* installing *source* package ‘spNNGP’ ...
** package ‘spNNGP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spNNGP/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PGLogit.cpp -o PGLogit.o
PGLogit.cpp: In function 'SEXPREC* PGLogit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
PGLogit.cpp:27:18: warning: unused variable 'negOne' [-Wunused-variable]
27 | const double negOne = -1.0;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cNNGP.cpp -o cNNGP.o
cNNGP.cpp: In function 'SEXPREC* cNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cSLGP.cpp -o cSLGP.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c init.cpp -o init.o
cSLGP.cpp: In function 'SEXPREC* cSLGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c nn.cpp -o nn.o
nn.cpp: In function 'SEXPREC* mkUIndx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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: In function 'void fastNN(int, int, double*, int, double*, int*, int*, double*)':
nn.cpp:134:11: warning: unused variable 'k' [-Wunused-variable]
134 | int i,j,k;
| ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rNNGP.cpp -o rNNGP.o
rNNGP.cpp: In function 'SEXPREC* rNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rNNGPPredict.cpp -o rNNGPPredict.o
rNNGPPredict.cpp: In function 'SEXPREC* rNNGPPredict(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rNNGPReplicated.cpp -o rNNGPReplicated.o
rNNGPReplicated.cpp: In function 'SEXPREC* rNNGPReplicated(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rpg.cpp -o rpg.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sNNGP.cpp -o sNNGP.o
sNNGP.cpp: In function 'SEXPREC* sNNGP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~~~
sNNGP.cpp:319:9: warning: 'logDet' may be used uninitialized [-Wmaybe-uninitialized]
319 | #pragma omp parallel for private (e, j, b) reduction(+:a, logDet)
| ^~~
sNNGP.cpp:222:41: note: 'logDet' was declared here
222 | double logPostCand, logPostCurrent, logDet;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sNNGPLogit.cpp -o sNNGPLogit.o
sNNGPLogit.cpp: In function 'SEXPREC* sNNGPLogit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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;
| ^~~~~~
sNNGPLogit.cpp:331:9: warning: 'logDet' may be used uninitialized [-Wmaybe-uninitialized]
331 | #pragma omp parallel for private (e, j, b) reduction(+:a, logDet)
| ^~~
sNNGPLogit.cpp:227:41: note: 'logDet' was declared here
227 | double logPostCand, logPostCurrent, logDet;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sNNGPPredict.cpp -o sNNGPPredict.o
sNNGPPredict.cpp: In function 'SEXPREC* sNNGPPredict(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
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);
| ^
sNNGPPredict.cpp:84:50: warning: 'nuIndx' may be used uninitialized [-Wmaybe-uninitialized]
84 | int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c util.cpp -o util.o
util.cpp: In function 'void mvrnorm(double*, double*, double*, int)':
util.cpp:29:10: warning: unused variable 'zero' [-Wunused-variable]
29 | double zero = 0.0;
| ^~~~
util.cpp: In function 'void mkUIndx2(int, int, int*, int*, int*, int*)':
util.cpp:113:10: warning: unused variable 'j' [-Wunused-variable]
113 | int i, j, k;
| ^
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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 -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spNNGP/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/spNNGP/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/spNNGP/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)