* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘spBayes’ ...
** package ‘spBayes’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpNa8dSx/R.INSTALL3f00a5b862e92/spBayes/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c adaptMetropGibbs.cpp -o adaptMetropGibbs.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c idist.cpp -o idist.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o 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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mkSpCov.cpp -o mkSpCov.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nonSpGLM_AMCMC.cpp -o nonSpGLM_AMCMC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ptsInPoly.cpp -o ptsInPoly.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spDynLM.cpp -o spDynLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spGLM.cpp -o spGLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spGLM_AMCMC.cpp -o spGLM_AMCMC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spLM.cpp -o spLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spLMPredict.cpp -o spLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spLMRecover.cpp -o spLMRecover.o
spLMRecover.cpp: In function ‘SEXPREC* spLMRecover(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spLMRecover.cpp:187:20: warning: ‘betaSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
187 | mvrnorm(&REAL(betaSamples_r)[s*p], bb, B, p, false);
| ~~~~^~~~~~~~~~~~~~~
spLMRecover.cpp:82:10: note: ‘betaSamples_r’ was declared here
82 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~~~~
spLMRecover.cpp:237:17: warning: ‘wSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
237 | REAL(wSamples_r)[s*n+k] = vU[k] + vU[n+k];
| ~~~~^~~~~~~~~~~~
spLMRecover.cpp:82:25: note: ‘wSamples_r’ was declared here
82 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~
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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMPPMvDIC.cpp -o spMPPMvDIC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMisalign.cpp -o spMisalign.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMisalignGLM.cpp -o spMisalignGLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMisalignGLMPredict.cpp -o spMisalignGLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMisalignPredict.cpp -o spMisalignPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMisalignRecover.cpp -o spMisalignRecover.o
spMisalignRecover.cpp: In function ‘SEXPREC* spMisalignRecover(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spMisalignRecover.cpp:241:20: warning: ‘betaSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
241 | mvrnorm(&REAL(betaSamples_r)[s*P], bb, B, P, false);
| ~~~~^~~~~~~~~~~~~~~
spMisalignRecover.cpp:102:10: note: ‘betaSamples_r’ was declared here
102 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~~~~
spMisalignRecover.cpp:298:24: warning: ‘wSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
298 | mvrnorm(&REAL(wSamples_r)[s*N], vU, C, N, false);
| ~~~~^~~~~~~~~~~~
spMisalignRecover.cpp:102:25: note: ‘wSamples_r’ was declared here
102 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~
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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvGLM.cpp -o spMvGLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvGLMPredict.cpp -o spMvGLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvGLM_AMCMC.cpp -o spMvGLM_AMCMC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvLM.cpp -o spMvLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvLMPredict.cpp -o spMvLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spMvLMRecover.cpp -o spMvLMRecover.o
spMvLMRecover.cpp: In function ‘SEXPREC* spMvLMRecover(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spMvLMRecover.cpp:258:20: warning: ‘betaSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
258 | mvrnorm(&REAL(betaSamples_r)[s*p], bb, B, p, false);
| ~~~~^~~~~~~~~~~~~~~
spMvLMRecover.cpp:107:10: note: ‘betaSamples_r’ was declared here
107 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~~~~
spMvLMRecover.cpp:366:17: warning: ‘wSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
366 | REAL(wSamples_r)[s*nm+k] = vU[nm+k] + vU[k];
| ~~~~^~~~~~~~~~~~
spMvLMRecover.cpp:107:25: note: ‘wSamples_r’ was declared here
107 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~
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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPDynLM.cpp -o spPPDynLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPGLM.cpp -o spPPGLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPGLM_AMCMC.cpp -o spPPGLM_AMCMC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPLM.cpp -o spPPLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPLMPredict.cpp -o spPPLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPLMRecover.cpp -o spPPLMRecover.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvGLM.cpp -o spPPMvGLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvGLMPredict.cpp -o spPPMvGLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvGLM_AMCMC.cpp -o spPPMvGLM_AMCMC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvLM.cpp -o spPPMvLM.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvLMPredict.cpp -o spPPMvLMPredict.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spPPMvLMRecover.cpp -o spPPMvLMRecover.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spSVC.cpp -o spSVC.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spSVCPredictJoint.cpp -o spSVCPredictJoint.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spSVCPredictMarg.cpp -o spSVCPredictMarg.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c spSVCRecover.cpp -o spSVCRecover.o
spSVCRecover.cpp: In function ‘SEXPREC* spSVCRecover(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
spSVCRecover.cpp:290:20: warning: ‘betaSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
290 | mvrnorm(&REAL(betaSamples_r)[s*p], bb, B, p, false);
| ~~~~^~~~~~~~~~~~~~~
spSVCRecover.cpp:95:10: note: ‘betaSamples_r’ was declared here
95 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~~~~
spSVCRecover.cpp:332:24: warning: ‘wSamples_r’ may be used uninitialized [-Wmaybe-uninitialized]
332 | mvrnorm(&REAL(wSamples_r)[s*nm], tmp_nm2, K, nm, false);
| ~~~~^~~~~~~~~~~~
spSVCRecover.cpp:95:25: note: ‘wSamples_r’ was declared here
95 | SEXP betaSamples_r, wSamples_r;
| ^~~~~~~~~~
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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c util.cpp -o util.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o spBayes.so adaptMetropGibbs.o idist.o init.o mkSpCov.o nonSpGLM_AMCMC.o ptsInPoly.o spDynLM.o spGLM.o spGLM_AMCMC.o spLM.o spLMPredict.o spLMRecover.o spMPPMvDIC.o spMisalign.o spMisalignGLM.o spMisalignGLMPredict.o spMisalignPredict.o spMisalignRecover.o spMvGLM.o spMvGLMPredict.o spMvGLM_AMCMC.o spMvLM.o spMvLMPredict.o spMvLMRecover.o spPPDynLM.o spPPGLM.o spPPGLM_AMCMC.o spPPLM.o spPPLMPredict.o spPPLMRecover.o spPPMvGLM.o spPPMvGLMPredict.o spPPMvGLM_AMCMC.o spPPMvLM.o spPPMvLMPredict.o spPPMvLMRecover.o spSVC.o spSVCPredictJoint.o spSVCPredictMarg.o spSVCRecover.o util.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpNa8dSx/R.INSTALL3f00a5b862e92/spBayes/src'
make[1]: Entering directory '/tmp/RtmpNa8dSx/R.INSTALL3f00a5b862e92/spBayes/src'
make[1]: Leaving directory '/tmp/RtmpNa8dSx/R.INSTALL3f00a5b862e92/spBayes/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-spBayes/00new/spBayes/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘spBayes’
finding HTML links ... done
BEF.dat html
FBC07.dat html
FORMGMT.dat html
NETemp.dat html
NYOzone.dat html
PM10.dat html
PM10.poly html
SVCMvData.dat html
WEF.dat html
Zurich.dat html
adaptMetropGibbs html
bayesGeostatExact html
bayesLMConjugate html
bayesLMRef html
iDist html
mkMvX html
mkSpCov html
pointsInPoly html
spDiag html
spDynLM html
spGLM html
spLM html
spMisalignGLM html
spMisalignLM html
spMvGLM html
spMvLM html
spPredict html
spRecover html
spSVC 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 (spBayes)