* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bayesSurv’ ...
** this is package ‘bayesSurv’ version ‘3.8’
** package ‘bayesSurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpz4OrKv/R.INSTALL758139aba7e0/bayesSurv/src'
g++-16 -std=gnu++20 -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 00bayesSurv_init.cpp -o 00bayesSurv_init.o
g++-16 -std=gnu++20 -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_LAPACK.cpp -o AK_BLAS_LAPACK.o
g++-16 -std=gnu++20 -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 ARS2.cpp -o ARS2.o
g++-16 -std=gnu++20 -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 GMRF.cpp -o GMRF.o
GMRF.cpp: In function ‘void GMRF::dGMRF_inputArgs(double*, double*, double*, const double*, const double*, const double*, const double*, const int*, const int*, const int*, const int*, double*)’:
GMRF.cpp:705:17: warning: variable ‘nx_nc’ set but not used [-Wunused-but-set-variable=]
705 | static int j, nx_nc, info;
| ^~~~~
g++-16 -std=gnu++20 -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 GMRF_Gspline.cpp -o GMRF_Gspline.o
GMRF_Gspline.cpp: In function ‘void GMRF_Gspline::mcmc_GMRF_Gspline(int*, double*, double*, double*, int*, const int*, const int*, const double*, const double*, const int*, const int*, const int*, const int*, const int*, const int*, const int*)’:
GMRF_Gspline.cpp:876:11: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
876 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
GMRF_Gspline.cpp:877:11: warning: variable ‘iterTotalNow’ set but not used [-Wunused-but-set-variable=]
877 | int iterTotalNow = 0;
| ^~~~~~~~~~~~
GMRF_Gspline.cpp:879:11: warning: variable ‘writeAll’ set but not used [-Wunused-but-set-variable=]
879 | int writeAll = 0;
| ^~~~~~~~
g++-16 -std=gnu++20 -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 GMRF_Gspline_Util.cpp -o GMRF_Gspline_Util.o
g++-16 -std=gnu++20 -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 Gspline.cpp -o Gspline.o
Gspline.cpp: In member function ‘void Gspline::print() const’:
Gspline.cpp:1052:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1052 | for (j = 0; j < _dim-1; j++) Rprintf("%g, ", _penalty[j]); Rprintf("%g\n", _penalty[_dim-1]);
| ^~~
Gspline.cpp:1052:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1052 | for (j = 0; j < _dim-1; j++) Rprintf("%g, ", _penalty[j]); Rprintf("%g\n", _penalty[_dim-1]);
| ^~~~~~~
Gspline.cpp:1079:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1079 | for (j = 0; j < _dim-1; j++) Rprintf("%d, ", _k_overrelax_scale[j]); Rprintf("%d\n", _k_overrelax_scale[_dim-1]);
| ^~~
Gspline.cpp:1079:74: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1079 | for (j = 0; j < _dim-1; j++) Rprintf("%d, ", _k_overrelax_scale[j]); Rprintf("%d\n", _k_overrelax_scale[_dim-1]);
| ^~~~~~~
Gspline.cpp:1081:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
1081 | for (j = 0; j < _dim-1; j++) Rprintf("%d, ", _k_overrelax_sigma[j]); Rprintf("%d\n", _k_overrelax_sigma[_dim-1]);
| ^~~
Gspline.cpp:1081:74: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1081 | for (j = 0; j < _dim-1; j++) Rprintf("%d, ", _k_overrelax_sigma[j]); Rprintf("%d\n", _k_overrelax_sigma[_dim-1]);
| ^~~~~~~
g++-16 -std=gnu++20 -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 Gspline_update_Intcpt.cpp -o Gspline_update_Intcpt.o
g++-16 -std=gnu++20 -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 Gspline_update_Scale.cpp -o Gspline_update_Scale.o
g++-16 -std=gnu++20 -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 Gspline_update_a.cpp -o Gspline_update_a.o
g++-16 -std=gnu++20 -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 Gspline_update_gamma.cpp -o Gspline_update_gamma.o
g++-16 -std=gnu++20 -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 Gspline_update_lambda.cpp -o Gspline_update_lambda.o
