* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mixAK’ ...
** package ‘mixAK’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/RtmpER8x4L/R.INSTALL23b6ba5b9fb99/mixAK/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c 00mixAK_init.cpp -o 00mixAK_init.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c AK_BLAS.cpp -o AK_BLAS.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c AK_BSTAT.cpp -o AK_BSTAT.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c AK_LAPACK.cpp -o AK_LAPACK.o
AK_LAPACK.cpp: In function ‘void AK_LAPACK::MPpinvSP(double*, double*, int*, const int*)’:
AK_LAPACK.cpp:1001:17: warning: variable ‘LTp’ set but not used [-Wunused-but-set-variable]
 1001 |   static int i, LTp, p_p;
      |                 ^~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c AK_Utils.cpp -o AK_Utils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_Dirichlet.cpp -o Dist_Dirichlet.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_Discrete.cpp -o Dist_Discrete.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_MVN.cpp -o Dist_MVN.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_MVT.cpp -o Dist_MVT.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_TMVN.cpp -o Dist_TMVN.o
Dist_TMVN.cpp: In function ‘void Dist::rTMVN2(double*, double*, const double*, const double*, const int*, const double*, const double*, const int*, const int*)’:
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;
      |                     ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_TNorm.cpp -o Dist_TNorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_TmixMVN.cpp -o Dist_TmixMVN.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_TmixNorm.cpp -o Dist_TmixNorm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_Wishart.cpp -o Dist_Wishart.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_mixMVN.cpp -o Dist_mixMVN.o
Dist_mixMVN.cpp: In function ‘void Dist::dmixMVN_R(double*, double*, double*, double*, int*, const double*, const int*, const double*, const int*, const int*)’:
Dist_mixMVN.cpp:212:13: warning: unused variable ‘LTnx’ [-Wunused-variable]
  212 |   const int LTnx = (*nx * (*nx + 1))/2;
      |             ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Dist_mixNorm.cpp -o Dist_mixNorm.o
Dist_mixNorm.cpp: In function ‘void Dist::dmixNorm_R(double*, const double*, const int*, const double*, const double*, const double*, const int*)’:
Dist_mixNorm.cpp:91:7: warning: unused variable ‘k’ [-Wunused-variable]
   91 |   int k, j;
      |       ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_Deviance.cpp -o GLMM_Deviance.o
GLMM_Deviance.cpp: In function ‘void GLMM::Deviance(double*, double*, double*, double*, double*, double*, double*, double**, int**, double**, double**, double**, double**, double**, int**, int*, double*, int*, double**, int**, double**, double**, double**, double**, double**, int**, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*)’:
GLMM_Deviance.cpp:139:10: warning: unused variable ‘U2_g’ [-Wunused-variable]
  139 |   double U2_g[5];
      |          ^~~~
GLMM_Deviance.cpp:140:10: warning: unused variable ‘H2_g’ [-Wunused-variable]
  140 |   double H2_g[15];
      |          ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_Deviance2.cpp -o GLMM_Deviance2.o
GLMM_Deviance2.cpp: In function ‘void GLMM::Deviance2(double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, double**, int**, double**, double**, double**, double**, double**, int**, int*, double*, int*, double**, int**, double**, double**, double**, double**, double**, int**, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*)’:
GLMM_Deviance2.cpp:103:28: warning: unused variable ‘bDb’ [-Wunused-variable]
  103 |   static double log_det_R, bDb, loglik_ik, max_log_pi_ik;
      |                            ^~~
GLMM_Deviance2.cpp:129:18: warning: unused variable ‘bscaled_hatP’ [-Wunused-variable]
  129 |   static double *bscaled_hatP;
      |                  ^~~~~~~~~~~~
GLMM_Deviance2.cpp:159:10: warning: unused variable ‘U2_g’ [-Wunused-variable]
  159 |   double U2_g[5];
      |          ^~~~
GLMM_Deviance2.cpp:160:10: warning: unused variable ‘H2_g’ [-Wunused-variable]
  160 |   double H2_g[15];
      |          ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_Deviance2Pr_obs.cpp -o GLMM_Deviance2Pr_obs.o
GLMM_Deviance2Pr_obs.cpp: In function ‘void GLMM::Deviance2Pr_obs(double*, const double*, const double*, const double*, const int*, const int*)’:
