* 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
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
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
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
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
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
cNNGP.cpp:77:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
cNNGP.cpp:77:24: warning: unused variable 's' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
cNNGP.cpp:80:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
PGLogit.cpp:31:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
cSLGP.cpp:141:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
cSLGP.cpp:141:24: warning: unused variable 's' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
cSLGP.cpp:144:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
rNNGP.cpp:111:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGP.cpp:111:18: warning: unused variable 'k' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGP.cpp:111:21: warning: unused variable 'l' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGP.cpp:184:8: warning: variable 'nuIndx' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
if(corName != "matern"){
^~~~~~~~~~~~~~~~~~~
rNNGP.cpp:255:114: 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:184:5: note: remove the 'if' if its condition is always false
if(corName != "matern"){
^~~~~~~~~~~~~~~~~~~~~~~~
rNNGP.cpp:182:56: note: initialize the variable 'nuIndx' to silence this warning
int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx;
^
= 0
rNNGPPredict.cpp:28:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPPredict.cpp:28:15: warning: unused variable 'j' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPPredict.cpp:31:18: 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 rNNGPReplicated.cpp -o rNNGPReplicated.o
nn.cpp:36:7: warning: unused variable 'nIndx' [-Wunused-variable]
int nIndx = static_cast<int>(static_cast<double>(1+m)/2*m+(n-m-1)*m);
^
nn.cpp:138:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
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 rpg.cpp -o rpg.o
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 sNNGP.cpp -o sNNGP.o
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 sNNGPLogit.cpp -o sNNGPLogit.o
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 sNNGPPredict.cpp -o sNNGPPredict.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 util.cpp -o util.o
3 warnings generated.
rNNGPReplicated.cpp:80:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPReplicated.cpp:80:18: warning: unused variable 'k' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPReplicated.cpp:80:21: warning: unused variable 'l' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPReplicated.cpp:80:27: warning: unused variable 'info' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
rNNGPReplicated.cpp:83:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
rNNGPReplicated.cpp:84:18: warning: unused variable 'zero' [-Wunused-variable]
const double zero = 0.0;
^
sNNGP.cpp:75:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGP.cpp:75:21: warning: unused variable 'l' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGP.cpp:78:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
6 warnings generated.
sNNGPLogit.cpp:76:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGPLogit.cpp:76:21: warning: unused variable 'l' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGPLogit.cpp:79:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
util.cpp:33:10: warning: unused variable 'zero' [-Wunused-variable]
double zero = 0.0;
^
util.cpp:117:10: warning: unused variable 'j' [-Wunused-variable]
int i, j, k;
^
sNNGPPredict.cpp:28:9: warning: unused variable 'h' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGPPredict.cpp:28:15: warning: unused variable 'j' [-Wunused-variable]
int h, i, j, k, l, s, info, nProtect=0;
^
sNNGPPredict.cpp:31:18: warning: unused variable 'negOne' [-Wunused-variable]
const double negOne = -1.0;
^
sNNGPPredict.cpp:36:13: warning: unused variable 'X' [-Wunused-variable]
double *X = REAL(X_r);
^
sNNGPPredict.cpp:37:13: warning: unused variable 'y' [-Wunused-variable]
double *y = REAL(y_r);
^
5 warnings generated.
2 warnings generated.
3 warnings generated.
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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/4.4/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)