Install log for 'mets'

* installing *source* package ‘mets’ ...
** this is package ‘mets’ version ‘1.3.11’
** package ‘mets’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using Fortran compiler: ‘GNU Fortran (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)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/mets/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 aalenfrailty.cpp -o aalenfrailty.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 apply.cpp -o apply.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 binomial-twostage.cpp -o binomial-twostage.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 biprobit.cpp -o biprobit.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 claytonoakes.cpp -o claytonoakes.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 clusterindex.cpp -o clusterindex.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 cor.cpp -o cor.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 fastcox.cpp -o fastcox.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 mvn.cpp -o mvn.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 pch.cpp -o pch.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 prop-odd.cpp -o prop-odd.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/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 randomF77.c -o randomF77.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 sim-tools.cpp -o sim-tools.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 survival-twostage.cpp -o survival-twostage.o
survival-twostage.cpp: In function ‘SEXPREC* twostageloglikeRV(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
survival-twostage.cpp:2076:57: warning: variable ‘sdj’ set but not used [-Wunused-but-set-variable=]
 2076 |  double dl1,dl2,ll1,ll2,ll=1,Li,Lk,diff=0,loglikecont=0,sdj=0;
      |                                                         ^~~
survival-twostage.cpp: In function ‘SEXPREC* survivalloglikeRVpairs(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
survival-twostage.cpp:2761:21: warning: variable ‘thetak’ set but not used [-Wunused-but-set-variable=]
 2761 |  double llt=1,ssf=0,thetak=0;
      |                     ^~~~~~
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 tools.cpp -o tools.o
gfortran  -fpic  -g -O2 -mtune=native -Wall -pedantic  -c tvpack.f -o tvpack.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/mvtnorm/include' -I/usr/local/include   -fopenmp -I../inst/include -DNDEBUG -DARMA_DONT_USE_OPENMP -DARMA_NO_DEBUG -DARMA_WARN_LEVEL=1 -DRCPP_NO_MODULES -DRCPP_NO_RTTI -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 weibull.cpp -o weibull.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o mets.so RcppExports.o aalenfrailty.o apply.o binomial-twostage.o biprobit.o claytonoakes.o clusterindex.o cor.o fastcox.o mvn.o pch.o prop-odd.o randomF77.o sim-tools.o survival-twostage.o tools.o tvpack.o weibull.o -fopenmp -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/mets/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/mets/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/mets/src'
installing to /data/localhost/ripley/R/packages/tests-devel/mets.Rcheck/00LOCK-mets/00new/mets/libs
** R
** data
** demo
** 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 (mets)