g++-16 -std=gnu++20 -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 Gspline_update_sigma.cpp -o Gspline_update_sigma.o
Gspline_update_sigma.cpp: In member function ‘void Gspline::update_sigma(const double*, const int*, const int*, const int*)’:
Gspline_update_sigma.cpp:22:49: warning: variable ‘itmp’ set but not used [-Wunused-but-set-variable=]
22 | static int j, j_, iter_nr, err_nr, overrelax, itmp;
| ^~~~
g++-16 -std=gnu++20 -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 List.cpp -o List.o
g++-16 -std=gnu++20 -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 MHblocks.cpp -o MHblocks.o
g++-16 -std=gnu++20 -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 MHproposal.cpp -o MHproposal.o
g++-16 -std=gnu++20 -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 Mvtdist3.cpp -o Mvtdist3.o
g++-16 -std=gnu++20 -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 Slice_sampler2.cpp -o Slice_sampler2.o
g++-16 -std=gnu++20 -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 arms.cpp -o arms.o
arms.cpp: In function ‘int meet(POINT*, ENVELOPE*, METROPOLIS*)’:
arms.cpp:805:48: warning: ‘dr’ may be used uninitialized [-Wmaybe-uninitialized]
805 | q->y = (dl * q->pr->y + dr * q->pl->y + dl * dr)/(dl + dr);
| ~~~^~~~
arms.cpp:732:23: note: ‘dr’ was declared here
732 | double gl,gr,grl,dl,dr;
| ^~
g++-16 -std=gnu++20 -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 arrays2Mat.cpp -o arrays2Mat.o
g++-16 -std=gnu++20 -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 bayesBisurvreg.cpp -o bayesBisurvreg.o
bayesBisurvreg.cpp: In function ‘void bayesBisurvreg(char**, const int*, const double*, const double*, const double*, const double*, const int*, const double*, const double*, const int*, double*, double*, int*, int*, const int*, int*, double*, int*, double*, int*, double*, int*, double*, int*, int*, int*, const int*, int*)’:
bayesBisurvreg.cpp:472:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
472 | if (beta1->nbeta()) free(XXtb1); if (*doubly && beta2->nbeta()) free(XXtb2);
| ^~
bayesBisurvreg.cpp:472:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
472 | if (beta1->nbeta()) free(XXtb1); if (*doubly && beta2->nbeta()) free(XXtb2);
| ^~
bayesBisurvreg.cpp:114:9: warning: variable ‘n1_interval’ set but not used [-Wunused-but-set-variable=]
114 | int n1_interval = 0;
| ^~~~~~~~~~~
bayesBisurvreg.cpp:134:9: warning: variable ‘n2_interval’ set but not used [-Wunused-but-set-variable=]
134 | int n2_interval = 0;
| ^~~~~~~~~~~
bayesBisurvreg.cpp:135:9: warning: variable ‘n2_censored’ set but not used [-Wunused-but-set-variable=]
135 | int n2_censored = 0;
| ^~~~~~~~~~~
bayesBisurvreg.cpp:366:9: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
366 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 bayesDensity.cpp -o bayesDensity.o
g++-16 -std=gnu++20 -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 bayesGspline.cpp -o bayesGspline.o
g++-16 -std=gnu++20 -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 bayesHistogram.cpp -o bayesHistogram.o
bayesHistogram.cpp: In function ‘void bayesHistogram(char**, int*, double*, double*, int*, int*, double*, int*, const int*, int*, double*, int*, int*, const int*, int*)’:
bayesHistogram.cpp:68:9: warning: variable ‘n_interval’ set but not used [-Wunused-but-set-variable=]
68 | int n_interval = 0;
| ^~~~~~~~~~
bayesHistogram.cpp:184:9: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
184 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 bayessurvreg1.cpp -o bayessurvreg1.o
bayessurvreg1.cpp: In function ‘void bayessurvreg1(char**, int*, double*, double*, int*, int*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, int*, double*, int*, double*, int*, double*, int*, double*, int*, int*, double*, int*)’:
bayessurvreg1.cpp:527:12: warning: variable ‘ru’ set but not used [-Wunused-but-set-variable=]
