* installing *source* package ‘lnmixsurv’ ...
** this is package ‘lnmixsurv’ version ‘3.1.6’
** package ‘lnmixsurv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/lnmixsurv/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I/usr/local/include `/data/gannet/ripley/R/R-devel/bin/Rscript -e "RcppGSL:::CFlags()"` -DARMA_64BIT_WORD=1 -I../inst/include/ -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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I/usr/local/include `/data/gannet/ripley/R/R-devel/bin/Rscript -e "RcppGSL:::CFlags()"` -DARMA_64BIT_WORD=1 -I../inst/include/ -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 lognormal_mixture_gibbs.cpp -o lognormal_mixture_gibbs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I/usr/local/include `/data/gannet/ripley/R/R-devel/bin/Rscript -e "RcppGSL:::CFlags()"` -DARMA_64BIT_WORD=1 -I../inst/include/ -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 predict.cpp -o predict.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I/usr/local/include `/data/gannet/ripley/R/R-devel/bin/Rscript -e "RcppGSL:::CFlags()"` -DARMA_64BIT_WORD=1 -I../inst/include/ -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 simulate_data.cpp -o simulate_data.o
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from lognormal_mixture_gibbs.cpp:3:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from predict.cpp:3:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from simulate_data.cpp:3:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
predict.cpp: In function ‘double sob_lognormal_mix(const double&, const arma::rowvec&, const arma::vec&, const arma::vec&)’:
predict.cpp:17:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
17 | for (int i = 0; i < m.n_elem; i++) {
| ~~^~~~~~~~~~
predict.cpp: In function ‘double hazard_lognormal_mix(const double&, const arma::rowvec&, const arma::vec&, const arma::vec&)’:
predict.cpp:27:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
27 | for (int i = 0; i < m.n_elem; i++) {
| ~~^~~~~~~~~~
predict.cpp: In function ‘arma::mat predict_survival_gibbs_cpp(const arma::vec&, const arma::rowvec&, const arma::field<arma::Mat<double> >&, arma::mat, arma::mat, const bool&, const double&)’:
predict.cpp:77:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
77 | for(int time = 0; time < eval_time.n_elem; time++) {
| ~~~~~^~~~~~~~~~~~~~~~~~
predict.cpp: In function ‘arma::mat predict_hazard_gibbs_cpp(const arma::vec&, const arma::rowvec&, const arma::field<arma::Mat<double> >&, arma::mat, arma::mat, const bool&, const double&)’:
predict.cpp:140:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
140 | for(int time = 0; time < eval_time.n_elem; time++) {
| ~~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o lnmixsurv.so RcppExports.o lognormal_mixture_gibbs.o predict.o simulate_data.o -lgsl -lgslcblas -lm -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/lnmixsurv/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/lnmixsurv/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/lnmixsurv/src'
installing to /data/gannet/ripley/R/packages/tests-devel/lnmixsurv.Rcheck/00LOCK-lnmixsurv/00new/lnmixsurv/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 (lnmixsurv)