* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mets’ ...
** this is package ‘mets’ version ‘1.3.7’
** package ‘mets’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-8) 14.3.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.3.0-8) 14.3.0’
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphKNLUf/R.INSTALL3ad407646f6323/mets/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:192,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /home/hornik/tmp/R.check/r-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-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-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c tvpack.f -o tvpack.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphKNLUf/R.INSTALL3ad407646f6323/mets/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphKNLUf/R.INSTALL3ad407646f6323/mets/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphKNLUf/R.INSTALL3ad407646f6323/mets/src'
installing to /home/hornik/tmp/R.check/r-patched-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
converting help for package ‘mets’
finding HTML links ... done
ACTG175 html
BinAugmentCifstrata html
Bootphreg html
CPH_HPN_CRBSI html
ClaytonOakes html
Dbvn html
EVaddGam html
Effbinreg html
Event html
EventSplit2 html
FG_AugmentCifstrata html
Grandom.cif html
LinSpline html
TRACE html
WA_recurrent html
aalenMets html
aalenfrailty html
back2timereg html
basehazplot.phreg html
bicomprisk html
binomial.twostage html
binreg html
binregATE html
binregCasewise html
binregG html
binregRatio html
binregTSR html
biprobit html
blocksample html
bmt html
bptwin html
calgb8923 html
casewise html
casewise.test html
cif html
cifreg html
cluster.index html
concordanceCor html
cor.cif html
count.history html
daggregate html
dby html
dcor html
dcut html
dermalridges html
dermalridgesMZ html
diabetes html
divide.conquer html
divide.conquer.timereg html
dlag html
doubleFGR html
dprint html
dreg html
drelevel html
dsort html
dspline html
dtable html
dtransform html
easy.binomial.twostage html
evalTerminal html
event.split html
eventpois html
familycluster.index html
familyclusterWithProbands.index html
fast.approx html
fast.pattern html
fast.reshape html
glm_IPTW html
gof.phreg html
gofG.phreg html
gofM.phreg html
gofZ.phreg html
haplo html
haplo.surv.discrete html
hfactioncpx12 html
iidBaseline html
internal html
interval.logitsurv.discrete html
ipw html
ipw2 html
km html
lifecourse html
lifetable.matrix html
logitSurv html
mediatorSurv html
medweight html
melanoma html
mena html
mets-package html
mets.options html
migr html
mlogit html
multcif html
np html
phreg html
phregR html
phreg_IPTW html
phreg_rct html
plack.cif html
plot.phreg html
plot_twin html
pmvn html
predict.phreg html
predictRisk html
predictRisk.binreg html
print.casewise html
prob.exceed.recurrent html
prt html
random.cif html
rchaz html
rchazC html
rcrisk html
recreg html
recurrentMarginal html
reexports html
resmean.phreg html
resmeanATE html
resmeanIPCW html
rpch html
sim.cause.cox html
sim.cif html
sim.cox html
sim.recurrent html
simAalenFrailty html
simClaytonOakes html
simClaytonOakesWei html
simGLcox html
simMultistate html
simRecurrentII html
simRecurrentTS html
summary.cor html
summaryGLM html
survival.twostage html
survivalG html
test.conc html
tetrachoric html
ttpd html
twin.clustertrunc html
twinbmi html
twinlm html
twinsim html
twinstut html
twostageMLE html
*** 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)