox.o
MCMC_Moments_NormalApprox.cpp:96:27: warning: unused variable 'QP' [-Wunused-variable]
96 | static double *cmeanP, *QP;
| ^~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c MCMC_Moments_NormalApprox_QR.cpp -o MCMC_Moments_NormalApprox_QR.o
MCMC_Moments_NormalApprox_QR.cpp:180:14: warning: unused variable 'one' [-Wunused-variable]
180 | static int one = 1;
| ^~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c MCMC_loglik_Zwork1_stres.cpp -o MCMC_loglik_Zwork1_stres.o
MCMC_loglik_Zwork1_stres.cpp:476:17: warning: unused variable 's2' [-Wunused-variable]
476 | static int s, s2, l;
| ^~
MCMC_loglik_Zwork1_stres.cpp:577:17: warning: unused variable 's2' [-Wunused-variable]
577 | static int s, s2, l;
| ^~
MCMC_loglik_Zwork1_stres.cpp:577:21: warning: unused variable 'l' [-Wunused-variable]
577 | static int s, s2, l;
| ^
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Misc_findIndexOfPermutation.cpp -o Misc_findIndexOfPermutation.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Misc_generatePermutations.cpp -o Misc_generatePermutations.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_ChainsDerived.cpp -o NMix_ChainsDerived.o
NMix_ChainsDerived.cpp:37:11: warning: unused variable 'dP' [-Wunused-variable]
37 | double *dP;
| ^~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Deviance.cpp -o NMix_Deviance.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_MCMC.cpp -o NMix_MCMC.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_NMixRelabel.cpp -o NMix_NMixRelabel.o
NMix_NMixRelabel.cpp:212:11: warning: unused variable 'hatPr_yP' [-Wunused-variable]
212 | double *hatPr_yP = NULL;
| ^~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PED.cpp -o NMix_PED.o
NMix_PED.cpp:56:15: warning: unused variable 'fname' [-Wunused-variable]
56 | const char *fname = "NMix_PED";
| ^~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PED_coreMulti.cpp -o NMix_PED_coreMulti.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PED_coreUni.cpp -o NMix_PED_coreUni.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PosterMeanMixParam.cpp -o NMix_PosterMeanMixParam.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Pr_y_and_cum_Pr_y.cpp -o NMix_Pr_y_and_cum_Pr_y.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredCDFMarg.cpp -o NMix_PredCDFMarg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredCondDensCDFMarg.cpp -o NMix_PredCondDensCDFMarg.o
NMix_PredCondDensCDFMarg.cpp:70:17: warning: unused variable 'wP' [-Wunused-variable]
70 | const double *wP = NULL;
| ^~
NMix_PredCondDensCDFMarg.cpp:71:17: warning: unused variable 'muP' [-Wunused-variable]
71 | const double *muP = NULL;
| ^~~
NMix_PredCondDensCDFMarg.cpp:72:17: warning: unused variable 'LiP' [-Wunused-variable]
72 | const double *LiP = NULL;
| ^~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredCondDensJoint2.cpp -o NMix_PredCondDensJoint2.o
NMix_PredCondDensJoint2.cpp:56:17: warning: unused variable 'wP' [-Wunused-variable]
56 | const double *wP = NULL;
| ^~
NMix_PredCondDensJoint2.cpp:57:17: warning: unused variable 'muP' [-Wunused-variable]
57 | const double *muP = NULL;
| ^~~
NMix_PredCondDensJoint2.cpp:58:17: warning: unused variable 'LiP' [-Wunused-variable]
58 | const double *LiP = NULL;
| ^~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredDA.cpp -o NMix_PredDA.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredDensJoint2.cpp -o NMix_PredDensJoint2.o
