* 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<int>(static_cast<double>(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)