* installing *source* package ‘spNNGP’ ... ** package ‘spNNGP’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/spNNGP/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PGLogit.cpp -o PGLogit.o PGLogit.cpp:27:18: warning: unused variable 'negOne' [-Wunused-variable] 27 | const double negOne = -1.0; | ^~~~~~ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cNNGP.cpp -o cNNGP.o 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; | ^~~~~~ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cSLGP.cpp -o cSLGP.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c init.cpp -o init.o 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; | ^~~~~~ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nn.cpp -o nn.o 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:134:11: warning: unused variable 'k' [-Wunused-variable] 134 | int i,j,k; | ^ 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rNNGP.cpp -o rNNGP.o 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; | ^ rNNGP.cpp:180:8: warning: variable 'nuIndx' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] 180 | if(corName != "matern"){ | ^~~~~~~~~~~~~~~~~~~ rNNGP.cpp:251:114: note: uninitialized use occurs here 251 | logDetCurrent = updateBF(B, F, c, C, coords, nnIndx, nnIndxLU, n, m, theta, tauSqIndx, sigmaSqIndx, phiIndx, nuIndx, covModel, bk, nuUnifb); | ^~~~~~ rNNGP.cpp:180:5: note: remove the 'if' if its condition is always false 180 | if(corName != "matern"){ | ^~~~~~~~~~~~~~~~~~~~~~~~ 181 | nTheta = 3;//sigma^2, tau^2, phi | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 | sigmaSqIndx = 0; tauSqIndx = 1; phiIndx = 2; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 | }else{ | ~~~~~ rNNGP.cpp:178:56: note: initialize the variable 'nuIndx' to silence this warning 178 | int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx; | ^ | = 0 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rNNGPPredict.cpp -o rNNGPPredict.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rNNGPReplicated.cpp -o rNNGPReplicated.o 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; | ^~~~~~ 3 warnings generated. 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; | ^~~~ 6 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rpg.cpp -o rpg.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sNNGP.cpp -o sNNGP.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sNNGPLogit.cpp -o sNNGPLogit.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c sNNGPPredict.cpp -o sNNGPPredict.o 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; | ^~~~~~ 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; | ^~~~~~ 3 warnings generated. 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); | ^ 3 warnings generated. 5 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c util.cpp -o util.o util.cpp:29:10: warning: unused variable 'zero' [-Wunused-variable] 29 | double zero = 0.0; | ^~~~ util.cpp:113:10: warning: unused variable 'j' [-Wunused-variable] 113 | int i, j, k; | ^ 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -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 -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/spNNGP/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/spNNGP/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/spNNGP/src' installing to /data/gannet/ripley/R/packages/tests-clang/spNNGP.Rcheck/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 * DONE (spNNGP)