527 | void (*ru) (double*, const double*);
| ^~
bayessurvreg1.cpp:616:9: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
616 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 bayessurvreg2.cpp -o bayessurvreg2.o
bayessurvreg2.cpp: In function ‘void bayessurvreg2(char**, const int*, const double*, const double*, const double*, const double*, const int*, const double*, const double*, const int*, double*, double*, double*, int*, int*, const int*, int*, int*, const int*, int*, double*, int*, double*, int*, double*, int*, double*, int*, double*, int*, double*, int*, double*, int*, double*, double*, int*, const int*, const double*, double*, const double*, const int*, const int*, const double*, int*, int*, int*, const int*, const int*, int*)’:
bayessurvreg2.cpp:338:9: warning: variable ‘n1_interval’ set but not used [-Wunused-but-set-variable=]
338 | int n1_interval = 0;
| ^~~~~~~~~~~
bayessurvreg2.cpp:358:9: warning: variable ‘n2_interval’ set but not used [-Wunused-but-set-variable=]
358 | int n2_interval = 0;
| ^~~~~~~~~~~
bayessurvreg2.cpp:359:9: warning: variable ‘n2_censored’ set but not used [-Wunused-but-set-variable=]
359 | int n2_censored = 0;
| ^~~~~~~~~~~
bayessurvreg2.cpp:381:16: warning: unused variable ‘RandomIntcpt1’ [-Wunused-variable]
381 | const int *RandomIntcpt1 = priorBeta1I + 3; /** indication of random intercept in model **/
| ^~~~~~~~~~~~~
bayessurvreg2.cpp:382:16: warning: unused variable ‘RandomIntcpt2’ [-Wunused-variable]
382 | const int *RandomIntcpt2 = priorBeta2I + 3; /** introduced on 26/11/2008 **/
| ^~~~~~~~~~~~~
bayessurvreg2.cpp:937:9: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
937 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 bblocks.cpp -o bblocks.o
g++-16 -std=gnu++20 -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 birthDeath.cpp -o birthDeath.o
g++-16 -std=gnu++20 -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 checkImputeData.cpp -o checkImputeData.o
g++-16 -std=gnu++20 -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 cholesky.cpp -o cholesky.o
g++-16 -std=gnu++20 -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 classBetaGamma.cpp -o classBetaGamma.o
classBetaGamma.cpp: In constructor ‘BetaGamma::BetaGamma(const int*, const double*)’:
classBetaGamma.cpp:109:9: warning: ‘*this.BetaGamma::_indbinXA’ may be used uninitialized [-Wmaybe-uninitialized]
109 | _indbinXA[irandom] = i;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 classBetaGammaExtend.cpp -o classBetaGammaExtend.o
g++-16 -std=gnu++20 -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 classCovMatrix.cpp -o classCovMatrix.o
g++-16 -std=gnu++20 -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 classCovMatrixExtend.cpp -o classCovMatrixExtend.o
g++-16 -std=gnu++20 -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 classRandomEff.cpp -o classRandomEff.o
classRandomEff.cpp: In member function ‘void RandomEff::print() const’:
classRandomEff.cpp:244:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
244 | for (j = 0; j < _nCluster; j++) Rprintf("%d, ", _nwithinCl[j]); Rprintf("\n");
| ^~~
classRandomEff.cpp:244:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
244 | for (j = 0; j < _nCluster; j++) Rprintf("%d, ", _nwithinCl[j]); Rprintf("\n");
| ^~~~~~~
g++-16 -std=gnu++20 -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 classRandomEff_rhoNorm.cpp -o classRandomEff_rhoNorm.o
g++-16 -std=gnu++20 -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 covMatrix.cpp -o covMatrix.o
g++-16 -std=gnu++20 -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 in_output.cpp -o in_output.o
g++-16 -std=gnu++20 -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 in_output_GS.cpp -o in_output_GS.o
g++-16 -std=gnu++20 -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 logLikelihood.cpp -o logLikelihood.o