NMix_PredDA.cpp:39:13: warning: unused variable 'debug' [-Wunused-variable]
39 | const int debug = 0;
| ^~~~~
NMix_PredDA.cpp:40:15: warning: unused variable 'fname' [-Wunused-variable]
40 | const char *fname = "NMix_PredDA";
| ^~~~~
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_PredDensMarg.cpp -o NMix_PredDensMarg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMC_aux_vector_u.cpp -o NMix_RJMCMC_aux_vector_u.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMC_logJacLambdaVSigma.cpp -o NMix_RJMCMC_logJacLambdaVSigma.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMC_logJac_part3.cpp -o NMix_RJMCMC_logJac_part3.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMCbirth.cpp -o NMix_RJMCMCbirth.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMCcombine.cpp -o NMix_RJMCMCcombine.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMCdeath.cpp -o NMix_RJMCMCdeath.o
NMix_RJMCMCbirth.cpp:54:39: warning: variable 'dwork_orderComp' set but not used [-Wunused-but-set-variable]
54 | static double *dwork_misc, *Li4mu, *dwork_orderComp;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_RJMCMCsplit.cpp -o NMix_RJMCMCsplit.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Stephens_costMatrix.cpp -o NMix_Stephens_costMatrix.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Stephens_step1.cpp -o NMix_Stephens_step1.o
NMix_RJMCMCsplit.cpp:68:18: warning: variable 'dlambdaV_dSigma' set but not used [-Wunused-but-set-variable]
68 | static double *dlambdaV_dSigma;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Stephens_step2_search.cpp -o NMix_Stephens_step2_search.o
NMix_Stephens_step2_search.cpp:37:37: warning: unused variable 'pij_q' [-Wunused-variable]
37 | static double minLoss, Loss, pij, pij_q;
| ^~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Stephens_step2_transport.cpp -o NMix_Stephens_step2_transport.o
NMix_Stephens_step2_transport.cpp:37:15: warning: variable 'orderP' set but not used [-Wunused-but-set-variable]
37 | static int *orderP, *rankP;
| ^
NMix_Stephens_step2_transport.cpp:37:24: warning: variable 'rankP' set but not used [-Wunused-but-set-variable]
37 | static int *orderP, *rankP;
| ^
NMix_Stephens_step2_transport.cpp:39:17: warning: unused variable 'minLoss' [-Wunused-variable]
39 | static double minLoss[1];
| ^~~~~~~
NMix_Stephens_step2_transport.cpp:40:14: warning: unused variable 'lp_status' [-Wunused-variable]
40 | static int lp_status[1];
| ^~~~~~~~~
NMix_Stephens_step2_transport.cpp:42:17: warning: unused variable 'IZERO' [-Wunused-variable]
42 | static int IZERO[1] = {0};
| ^~~~~
NMix_Stephens_step2_transport.cpp:43:17: warning: unused variable 'DZERO' [-Wunused-variable]
43 | static double DZERO[1] = {0};
| ^~~~~
6 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_Utils.cpp -o NMix_Utils.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_fullCondMean_WeightsMeansVars.cpp -o NMix_fullCondMean_WeightsMeansVars.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_orderComp.cpp -o NMix_orderComp.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_reorder_Pr_y.cpp -o NMix_reorder_Pr_y.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_sum_Ir.cpp -o NMix_sum_Ir.o
NMix_sum_Ir.cpp:26:17: warning: unused variable 'j' [-Wunused-variable]
