* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘spNNGP’ ... ** package ‘spNNGP’ 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 '/home/hornik/tmp/scratch/RtmpULdxmw/R.INSTALL1287dc37016d10/spNNGP/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PGLogit.cpp -o PGLogit.o PGLogit.cpp: In function ‘SEXPREC* PGLogit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: PGLogit.cpp:27:18: warning: unused variable ‘negOne’ [-Wunused-variable] 27 | const double negOne = -1.0; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cNNGP.cpp -o cNNGP.o cNNGP.cpp: In function ‘SEXPREC* cNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: cNNGP.cpp:73:9: warning: unused variable ‘h’ [-Wunused-variable] 73 | int h, i, j, k, l, s, info, nProtect=0; | ^ cNNGP.cpp:73:24: warning: unused variable ‘s’ [-Wunused-variable] 73 | int h, i, j, k, l, s, info, nProtect=0; | ^ cNNGP.cpp:76:18: warning: unused variable ‘negOne’ [-Wunused-variable] 76 | const double negOne = -1.0; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cSLGP.cpp -o cSLGP.o cSLGP.cpp: In function ‘SEXPREC* cSLGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: cSLGP.cpp:137:9: warning: unused variable ‘h’ [-Wunused-variable] 137 | int h, i, j, k, l, s, info, nProtect=0; | ^ cSLGP.cpp:137:24: warning: unused variable ‘s’ [-Wunused-variable] 137 | int h, i, j, k, l, s, info, nProtect=0; | ^ cSLGP.cpp:140:18: warning: unused variable ‘negOne’ [-Wunused-variable] 140 | const double negOne = -1.0; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nn.cpp -o nn.o nn.cpp: In function ‘SEXPREC* mkUIndx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: nn.cpp:32:7: warning: unused variable ‘nIndx’ [-Wunused-variable] 32 | int nIndx = static_cast(static_cast(1+m)/2*m+(n-m-1)*m); | ^~~~~ nn.cpp: In function ‘void fastNN(int, int, double*, int, double*, int*, int*, double*)’: nn.cpp:134:11: warning: unused variable ‘k’ [-Wunused-variable] 134 | int i,j,k; | ^ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rNNGP.cpp -o rNNGP.o rNNGP.cpp: In function ‘SEXPREC* rNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: rNNGP.cpp:107:9: warning: unused variable ‘h’ [-Wunused-variable] 107 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGP.cpp:107:18: warning: unused variable ‘k’ [-Wunused-variable] 107 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGP.cpp:107:21: warning: unused variable ‘l’ [-Wunused-variable] 107 | int h, i, j, k, l, s, info, nProtect=0; | ^ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rNNGPPredict.cpp -o rNNGPPredict.o rNNGPPredict.cpp: In function ‘SEXPREC* rNNGPPredict(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: rNNGPPredict.cpp:24:9: warning: unused variable ‘h’ [-Wunused-variable] 24 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGPPredict.cpp:24:15: warning: unused variable ‘j’ [-Wunused-variable] 24 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGPPredict.cpp:27:18: warning: unused variable ‘negOne’ [-Wunused-variable] 27 | const double negOne = -1.0; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rNNGPReplicated.cpp -o rNNGPReplicated.o rNNGPReplicated.cpp: In function ‘SEXPREC* rNNGPReplicated(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: rNNGPReplicated.cpp:76:9: warning: unused variable ‘h’ [-Wunused-variable] 76 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGPReplicated.cpp:76:18: warning: unused variable ‘k’ [-Wunused-variable] 76 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGPReplicated.cpp:76:21: warning: unused variable ‘l’ [-Wunused-variable] 76 | int h, i, j, k, l, s, info, nProtect=0; | ^ rNNGPReplicated.cpp:76:27: warning: unused variable ‘info’ [-Wunused-variable] 76 | int h, i, j, k, l, s, info, nProtect=0; | ^~~~ rNNGPReplicated.cpp:79:18: warning: unused variable ‘negOne’ [-Wunused-variable] 79 | const double negOne = -1.0; | ^~~~~~ rNNGPReplicated.cpp:80:18: warning: unused variable ‘zero’ [-Wunused-variable] 80 | const double zero = 0.0; | ^~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rpg.cpp -o rpg.