GLMM_Deviance2Pr_obs.cpp:34:17: warning: unused variable ‘sum_w_L_ik’ [-Wunused-variable]
   34 |   static double sum_w_L_ik;
      |                 ^~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_MCMC.cpp -o GLMM_MCMC.o
GLMM_MCMC.cpp: In function ‘void GLMM_MCMC(double*, int*, const int*, int*, const double*, double*, const int*, const double*, const double*, const int*, const double*, const double*, const double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, int*)’:
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;
      |                 ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_NMixRelabel.cpp -o GLMM_NMixRelabel.o
GLMM_NMixRelabel.cpp:346:1: warning: "/*" within comment [-Wcomment]
  346 | /***** %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *****/
      |  
GLMM_NMixRelabel.cpp: In function ‘void GLMM_NMixRelabel(const int*, const int*, const int*, double*, int*, const int*, const int*, const int*, int*, const double*, double*, const int*, const double*, const int*, const int*, const double*, const double*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, int*, int*, double*, int*, int*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, int*, int*, int*)’:
GLMM_NMixRelabel.cpp:543:5: warning: ‘simpleType’ may be used uninitialized [-Wmaybe-uninitialized]
  543 |     switch (simpleType){
      |     ^~~~~~
GLMM_NMixRelabel.cpp:392:7: note: ‘simpleType’ was declared here
  392 |   int simpleType;
      |       ^~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_PED.cpp -o GLMM_PED.o
GLMM_PED.cpp: In function ‘void GLMM_PED(double*, double*, double*, double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, const int*, int*, const double*, double*, const int*, const int*, const double*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const double*)’:
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 = Calloc(R, double*);
      |            ^~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_copy_shift_eta_meanY_Zresp.cpp -o GLMM_copy_shift_eta_meanY_Zresp.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_create_SZitZiS.cpp -o GLMM_create_SZitZiS.o
GLMM_create_SZitZiS.cpp: In function ‘void GLMM::create_SZitZiS(double*, double**, double**, const double*, const int*, const int*, const int*, const int*, const int*, const int*)’:
GLMM_create_SZitZiS.cpp:129:21: warning: ‘SZitZiS_is’ may be used uninitialized [-Wmaybe-uninitialized]
  129 |           SZitZiS_is++;
      |           ~~~~~~~~~~^~
GLMM_create_SZitZiS.cpp:34:11: note: ‘SZitZiS_is’ was declared here
   34 |   double *SZitZiS_is, *SZitZiSP;
      |           ^~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_create_SZitZiS_4longitDA.cpp -o GLMM_create_SZitZiS_4longitDA.o
GLMM_create_SZitZiS_4longitDA.cpp: In function ‘void GLMM::create_SZitZiS_4longitDA(double*, double*, double**, double**, const double*, const int*, const int*, const int*, const int*, const int*, const int*)’:
GLMM_create_SZitZiS_4longitDA.cpp:34:41: warning: unused variable ‘SZitZiSP’ [-Wunused-variable]
   34 |   double *SZitZiS_c_is, *SZitZiS_d_is, *SZitZiSP, *SZitZiS_prev;
      |                                         ^~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_create_XtX.cpp -o GLMM_create_XtX.o
GLMM_create_XtX.cpp: In function ‘void GLMM::create_XtX(double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*)’:
GLMM_create_XtX.cpp:109:16: warning: ‘XtX_s’ may be used uninitialized [-Wmaybe-uninitialized]
  109 |           XtX_s++;
      |           ~~~~~^~
GLMM_create_XtX.cpp:31:11: note: ‘XtX_s’ was declared here
   31 |   double *XtX_s, *XtXP;
      |           ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_create_ZS.cpp -o GLMM_create_ZS.o
GLMM_create_ZS.cpp: In function ‘void GLMM::create_ZS(double*, double**, int**, double**, int**, const double*, const int*, const int*, const int*, const int*)’:
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;
      |       ^~~
GLMM_create_ZS.cpp:96:31: warning: ‘ZP’ may be used uninitialized [-Wmaybe-uninitialized]
   96 |       if (*qP) ZrespP[s] = ZP - (*qP - 1);
      |                            ~~~^~~~~~~~~~~
GLMM_create_ZS.cpp:31:26: note: ‘ZP’ was declared here
   31 |   double *ZSP, *Zstart, *ZP;
