Install log for 'stLMM'

* installing *source* package ‘stLMM’ ...
** this is package ‘stLMM’ version ‘0.0.3’
** package ‘stLMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/stLMM/src'
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 Matrix_stubs.c -o Matrix_stubs.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 corModels.cpp -o corModels.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_common.cpp -o stLMM_common.o
stLMM_common.cpp: In function ‘double logDetFactor(cholmod_factor*)’:
stLMM_common.cpp:308:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  308 |   for(i = 0; i < L->nsuper; i++){
      |              ~~^~~~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_covariance.cpp -o stLMM_covariance.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_precision.cpp -o stLMM_precision.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_predict.cpp -o stLMM_predict.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_recover.cpp -o stLMM_recover.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_sampler.cpp -o stLMM_sampler.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 stLMM_state.cpp -o stLMM_state.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/BayesLogit/include' -I'/data/localhost/ripley/R/R-devel/library/Matrix/include' -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 utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o stLMM.so Matrix_stubs.o corModels.o init.o nn.o stLMM_common.o stLMM_covariance.o stLMM_precision.o stLMM_predict.o stLMM_recover.o stLMM_sampler.o stLMM_state.o utils.o -fopenmp -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/stLMM/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/stLMM/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/stLMM/src'
installing to /data/localhost/ripley/R/packages/tests-devel/stLMM.Rcheck/00LOCK-stLMM/00new/stLMM/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (stLMM)