* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘mets’ ...
** this is package ‘mets’ version ‘1.3.8’
** package ‘mets’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-11) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
make[1]: Entering directory '/tmp/Rtmp4daqjL/R.INSTALL1b87d538abd01d/mets/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aalenfrailty.cpp -o aalenfrailty.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c apply.cpp -o apply.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binomial-twostage.cpp -o binomial-twostage.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c biprobit.cpp -o biprobit.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c claytonoakes.cpp -o claytonoakes.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c clusterindex.cpp -o clusterindex.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cor.cpp -o cor.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastcox.cpp -o fastcox.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mvn.cpp -o mvn.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pch.cpp -o pch.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c prop-odd.cpp -o prop-odd.o
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c randomF77.c -o randomF77.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sim-tools.cpp -o sim-tools.o
sim-tools.cpp: In function ‘arma::uvec approx(const arma::mat&, const arma::mat&, unsigned int)’:
sim-tools.cpp:17:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
17 | for (int i=0; i<newtime.n_elem; i++) {
| ~^~~~~~~~~~~~~~~
sim-tools.cpp: In function ‘arma::uvec pmini(const arma::uvec&, int)’:
sim-tools.cpp:72:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
72 | for(int i=0; i<y.n_elem; ++i)
| ~^~~~~~~~~
sim-tools.cpp:73:22: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘const int’ [-Wsign-compare]
73 | if (y(i) < N) res(i) = y(i); else res(i) = N;
| ~~~~~^~~
sim-tools.cpp: In function ‘arma::colvec pminv(const arma::colvec&, double)’:
sim-tools.cpp:80:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
80 | for(int i=0; i<y.n_elem; ++i)
| ~^~~~~~~~~
sim-tools.cpp: In function ‘arma::mat interpolate2(const arma::mat&, const arma::colvec&)’:
sim-tools.cpp:98:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
98 | for(int i=0;i<N;++i)
| ~^~
sim-tools.cpp: In function ‘double interpolate3(const arma::mat&, double)’:
sim-tools.cpp:124:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
124 | for(int i=0;i<N;++i)
| ~^~
sim-tools.cpp: In function ‘arma::colvec simbase(const arma::mat&, double, double, double, int)’:
sim-tools.cpp:156:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
156 | for (unsigned i=0; i<maxit; i++) {
| ~^~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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:2077:57: warning: variable ‘sdj’ set but not used [-Wunused-but-set-variable]
2077 | 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:2762:21: warning: variable ‘thetak’ set but not used [-Wunused-but-set-variable]
2762 | double llt=1,ssf=0,thetak=0;
| ^~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:191,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from survival-twostage.cpp:1:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:471:46,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:495:40,
inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:744:34,
inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
inlined from ‘Rcpp::internal::generic_name_proxy<RTYPE, StoragePolicy>& Rcpp::internal::generic_name_proxy<RTYPE, StoragePolicy>::operator=(const T&) [with T = double; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/proxy.h:157:11,
inlined from ‘SEXPREC* claytonoakesbinRV(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’ at survival-twostage.cpp:1800:16:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: ‘like’ may be used uninitialized [-Wmaybe-uninitialized]
448 | r_vector_start<RTYPE>(x)[0] = object;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
survival-twostage.cpp: In function ‘SEXPREC* claytonoakesbinRV(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
survival-twostage.cpp:1786:16: note: ‘like’ was declared here
1786 | double like;
| ^~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tools.cpp -o tools.o
gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c tvpack.f -o tvpack.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/tmp/Rtmp4daqjL/R.INSTALL1b87d538abd01d/mets/src'
make[1]: Entering directory '/tmp/Rtmp4daqjL/R.INSTALL1b87d538abd01d/mets/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/tmp/Rtmp4daqjL/R.INSTALL1b87d538abd01d/mets/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)