      |                          ^~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_create_ZiS.cpp -o GLMM_create_ZiS.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_dY_meanY.cpp -o GLMM_dY_meanY.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_eta_fixed_random2eta_meanY.cpp -o GLMM_eta_fixed_random2eta_meanY.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_fitted_Bernoulli_Logit.cpp -o GLMM_fitted_Bernoulli_Logit.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_fitted_Poisson_Log.cpp -o GLMM_fitted_Poisson_Log.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_linear_predictors.cpp -o GLMM_linear_predictors.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_longitDA.cpp -o GLMM_longitDA.o
GLMM_longitDA.cpp: In function ‘void GLMM_longitDA(double*, const int*, int*, const int*, const int*, const int*, const int*, const int*, const double*, const int*, const int*, double*, const int*, const int*, const double*, const int*, const int*, const int*, const double*, const int*, const double*, const double*, const double*, const double*, double*, double*, double*, int*)’:
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;
      |       ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_longitDA2.cpp -o GLMM_longitDA2.o
GLMM_longitDA2.cpp: In function ‘void GLMM_longitDA2(const int*, double*, const int*, int*, const int*, const int*, const int*, const int*, int*, const double*, const int*, const int*, double*, const int*, const int*, const double*, const int*, const int*, const int*, const int*, const int*, const double*, const int*, const double*, const double*, const double*, const double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*)’:
GLMM_longitDA2.cpp:435:22: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  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;
      |       ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_longitPred_nmix_gauss.cpp -o GLMM_longitPred_nmix_gauss.o
GLMM_longitPred_nmix_gauss.cpp: In function ‘void GLMM::longitPred_nmix_gauss(double*, double*, double*, double**, double*, double*, double*, int*, double**, int**, double**, double**, double**, int*, double**, int**, double**, const double*, double**, const double*, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const double*, const double*)’:
GLMM_longitPred_nmix_gauss.cpp:82:31: warning: unused variable ‘eta_randomP’ [-Wunused-variable]
   82 |   static double *eta_fixedP, *eta_randomP, *eta_zsP;
      |                               ^~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_newData.cpp -o GLMM_newData.o
GLMM_newData.cpp: In function ‘void GLMM::newData(double*, int*, double*, double*, double*, double*, double*, double*, double*, const double*, const double*, const int*, const int*, const int*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*)’:
GLMM_newData.cpp:47:15: warning: unused variable ‘fname’ [-Wunused-variable]
   47 |   const char *fname = "GLMM::newData";
      |               ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_scale_ZitZi.cpp -o GLMM_scale_ZitZi.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_updateFixEf.cpp -o GLMM_updateFixEf.o
GLMM_updateFixEf.cpp: In function ‘void GLMM::updateFixEf(double*, double*, double*, double*, double*, double*, int*, int*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*)’:
GLMM_updateFixEf.cpp:72:40: warning: unused variable ‘dworkP’ [-Wunused-variable]
   72 |   static double *mu_fullP, *Li_fullP, *dworkP, *beta_propP;
      |                                        ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_updateHyperVars_eps.cpp -o GLMM_updateHyperVars_eps.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_updateRanEf.cpp -o GLMM_updateRanEf.o
GLMM_updateRanEf.cpp:498:5: warning: "/*" within comment [-Wcomment]
  498 |     /*** +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ***/
      |      
GLMM_updateRanEf.cpp: In function ‘void GLMM::updateRanEf(double*, double*, double**, double**, double**, double*, double*, double**, int**, double**, double**, double**, double**, double**, double**, double**, int**, int*, int*, double**, int**, double**, double**, double**, double**, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, int**, const int*, const double*, const int*, const double*, const double*, const double*, const double*, const int*, const double*, const double*)’:
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;