g++-16 -std=gnu++20 -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 marginal_bayesGspline.cpp -o marginal_bayesGspline.o
g++-16 -std=gnu++20 -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 miscellaneous.cpp -o miscellaneous.o
g++-16 -std=gnu++20 -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 miscellaneous_GS.cpp -o miscellaneous_GS.o
g++-16 -std=gnu++20 -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 mixMoments.cpp -o mixMoments.o
g++-16 -std=gnu++20 -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 moodyRing.cpp -o moodyRing.o
g++-16 -std=gnu++20 -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 mvtdist.cpp -o mvtdist.o
g++-16 -std=gnu++20 -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 newton_raphson.cpp -o newton_raphson.o
g++-16 -std=gnu++20 -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 openFile.cpp -o openFile.o
g++-16 -std=gnu++20 -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 predictMisc.cpp -o predictMisc.o
g++-16 -std=gnu++20 -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 predictive.cpp -o predictive.o
g++-16 -std=gnu++20 -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 predictive_GS.cpp -o predictive_GS.o
predictive_GS.cpp: In function ‘void predictive_GS(double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, const int*, const double*, const int*, int*, char**, char**, char**, const int*, const int*, const double*, const int*, const double*, const int*, const double*, const double*, const int*, double*, const int*, int*, const int*, const int*, const int*, const int*, const int*, const int*, const int*, int*)’:
predictive_GS.cpp:171:9: warning: variable ‘sum_ngrid’ set but not used [-Wunused-but-set-variable=]
171 | int sum_ngrid = 0;
| ^~~~~~~~~
g++-16 -std=gnu++20 -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 printArray.cpp -o printArray.o
g++-16 -std=gnu++20 -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 propVector.cpp -o propVector.o
g++-16 -std=gnu++20 -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 qrdecomp.cpp -o qrdecomp.o
g++-16 -std=gnu++20 -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 quantile.cpp -o quantile.o
g++-16 -std=gnu++20 -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 random.cpp -o random.o
g++-16 -std=gnu++20 -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 randomLogLikelihood.cpp -o randomLogLikelihood.o
g++-16 -std=gnu++20 -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 regresResidual_GS.cpp -o regresResidual_GS.o
g++-16 -std=gnu++20 -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 rhoNorm.cpp -o rhoNorm.o
rhoNorm.cpp: In function ‘void rhoNorm::mcmc_rhoNorm(int*, double*, double*, int*, const double*, const double*, const double*, const int*, const int*, const int*, const double*)’:
rhoNorm.cpp:459:11: warning: variable ‘iterTotal’ set but not used [-Wunused-but-set-variable=]
459 | int iterTotal = nullthIter*nthin;
| ^~~~~~~~~
rhoNorm.cpp:460:11: warning: variable ‘iterTotalNow’ set but not used [-Wunused-but-set-variable=]
460 | int iterTotalNow = 0;
| ^~~~~~~~~~~~
rhoNorm.cpp:462:11: warning: variable ‘writeAll’ set but not used [-Wunused-but-set-variable=]
462 | int writeAll = 0;
| ^~~~~~~~
g++-16 -std=gnu++20 -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 sampledKendallTau.cpp -o sampledKendallTau.o
g++-16 -std=gnu++20 -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 splitCombine.cpp -o splitCombine.o
g++-16 -std=gnu++20 -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 structRandomEff32.cpp -o structRandomEff32.o
g++-16 -std=gnu++20 -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 templatefun.cpp -o templatefun.o
g++-16 -std=gnu++20 -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 templatefun_GS.cpp -o templatefun_GS.o
