* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘surtvep’ ...
** package ‘surtvep’ successfully unpacked and MD5 sums checked
** using staged installation
./configure: 7: cannot create inst/cc: Directory nonexistent
./configure: 8: cannot create inst/cc: Directory nonexistent
gcc-13 13.2.0
zlib 1.3 is available ok
R CMD SHLIB supports OpenMP without any extra hint
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
make[1]: Entering directory '/tmp/RtmpZqpEKU/R.INSTALL3bdce61c5b629e/surtvep/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PenalizeStopCpp.cpp -o PenalizeStopCpp.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:188,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from PenalizeStopCpp.cpp:5:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = int]’,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = int]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:465:46,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = int]’ at /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 = int]’ 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 = int]’ 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 = int; 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 ‘Rcpp::List Lambda_estimate_ties2(int, arma::colvec&, arma::mat&, arma::mat&, arma::mat&, arma::vec&)’ at PenalizeStopCpp.cpp:2649:25:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized]
442 | r_vector_start<RTYPE>(x)[0] = object;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
PenalizeStopCpp.cpp: In function ‘Rcpp::List Lambda_estimate_ties2(int, arma::colvec&, arma::mat&, arma::mat&, arma::mat&, arma::vec&)’:
PenalizeStopCpp.cpp:2625:13: note: ‘index’ was declared here
2625 | int index;
| ^~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -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-patched-gcc/Work/build/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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c header.cpp -o header.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o surtvep.so PenalizeStopCpp.o RcppExports.o header.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpZqpEKU/R.INSTALL3bdce61c5b629e/surtvep/src'
make[1]: Entering directory '/tmp/RtmpZqpEKU/R.INSTALL3bdce61c5b629e/surtvep/src'
make[1]: Leaving directory '/tmp/RtmpZqpEKU/R.INSTALL3bdce61c5b629e/surtvep/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-surtvep/00new/surtvep/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘surtvep’
finding HTML links ... done
ExampleData html
ExampleDataBinary html
IC html
StrataExample html
baseline html
confint.coxtv html
coxtp html
coxtv html
cv.coxtp html
get.tvcoef html
plot.baseline html
plot.coxtp html
plot.coxtv html
support html
tvef.ph html
tvef.zero html
tvef.zero.time html
** building package indices
** 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
* creating tarball
packaged installation of ‘surtvep’ as ‘surtvep_1.0.0_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (surtvep)