      |                                                                                                          ^~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_updateRanEf_QR.cpp -o GLMM_updateRanEf_QR.o
GLMM_updateRanEf_QR.cpp: In function ‘void GLMM::updateRanEf_QR(double*, double*, double**, double**, double**, double*, int*, double*, double**, int**, double**, double**, double**, double**, double**, double**, int**, int*, int*, double**, int**, double**, double**, double**, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, int**, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const int*, const double*, const double*)’:
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;
      |                          ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GLMM_updateVars_eps.cpp -o GLMM_updateVars_eps.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c LogLik_Bernoulli_Logit.cpp -o LogLik_Bernoulli_Logit.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c LogLik_Gauss_Identity.cpp -o LogLik_Gauss_Identity.o
LogLik_Gauss_Identity.cpp: In function ‘void LogLik::Gauss_Identity1(double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*)’:
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: In function ‘void LogLik::Gauss_Identity_sqrt_w_phi1(double*, double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*)’:
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: In function ‘void LogLik::Gauss_Identity_sqrt_w_phi_stres1(double*, double*, double*, double*, double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*)’:
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: In function ‘void LogLik::Gauss_Identity3(double*, double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*)’:
LogLik_Gauss_Identity.cpp:460:20: warning: unused variable ‘k’ [-Wunused-variable]
  460 |   static int i, j, k;
      |                    ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c LogLik_Poisson_Log.cpp -o LogLik_Poisson_Log.o
LogLik_Poisson_Log.cpp: In function ‘void LogLik::Poisson_Log_sqrt_w_phi_stres2(double*, double*, double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*)’:
LogLik_Poisson_Log.cpp:295:17: warning: unused variable ‘eta_now’ [-Wunused-variable]
  295 |   static double eta_now, ll_now;
      |                 ^~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MCMC_Moments_NormalApprox.cpp -o MCMC_Moments_NormalApprox.o
MCMC_Moments_NormalApprox.cpp: In function ‘void MCMC::Moments_NormalApprox(double*, double*, const double*, const double*, const double*, const int*)’:
MCMC_Moments_NormalApprox.cpp:96:27: warning: unused variable ‘QP’ [-Wunused-variable]
   96 |   static double *cmeanP, *QP;
      |                           ^~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MCMC_Moments_NormalApprox_QR.cpp -o MCMC_Moments_NormalApprox_QR.o
MCMC_Moments_NormalApprox_QR.cpp: In function ‘void MCMC::Moments_NormalApprox_QR(double*, double*, int*, int*, double*, double*, int*, const double*, const double*, const int*, const int*, const char*)’:
MCMC_Moments_NormalApprox_QR.cpp:180:14: warning: unused variable ‘one’ [-Wunused-variable]
  180 |   static int one = 1;
      |              ^~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c MCMC_loglik_Zwork1_stres.cpp -o MCMC_loglik_Zwork1_stres.o
MCMC_loglik_Zwork1_stres.cpp: In function ‘void MCMC::loglik(double*, double*, int*, double**, double**, double**, int**, int**, double**, const double*, const double*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*)’:
MCMC_loglik_Zwork1_stres.cpp:476:17: warning: unused variable ‘s2’ [-Wunused-variable]
  476 |   static int s, s2, l;
      |                 ^~
MCMC_loglik_Zwork1_stres.cpp: In function ‘void MCMC::loglik(double*, int*, double**, double**, double**, int**, int**, double**, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*)’:
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;
      |                     ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Misc_findIndexOfPermutation.cpp -o Misc_findIndexOfPermutation.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Misc_generatePermutations.cpp -o Misc_generatePermutations.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_ChainsDerived.cpp -o NMix_ChainsDerived.o
NMix_ChainsDerived.cpp: In function ‘void NMix_ChainsDerived(double*, double*, int*, const int*, const double*, const int*, const double*, const double*, const double*, const int*, const int*)’:
NMix_ChainsDerived.cpp:37:11: warning: unused variable ‘dP’ [-Wunused-variable]
   37 |   double *dP;
      |           ^~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Deviance.cpp -o NMix_Deviance.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_MCMC.cpp -o NMix_MCMC.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_NMixRelabel.cpp -o NMix_NMixRelabel.o
NMix_NMixRelabel.cpp: In function ‘void NMix_NMixRelabel(const int*, const int*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, int*, int*, double*, int*, double*, double*, double*, double*, double*, int*, double*, double*, int*, int*, int*)’:
NMix_NMixRelabel.cpp:212:11: warning: unused variable ‘hatPr_yP’ [-Wunused-variable]
  212 |   double *hatPr_yP = NULL;
      |           ^~~~~~~~
NMix_NMixRelabel.cpp:329:5: warning: ‘simpleType’ may be used uninitialized [-Wmaybe-uninitialized]
  329 |     switch (simpleType){
      |     ^~~~~~
NMix_NMixRelabel.cpp:207:7: note: ‘simpleType’ was declared here
  207 |   int simpleType;
      |       ^~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PED.cpp -o NMix_PED.o
NMix_PED.cpp: In function ‘void NMix_PED(double*, double*, double*, double*, int*, int*, int*, double*, int*, const double*, const double*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const int*, const double*, const double*, const double*, const int*, const int*, const int*, const double*, const double*)’:
NMix_PED.cpp:56:15: warning: unused variable ‘fname’ [-Wunused-variable]
   56 |   const char *fname = "NMix_PED";
      |               ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PED_coreMulti.cpp -o NMix_PED_coreMulti.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PED_coreUni.cpp -o NMix_PED_coreUni.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PosterMeanMixParam.cpp -o NMix_PosterMeanMixParam.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Pr_y_and_cum_Pr_y.cpp -o NMix_Pr_y_and_cum_Pr_y.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredCDFMarg.cpp -o NMix_PredCDFMarg.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredCondDensCDFMarg.cpp -o NMix_PredCondDensCDFMarg.o
NMix_PredCondDensCDFMarg.cpp: In function ‘void NMix_PredCondDensCDFMarg(double*, double*, int*, const int*, const int*, const double*, const int*, const double*, const int*, const int*, const int*, const double*, const double*, const double*, const int*)’:
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;
      |                 ^~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredCondDensJoint2.cpp -o NMix_PredCondDensJoint2.o
NMix_PredCondDensJoint2.cpp: In function ‘void NMix_PredCondDensJoint2(double*, double*, int*, const int*, const double*, const int*, const int*, const int*, const double*, const double*, const double*, const int*)’:
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;
      |                 ^~~
NMix_PredCondDensJoint2.cpp:105:29: warning: ‘lcgrid’ may be used uninitialized [-Wmaybe-uninitialized]
  105 |   dens_numer = dens_denom + lcgrid;           /** space to store numerator when computing conditional densities         **/
      |                             ^~~~~~
NMix_PredCondDensJoint2.cpp:72:7: note: ‘lcgrid’ was declared here
   72 |   int lcgrid;
      |       ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredDA.cpp -o NMix_PredDA.o
NMix_PredDA.cpp: In function ‘void NMix_PredDA(const double*, const double*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const int*, double*, int*, int*, double*, int*)’:
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";
      |               ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredDensJoint2.cpp -o NMix_PredDensJoint2.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_PredDensMarg.cpp -o NMix_PredDensMarg.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMC_aux_vector_u.cpp -o NMix_RJMCMC_aux_vector_u.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMC_logJacLambdaVSigma.cpp -o NMix_RJMCMC_logJacLambdaVSigma.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMC_logJac_part3.cpp -o NMix_RJMCMC_logJac_part3.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMCbirth.cpp -o NMix_RJMCMCbirth.o
NMix_RJMCMCbirth.cpp: In function ‘void NMix::RJMCMCbirth(int*, double*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, double*, int*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*)’:
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;
