* installing *source* package ‘spNNGP’ ...
** package ‘spNNGP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PGLogit.cpp -o PGLogit.o
PGLogit.cpp:27:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cNNGP.cpp -o cNNGP.o
cNNGP.cpp:73:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
cNNGP.cpp:73:24: warning: unused variable 's' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                       ^
cNNGP.cpp:76:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cSLGP.cpp -o cSLGP.o
cSLGP.cpp:137:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
cSLGP.cpp:137:24: warning: unused variable 's' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                       ^
cSLGP.cpp:140:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nn.cpp -o nn.o
nn.cpp:32:7: warning: unused variable 'nIndx' [-Wunused-variable]
  int nIndx = static_cast<int>(static_cast<double>(1+m)/2*m+(n-m-1)*m);
      ^
nn.cpp:134:11: warning: unused variable 'k' [-Wunused-variable]
  int i,j,k;
          ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rNNGP.cpp -o rNNGP.o
rNNGP.cpp:107:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
rNNGP.cpp:107:18: warning: unused variable 'k' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                 ^
rNNGP.cpp:107:21: warning: unused variable 'l' [-Wunused-variable]
    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]
    if(corName != "matern"){
       ^~~~~~~~~~~~~~~~~~~
rNNGP.cpp:251:114: note: uninitialized use occurs here
    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
    if(corName != "matern"){
    ^~~~~~~~~~~~~~~~~~~~~~~~
rNNGP.cpp:178:56: note: initialize the variable 'nuIndx' to silence this warning
    int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx;
                                                       ^
                                                        = 0
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rNNGPPredict.cpp -o rNNGPPredict.o
rNNGPPredict.cpp:24:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
rNNGPPredict.cpp:24:15: warning: unused variable 'j' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
              ^
rNNGPPredict.cpp:27:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rNNGPReplicated.cpp -o rNNGPReplicated.o
rNNGPReplicated.cpp:76:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
rNNGPReplicated.cpp:76:18: warning: unused variable 'k' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                 ^
rNNGPReplicated.cpp:76:21: warning: unused variable 'l' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                    ^
rNNGPReplicated.cpp:76:27: warning: unused variable 'info' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                          ^
rNNGPReplicated.cpp:79:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
rNNGPReplicated.cpp:80:18: warning: unused variable 'zero' [-Wunused-variable]
    const double zero = 0.0;
                 ^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rpg.cpp -o rpg.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sNNGP.cpp -o sNNGP.o
sNNGP.cpp:71:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
sNNGP.cpp:71:21: warning: unused variable 'l' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                    ^
sNNGP.cpp:74:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sNNGPLogit.cpp -o sNNGPLogit.o
sNNGPLogit.cpp:72:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
sNNGPLogit.cpp:72:21: warning: unused variable 'l' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
                    ^
sNNGPLogit.cpp:75:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sNNGPPredict.cpp -o sNNGPPredict.o
sNNGPPredict.cpp:24:9: warning: unused variable 'h' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
        ^
sNNGPPredict.cpp:24:15: warning: unused variable 'j' [-Wunused-variable]
    int h, i, j, k, l, s, info, nProtect=0;
              ^
sNNGPPredict.cpp:27:18: warning: unused variable 'negOne' [-Wunused-variable]
    const double negOne = -1.0;
                 ^
sNNGPPredict.cpp:32:13: warning: unused variable 'X' [-Wunused-variable]
    double *X = REAL(X_r);
            ^
sNNGPPredict.cpp:33:13: warning: unused variable 'y' [-Wunused-variable]
    double *y = REAL(y_r);
            ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c util.cpp -o util.o
util.cpp:29:10: warning: unused variable 'zero' [-Wunused-variable]
  double zero = 0.0;
         ^
util.cpp:113:10: warning: unused variable 'j' [-Wunused-variable]
  int i, j, k;
         ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/spNNGP.Rcheck/00LOCK-spNNGP/00new/spNNGP/libs
** generating debug symbols (dSYM)
** 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)