Install log for 'mets'

* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’
* installing *source* package ‘mets’ ...
** package ‘mets’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpi6reM4/R.INSTALL1afb5456d0431b/mets/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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
fastcox.cpp: In function ‘SEXPREC* cumsumstratasumR(SEXP, SEXP, SEXP)’:
fastcox.cpp:993:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  993 |                 if ((first>0.1) && (i>=1)&& (ss<nstrata) && (ss>=0))
      |                 ^~
fastcox.cpp:995:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  995 |                         lagressum(i)=tmpsum(ss);
      |                         ^~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/mvtnorm/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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
mvn.cpp: In function ‘arma::vec loglikmvn(arma::mat&, arma::mat&, arma::uvec&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, double)’:
mvn.cpp:297:20: warning: unused variable ‘logdetS’ [-Wunused-variable]
  297 |   double logdetS0, logdetS, sign;
      |                    ^~~~~~~
mvn.cpp:297:29: warning: unused variable ‘sign’ [-Wunused-variable]
  297 |   double logdetS0, logdetS, sign;
      |                             ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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-13 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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::mat interpolate(const arma::mat&, double, bool)’:
sim-tools.cpp:60:14: warning: unused variable ‘delta’ [-Wunused-variable]
   60 |       double delta = curtime-time(cur);
      |              ^~~~~
sim-tools.cpp:64:12: warning: unused variable ‘tau2’ [-Wunused-variable]
   64 |     double tau2 = tn-input2(N-2,0);
      |            ^~~~
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++) {
      |                            ~^~~~~~
sim-tools.cpp: In function ‘arma::mat simGL(const arma::mat&, const arma::colvec&, const arma::colvec&, const arma::colvec&, const arma::colvec&, const arma::colvec&, const arma::colvec&, int, double, int, double)’:
sim-tools.cpp:195:6: warning: label ‘arma’ defined but not used [-Wunused-label]
  195 |      arma:mat basei=dcum;
      |      ^~~~
sim-tools.cpp: In function ‘arma::mat simSurvZ(const arma::mat&, const arma::colvec&, const arma::colvec&, double, int)’:
sim-tools.cpp:241:5: warning: label ‘arma’ defined but not used [-Wunused-label]
  241 |     arma:mat basei=St;
      |     ^~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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;
      |                     ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-release-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-13  -fpic  -g -O2 -Wall -mtune=native  -c tvpack.f -o tvpack.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-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 init.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-release-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpi6reM4/R.INSTALL1afb5456d0431b/mets/src'
make[1]: Entering directory '/tmp/Rtmpi6reM4/R.INSTALL1afb5456d0431b/mets/src'
make[1]: Leaving directory '/tmp/Rtmpi6reM4/R.INSTALL1afb5456d0431b/mets/src'
installing to /home/hornik/tmp/R.check/r-release-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)