26 | static int l, j, m;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_updateAlloc.cpp -o NMix_updateAlloc.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_updateCensObs.cpp -o NMix_updateCensObs.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_updateHyperVars.cpp -o NMix_updateHyperVars.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_updateMeansVars.cpp -o NMix_updateMeansVars.o
NMix_updateMeansVars.cpp:477:38: warning: unused variable 'log_detsP' [-Wunused-variable]
477 | static double *QP, *SigmaP, *LiP, *log_detsP, *muP, *mixSSmP, *dP;
| ^~~~~~~~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_updateWeights.cpp -o NMix_updateWeights.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix_update_sum_Ir_and_sum_Pr_y.cpp -o NMix_update_sum_Ir_and_sum_Pr_y.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Rand_RotationMatrix.cpp -o Rand_RotationMatrix.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Rand_SamplePair.cpp -o Rand_SamplePair.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Stat_BLA.cpp -o Stat_BLA.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c Stat_Quantile.cpp -o Stat_Quantile.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o mixAK.so 00mixAK_init.o AK_BLAS.o AK_BSTAT.o AK_LAPACK.o AK_Utils.o Dist_Dirichlet.o Dist_Discrete.o Dist_MVN.o Dist_MVT.o Dist_TMVN.o Dist_TNorm.o Dist_TmixMVN.o Dist_TmixNorm.o Dist_Wishart.o Dist_mixMVN.o Dist_mixNorm.o GLMM_Deviance.o GLMM_Deviance2.o GLMM_Deviance2Pr_obs.o GLMM_MCMC.o GLMM_NMixRelabel.o GLMM_PED.o GLMM_copy_shift_eta_meanY_Zresp.o GLMM_create_SZitZiS.o GLMM_create_SZitZiS_4longitDA.o GLMM_create_XtX.o GLMM_create_ZS.o GLMM_create_ZiS.o GLMM_dY_meanY.o GLMM_eta_fixed_random2eta_meanY.o GLMM_fitted_Bernoulli_Logit.o GLMM_fitted_Poisson_Log.o GLMM_linear_predictors.o GLMM_longitDA.o GLMM_longitDA2.o GLMM_longitPred_nmix_gauss.o GLMM_newData.o GLMM_scale_ZitZi.o GLMM_updateFixEf.o GLMM_updateHyperVars_eps.o GLMM_updateRanEf.o GLMM_updateRanEf_QR.o GLMM_updateVars_eps.o LogLik_Bernoulli_Logit.o LogLik_Gauss_Identity.o LogLik_Poisson_Log.o MCMC_Moments_NormalApprox.o MCMC_Moments_NormalApprox_QR.o MCMC_loglik_Zwork1_stres.o Misc_findIndexOfPermutation.o Misc_generatePermutations.o NMix_ChainsDerived.o NMix_Deviance.o NMix_MCMC.o NMix_NMixRelabel.o NMix_PED.o NMix_PED_coreMulti.o NMix_PED_coreUni.o NMix_PosterMeanMixParam.o NMix_Pr_y_and_cum_Pr_y.o NMix_PredCDFMarg.o NMix_PredCondDensCDFMarg.o NMix_PredCondDensJoint2.o NMix_PredDA.o NMix_PredDensJoint2.o NMix_PredDensMarg.o NMix_RJMCMC_aux_vector_u.o NMix_RJMCMC_logJacLambdaVSigma.o NMix_RJMCMC_logJac_part3.o NMix_RJMCMCbirth.o NMix_RJMCMCcombine.o NMix_RJMCMCdeath.o NMix_RJMCMCsplit.o NMix_Stephens_costMatrix.o NMix_Stephens_step1.o NMix_Stephens_step2_search.o NMix_Stephens_step2_transport.o NMix_Utils.o NMix_fullCondMean_WeightsMeansVars.o NMix_orderComp.o NMix_reorder_Pr_y.o NMix_sum_Ir.o NMix_updateAlloc.o NMix_updateCensObs.o NMix_updateHyperVars.o NMix_updateMeansVars.o NMix_updateWeights.o NMix_update_sum_Ir_and_sum_Pr_y.o Rand_RotationMatrix.o Rand_SamplePair.o Stat_BLA.o Stat_Quantile.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/mixAK/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/mixAK/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/mixAK/src'
installing to /data/gannet/ripley/R/packages/tests-clang/mixAK.Rcheck/00LOCK-mixAK/00new/mixAK/libs
** R
** data
** inst
** 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 (mixAK)