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c sNNGP.cpp -o sNNGP.o sNNGP.cpp: In function ‘SEXPREC* sNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: sNNGP.cpp:71:9: warning: unused variable ‘h’ [-Wunused-variable] 71 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGP.cpp:71:21: warning: unused variable ‘l’ [-Wunused-variable] 71 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGP.cpp:74:18: warning: unused variable ‘negOne’ [-Wunused-variable] 74 | const double negOne = -1.0; | ^~~~~~ sNNGP.cpp:319:9: warning: ‘logDet’ may be used uninitialized [-Wmaybe-uninitialized] 319 | #pragma omp parallel for private (e, j, b) reduction(+:a, logDet) | ^~~ sNNGP.cpp:222:41: note: ‘logDet’ was declared here 222 | double logPostCand, logPostCurrent, logDet; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c sNNGPLogit.cpp -o sNNGPLogit.o sNNGPLogit.cpp: In function ‘SEXPREC* sNNGPLogit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: sNNGPLogit.cpp:72:9: warning: unused variable ‘h’ [-Wunused-variable] 72 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGPLogit.cpp:72:21: warning: unused variable ‘l’ [-Wunused-variable] 72 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGPLogit.cpp:75:18: warning: unused variable ‘negOne’ [-Wunused-variable] 75 | const double negOne = -1.0; | ^~~~~~ sNNGPLogit.cpp:331:9: warning: ‘logDet’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #pragma omp parallel for private (e, j, b) reduction(+:a, logDet) | ^~~ sNNGPLogit.cpp:227:41: note: ‘logDet’ was declared here 227 | double logPostCand, logPostCurrent, logDet; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c sNNGPPredict.cpp -o sNNGPPredict.o sNNGPPredict.cpp: In function ‘SEXPREC* sNNGPPredict(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: sNNGPPredict.cpp:24:9: warning: unused variable ‘h’ [-Wunused-variable] 24 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGPPredict.cpp:24:15: warning: unused variable ‘j’ [-Wunused-variable] 24 | int h, i, j, k, l, s, info, nProtect=0; | ^ sNNGPPredict.cpp:27:18: warning: unused variable ‘negOne’ [-Wunused-variable] 27 | const double negOne = -1.0; | ^~~~~~ sNNGPPredict.cpp:32:13: warning: unused variable ‘X’ [-Wunused-variable] 32 | double *X = REAL(X_r); | ^ sNNGPPredict.cpp:33:13: warning: unused variable ‘y’ [-Wunused-variable] 33 | double *y = REAL(y_r); | ^ sNNGPPredict.cpp:84:50: warning: ‘nuIndx’ may be used uninitialized [-Wmaybe-uninitialized] 84 | int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-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 util.cpp: In function ‘void mvrnorm(double*, double*, double*, int)’: util.cpp:29:10: warning: unused variable ‘zero’ [-Wunused-variable] 29 | double zero = 0.0; | ^~~~ util.cpp: In function ‘void mkUIndx2(int, int, int*, int*, int*, int*)’: util.cpp:113:10: warning: unused variable ‘j’ [-Wunused-variable] 113 | int i, j, k; | ^ g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o spNNGP.so PGLogit.o cNNGP.o cSLGP.o init.o nn.o rNNGP.o rNNGPPredict.o rNNGPReplicated.o rpg.o sNNGP.o sNNGPLogit.o sNNGPPredict.o util.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpULdxmw/R.INSTALL1287dc37016d10/spNNGP/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpULdxmw/R.INSTALL1287dc37016d10/spNNGP/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpULdxmw/R.INSTALL1287dc37016d10/spNNGP/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-spNNGP/00new/spNNGP/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * creating tarball packaged installation of ‘spNNGP’ as ‘spNNGP_1.0.0_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (spNNGP)