      |                                       ^~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMCcombine.cpp -o NMix_RJMCMCcombine.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMCdeath.cpp -o NMix_RJMCMCdeath.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_RJMCMCsplit.cpp -o NMix_RJMCMCsplit.o
NMix_RJMCMCsplit.cpp: In function ‘void NMix::RJMCMCsplit(int*, double*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int**, double*, double*, double*, double*, int*, int*, const double*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const double*, void (*)(double*, double*, const double*, const int*))’:
NMix_RJMCMCsplit.cpp:68:18: warning: variable ‘dlambdaV_dSigma’ set but not used [-Wunused-but-set-variable]
   68 |   static double *dlambdaV_dSigma;
      |                  ^~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Stephens_costMatrix.cpp -o NMix_Stephens_costMatrix.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Stephens_step1.cpp -o NMix_Stephens_step1.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Stephens_step2_search.cpp -o NMix_Stephens_step2_search.o
NMix_Stephens_step2_search.cpp: In function ‘void NMix::Stephens_step2_search(int*, int*, int*, int*, const double*, const double*, const int*, const int*, const int*, const int*, const int*)’:
NMix_Stephens_step2_search.cpp:37:37: warning: unused variable ‘pij_q’ [-Wunused-variable]
   37 |   static double minLoss, Loss, pij, pij_q;
      |                                     ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Stephens_step2_transport.cpp -o NMix_Stephens_step2_transport.o
NMix_Stephens_step2_transport.cpp: In function ‘void NMix::Stephens_step2_transport(int*, int*, int*, double*, double*, int*, double*, int*, double*, int*, const double*, const double*, const int*, const int*, const int*)’:
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};
      |                 ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_Utils.cpp -o NMix_Utils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_fullCondMean_WeightsMeansVars.cpp -o NMix_fullCondMean_WeightsMeansVars.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_orderComp.cpp -o NMix_orderComp.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_reorder_Pr_y.cpp -o NMix_reorder_Pr_y.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_sum_Ir.cpp -o NMix_sum_Ir.o
NMix_sum_Ir.cpp: In function ‘void NMix::sum_Ir(int*, const int*, const int*, const int*, const int*, const int*)’:
NMix_sum_Ir.cpp:26:17: warning: unused variable ‘j’ [-Wunused-variable]
   26 |   static int l, j, m;
      |                 ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_updateAlloc.cpp -o NMix_updateAlloc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_updateCensObs.cpp -o NMix_updateCensObs.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_updateHyperVars.cpp -o NMix_updateHyperVars.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_updateMeansVars.cpp -o NMix_updateMeansVars.o
NMix_updateMeansVars.cpp: In function ‘void NMix::updateMeansVars_IC_homoscedastic(double*, double*, double*, double*, double*, int*, int*, double*, int*, const double*, const int*, const int*, const int*, const int*, const int*, const double*, const double*, const double*, const double*, const double*, const double*, const double*)’:
NMix_updateMeansVars.cpp:477:38: warning: unused variable ‘log_detsP’ [-Wunused-variable]
  477 |   static double *QP, *SigmaP, *LiP, *log_detsP, *muP, *mixSSmP, *dP;
      |                                      ^~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_updateWeights.cpp -o NMix_updateWeights.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c NMix_update_sum_Ir_and_sum_Pr_y.cpp -o NMix_update_sum_Ir_and_sum_Pr_y.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Rand_RotationMatrix.cpp -o Rand_RotationMatrix.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Rand_SamplePair.cpp -o Rand_SamplePair.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Stat_BLA.cpp -o Stat_BLA.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Stat_Quantile.cpp -o Stat_Quantile.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpER8x4L/R.INSTALL23b6ba5b9fb99/mixAK/src'
make[1]: Entering directory '/tmp/RtmpER8x4L/R.INSTALL23b6ba5b9fb99/mixAK/src'
