* 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-14 14.2.0 zlib 1.3.1 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3AsMp7/R.INSTALL2fca7f5e66606a/surtvep/src' g++-14 -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:189, 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& Rcpp::internal::generic_name_proxy::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(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++-14 -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++-14 -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++-14 -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 '/home/hornik/tmp/scratch/Rtmp3AsMp7/R.INSTALL2fca7f5e66606a/surtvep/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3AsMp7/R.INSTALL2fca7f5e66606a/surtvep/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3AsMp7/R.INSTALL2fca7f5e66606a/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 * DONE (surtvep)