* installing *source* package 'mets' ...
** package 'mets' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using Fortran compiler: 'GNU Fortran (GCC) 13.2.0'
using C++ compiler: 'g++.exe (GCC) 13.2.0'
make[1]: Entering directory '/d/temp/Rtmp2Zetqo/R.INSTALL2af4838e57aba/mets/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c aalenfrailty.cpp -o aalenfrailty.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c apply.cpp -o apply.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c binomial-twostage.cpp -o binomial-twostage.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biprobit.cpp -o biprobit.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c claytonoakes.cpp -o claytonoakes.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clusterindex.cpp -o clusterindex.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cor.cpp -o cor.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pch.cpp -o pch.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c prop-odd.cpp -o prop-odd.o
gcc -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c randomF77.c -o randomF77.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:188,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:29,
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 D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/internal/wrap.h:465:46,
inlined from 'SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]' at D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/internal/wrap.h:489:40,
inlined from 'SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]' at D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/internal/wrap.h:744:34,
inlined from 'SEXPREC* Rcpp::wrap(const T&) [with T = double]' at D:/RCompile/CRANpkg/lib/4.4/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 D:/RCompile/CRANpkg/lib/4.4/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:
D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: 'like' may be used uninitialized [-Wmaybe-uninitialized]
442 | 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++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include -I. -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/mvtnorm/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tools.cpp -o tools.o
gfortran -pedantic -O2 -mfpmath=sse -msse2 -mstackrealign -c tvpack.f -o tvpack.o
g++ -std=gnu++17 -shared -s -static-libgcc -o mets.dll tmp.def 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 -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LD:/RCompile/recent/R-4.4.0/bin/x64 -lR
make[1]: Leaving directory '/d/temp/Rtmp2Zetqo/R.INSTALL2af4838e57aba/mets/src'
make[1]: Entering directory '/d/temp/Rtmp2Zetqo/R.INSTALL2af4838e57aba/mets/src'
make[1]: Leaving directory '/d/temp/Rtmp2Zetqo/R.INSTALL2af4838e57aba/mets/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-mets/00new/mets/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'mets' as mets_1.3.4.zip
* DONE (mets)