make[1]: Leaving directory '/tmp/RtmpER8x4L/R.INSTALL23b6ba5b9fb99/mixAK/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mixAK/00new/mixAK/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘mixAK’
    finding HTML links ... done
    Acidity                                 html  
    BLA                                     html  
    BsBasis                                 html  
    Dirichlet                               html  
    Enzyme                                  html  
    Faithful                                html  
    GLMMMCMC                                html  
    GLMMMCMCdata                            html  
    GLMMMCMCifit                            html  
    GLMMMCMCinit.alpha                      html  
    GLMMMCMCinit.b                          html  
    GLMMMCMCinit.eps                        html  
    GLMMMCMCprior.alpha                     html  
    GLMMMCMCprior.b                         html  
    GLMMMCMCprior.eps                       html  
    GLMMMCMCscale.b                         html  
    GLMMMCMCwrapper                         html  
    GLMMlongitDA                            html  
    GLMMlongitDA2                           html  
    Galaxy                                  html  
    MVN                                     html  
    MVNmixture                              html  
    MVT                                     html  
    MatMPpinv                               html  
    MatSqrt                                 html  
    NMixChainComp                           html  
    NMixChainsDerived                       html  
    NMixCluster                             html  
    NMixEM                                  html  
    NMixMCMC                                html  
    NMixMCMCdata                            html  
    NMixMCMCinitr                           html  
    NMixMCMCinity                           html  
    NMixMCMCwrapper                         html  
    NMixPlugCondDensJoint2                  html  
    NMixPlugCondDensMarg                    html  
    NMixPlugDA                              html  
    NMixPlugDensJoint2                      html  
    NMixPlugDensMarg                        html  
    NMixPredCDFMarg                         html  
    NMixPredCondCDFMarg                     html  
    NMixPredCondDensJoint2                  html  
    NMixPredCondDensMarg                    html  
    NMixPredDA                              html  
    NMixPredDensJoint2                      html  
    NMixPredDensMarg                        html  
    NMixPseudoGOF                           html  
    NMixRelabel                             html  
    NMixRelabelAlgorithm                    html  
    NMixSummComp                            html  
    PBC910                                  html  
    PBCseq                                  html  
    SP2Rect                                 html  
    SimData                                 html  
    TMVN                                    html  
    TNorm                                   html  
    Tandmob                                 html  
    TandmobEmer                             html  
    Wishart                                 html  
    Y2T                                     html  
    autolayout                              html  
    cbplot                                  html  
    fitted.GLMMMCMC                         html  
    generatePermutations                    html  
    getProfiles                             html  
    plot.NMixPlugCondDensJoint2             html  
    plot.NMixPlugCondDensMarg               html  
    plot.NMixPlugDensJoint2                 html  
    plot.NMixPlugDensMarg                   html  
    plot.NMixPredCDFMarg                    html  
    plot.NMixPredCondCDFMarg                html  
    plot.NMixPredCondDensJoint2             html  
    plot.NMixPredCondDensMarg               html  
    plot.NMixPredDensJoint2                 html  
    plot.NMixPredDensMarg                   html  
    plotProfiles                            html  
    rRotationMatrix                         html  
    rSamplePair                             html  
    summaryDiff                             html  
    tracePlots                              html  
** 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
* creating tarball
packaged installation of ‘mixAK’ as ‘mixAK_5.7_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (mixAK)