* installing *source* package ‘spNNGP’ ...
** package ‘spNNGP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/spNNGP/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c PGLogit.cpp -o PGLogit.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c cNNGP.cpp -o cNNGP.o
PGLogit.cpp:31:18: warning: unused variable 'negOne' [-Wunused-variable]
31 | const double negOne = -1.0;
| ^~~~~~
1 warning generated.
cNNGP.cpp:77:9: warning: unused variable 'h' [-Wunused-variable]
77 | int h, i, j, k, l, s, info, nProtect=0;
| ^
cNNGP.cpp:77:24: warning: unused variable 's' [-Wunused-variable]
77 | int h, i, j, k, l, s, info, nProtect=0;
| ^
cNNGP.cpp:80:18: warning: unused variable 'negOne' [-Wunused-variable]
80 | const double negOne = -1.0;
| ^~~~~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c cSLGP.cpp -o cSLGP.o
cSLGP.cpp:141:9: warning: unused variable 'h' [-Wunused-variable]
141 | int h, i, j, k, l, s, info, nProtect=0;
| ^
cSLGP.cpp:141:24: warning: unused variable 's' [-Wunused-variable]
141 | int h, i, j, k, l, s, info, nProtect=0;
| ^
cSLGP.cpp:144:18: warning: unused variable 'negOne' [-Wunused-variable]
144 | const double negOne = -1.0;
| ^~~~~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c init.cpp -o init.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c nn.cpp -o nn.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rNNGP.cpp -o rNNGP.o
nn.cpp:36:7: warning: unused variable 'nIndx' [-Wunused-variable]
36 | 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]
138 | int i,j,k;
| ^
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rNNGPPredict.cpp -o rNNGPPredict.o
rNNGP.cpp:111:9: warning: unused variable 'h' [-Wunused-variable]
111 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGP.cpp:111:18: warning: unused variable 'k' [-Wunused-variable]
111 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGP.cpp:111:21: warning: unused variable 'l' [-Wunused-variable]
111 | 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]
184 | if(corName != "matern"){
| ^~~~~~~~~~~~~~~~~~~
rNNGP.cpp:255:114: note: uninitialized use occurs here
255 | 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
184 | if(corName != "matern"){
| ^~~~~~~~~~~~~~~~~~~~~~~~
185 | nTheta = 3;//sigma^2, tau^2, phi
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | sigmaSqIndx = 0; tauSqIndx = 1; phiIndx = 2;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | }else{
| ~~~~~
rNNGP.cpp:182:56: note: initialize the variable 'nuIndx' to silence this warning
182 | int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx;
| ^
| = 0
4 warnings generated.
rNNGPPredict.cpp:28:9: warning: unused variable 'h' [-Wunused-variable]
28 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGPPredict.cpp:28:15: warning: unused variable 'j' [-Wunused-variable]
28 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGPPredict.cpp:31:18: warning: unused variable 'negOne' [-Wunused-variable]
31 | const double negOne = -1.0;
| ^~~~~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rNNGPReplicated.cpp -o rNNGPReplicated.o
rNNGPReplicated.cpp:80:9: warning: unused variable 'h' [-Wunused-variable]
80 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGPReplicated.cpp:80:18: warning: unused variable 'k' [-Wunused-variable]
80 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGPReplicated.cpp:80:21: warning: unused variable 'l' [-Wunused-variable]
80 | int h, i, j, k, l, s, info, nProtect=0;
| ^
rNNGPReplicated.cpp:80:27: warning: unused variable 'info' [-Wunused-variable]
80 | int h, i, j, k, l, s, info, nProtect=0;
| ^~~~
rNNGPReplicated.cpp:83:18: warning: unused variable 'negOne' [-Wunused-variable]
83 | const double negOne = -1.0;
| ^~~~~~
rNNGPReplicated.cpp:84:18: warning: unused variable 'zero' [-Wunused-variable]
84 | const double zero = 0.0;
| ^~~~
6 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rpg.cpp -o rpg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sNNGP.cpp -o sNNGP.o
sNNGP.cpp:75:9: warning: unused variable 'h' [-Wunused-variable]
75 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGP.cpp:75:21: warning: unused variable 'l' [-Wunused-variable]
75 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGP.cpp:78:18: warning: unused variable 'negOne' [-Wunused-variable]
78 | const double negOne = -1.0;
| ^~~~~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sNNGPLogit.cpp -o sNNGPLogit.o
sNNGPLogit.cpp:76:9: warning: unused variable 'h' [-Wunused-variable]
76 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGPLogit.cpp:76:21: warning: unused variable 'l' [-Wunused-variable]
76 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGPLogit.cpp:79:18: warning: unused variable 'negOne' [-Wunused-variable]
79 | const double negOne = -1.0;
| ^~~~~~
3 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sNNGPPredict.cpp -o sNNGPPredict.o
sNNGPPredict.cpp:28:9: warning: unused variable 'h' [-Wunused-variable]
28 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGPPredict.cpp:28:15: warning: unused variable 'j' [-Wunused-variable]
28 | int h, i, j, k, l, s, info, nProtect=0;
| ^
sNNGPPredict.cpp:31:18: warning: unused variable 'negOne' [-Wunused-variable]
31 | const double negOne = -1.0;
| ^~~~~~
sNNGPPredict.cpp:36:13: warning: unused variable 'X' [-Wunused-variable]
36 | double *X = REAL(X_r);
| ^
sNNGPPredict.cpp:37:13: warning: unused variable 'y' [-Wunused-variable]
37 | double *y = REAL(y_r);
| ^
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c util.cpp -o util.o
util.cpp:33:10: warning: unused variable 'zero' [-Wunused-variable]
33 | double zero = 0.0;
| ^~~~
util.cpp:117:10: warning: unused variable 'j' [-Wunused-variable]
117 | int i, j, k;
| ^
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/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 -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)