g++-16 -std=gnu++20 -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 updateAlloc.cpp -o updateAlloc.o
g++-16 -std=gnu++20 -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 updateCovMatRandom.cpp -o updateCovMatRandom.o
g++-16 -std=gnu++20 -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 updateData.cpp -o updateData.o
g++-16 -std=gnu++20 -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 updateEta.cpp -o updateEta.o
g++-16 -std=gnu++20 -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 updateMeans.cpp -o updateMeans.o
g++-16 -std=gnu++20 -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 updateRandom.cpp -o updateRandom.o
g++-16 -std=gnu++20 -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 updateRegres.cpp -o updateRegres.o
g++-16 -std=gnu++20 -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 updateVars.cpp -o updateVars.o
g++-16 -std=gnu++20 -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 updateWeights.cpp -o updateWeights.o
g++-16 -std=gnu++20 -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 update_Alloc_GS.cpp -o update_Alloc_GS.o
g++-16 -std=gnu++20 -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 update_Data_GS.cpp -o update_Data_GS.o
g++-16 -std=gnu++20 -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 update_sens_spec_misclassification.cpp -o update_sens_spec_misclassification.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bayesSurv.so 00bayesSurv_init.o AK_BLAS_LAPACK.o ARS2.o GMRF.o GMRF_Gspline.o GMRF_Gspline_Util.o Gspline.o Gspline_update_Intcpt.o Gspline_update_Scale.o Gspline_update_a.o Gspline_update_gamma.o Gspline_update_lambda.o Gspline_update_sigma.o List.o MHblocks.o MHproposal.o Mvtdist3.o Slice_sampler2.o arms.o arrays2Mat.o bayesBisurvreg.o bayesDensity.o bayesGspline.o bayesHistogram.o bayessurvreg1.o bayessurvreg2.o bblocks.o birthDeath.o checkImputeData.o cholesky.o classBetaGamma.o classBetaGammaExtend.o classCovMatrix.o classCovMatrixExtend.o classRandomEff.o classRandomEff_rhoNorm.o covMatrix.o in_output.o in_output_GS.o logLikelihood.o marginal_bayesGspline.o miscellaneous.o miscellaneous_GS.o mixMoments.o moodyRing.o mvtdist.o newton_raphson.o openFile.o predictMisc.o predictive.o predictive_GS.o printArray.o propVector.o qrdecomp.o quantile.o random.o randomLogLikelihood.o regresResidual_GS.o rhoNorm.o sampledKendallTau.o splitCombine.o structRandomEff32.o templatefun.o templatefun_GS.o updateAlloc.o updateCovMatRandom.o updateData.o updateEta.o updateMeans.o updateRandom.o updateRegres.o updateVars.o updateWeights.o update_Alloc_GS.o update_Data_GS.o update_sens_spec_misclassification.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpz4OrKv/R.INSTALL758139aba7e0/bayesSurv/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpz4OrKv/R.INSTALL758139aba7e0/bayesSurv/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpz4OrKv/R.INSTALL758139aba7e0/bayesSurv/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bayesSurv/00new/bayesSurv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bayesSurv’
finding HTML links ... done
bayesBisurvreg html
bayesBisurvreg.help html
bayesDensity html
bayesGspline html
bayesHistogram html
bayesHistogram.help html
bayessurvreg.help html
bayessurvreg1 html
bayessurvreg1.files2init html
bayessurvreg1.help html
bayessurvreg2 html
bayessurvreg2.help html
bayessurvreg3 html
bayessurvreg3.help html
cgd html
credible.region html
densplot2 html
files.Gspline html
files2coda html
give.init html
give.summary html
marginal.bayesGspline html
plot.bayesDensity html
plot.bayesGspline html
plot.marginal.bayesGspline html
predictive html
predictive2 html
print.bayesDensity html
rMVNorm html
rWishart html
sampleCovMat html
sampled.kendall.tau html
scanFN html
simult.pvalue html
tandmob2 html
tandmobRoos html
traceplot2 html
vecr2matr 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
* DONE (bayesSurv)