* installing *source* package ‘BRISC’ ...
** package ‘BRISC’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking for g++-13 -std=gnu++17 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BRISC/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 BRISC.cpp -o BRISC.o
BRISC.cpp: In function 'SEXPREC* BRISC_bootstrapcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC.cpp:475:18: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
475 | int i_0, ret = 0;
| ^~~
BRISC.cpp: In function 'SEXPREC* BRISC_estimatecpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC.cpp:662:18: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
662 | int i_0, ret = 0;
| ^~~
BRISC.cpp: In function 'SEXPREC* BRISC_correlationcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC.cpp:914:16: warning: unused variable 'logDet' [-Wunused-variable]
914 | double logDet = updateBF(B, F, c, C, D, d, nnIndxLU, CIndx, n, theta, covModel, nThreads, fix_nugget);
| ^~~~~~
BRISC.cpp: In function 'SEXPREC* BRISC_decorrelationcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC.cpp:1076:16: warning: unused variable 'logDet' [-Wunused-variable]
1076 | double logDet = updateBF(B, F, c, C, D, d, nnIndxLU, CIndx, n, theta, covModel, nThreads, fix_nugget);
| ^~~~~~
BRISC.cpp: In function 'SEXPREC* BRISC_estimateneighborcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC.cpp:1238:13: warning: unused variable 'i' [-Wunused-variable]
1238 | int i, k, l, nProtect=0;
| ^
BRISC.cpp:1238:16: warning: unused variable 'k' [-Wunused-variable]
1238 | int i, k, l, nProtect=0;
| ^
BRISC.cpp:1238:19: warning: unused variable 'l' [-Wunused-variable]
1238 | int i, k, l, nProtect=0;
| ^
BRISC.cpp:1248:17: warning: unused variable 'coords' [-Wunused-variable]
1248 | double *coords = REAL(coords_r);
| ^~~~~~
BRISC.cpp:1323:18: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
1323 | int i_0, ret = 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 BRISC_Predict.cpp -o BRISC_Predict.o
BRISC_Predict.cpp: In function 'SEXPREC* BRISC_predictioncpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
BRISC_Predict.cpp:80:9: warning: variable 'nTheta' set but not used [-Wunused-but-set-variable]
80 | int nTheta, sigmaSqIndx, tauSqIndx, phiIndx, nuIndx;
| ^~~~~~
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lbfgs.c -o lbfgs.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 util.cpp -o util.o
util.cpp: In function 'void fastNN(int, int, double*, int, double*, int*, int*, double*)':
util.cpp:175:11: warning: unused variable 'k' [-Wunused-variable]
175 | 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 BRISC.so BRISC.o BRISC_Predict.o init.o lbfgs.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/BRISC/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BRISC/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BRISC/src'
installing to /data/gannet/ripley/R/packages/tests-devel/BRISC.Rcheck/00LOCK-BRISC/00new/BRISC/libs
** R
** 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 (BRISC)