* installing *source* package ‘surtvep’ ... ** package ‘surtvep’ successfully unpacked and MD5 sums checked ** using staged installation ./configure: line 7: inst/cc: No such file or directory ./configure: line 8: inst/cc: No such file or directory gcc-14 14.2.0 zlib 1.2.11 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs using C++ compiler: ‘g++-14 (GCC) 14.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/surtvep/src' g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c PenalizeStopCpp.cpp -o PenalizeStopCpp.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c header.cpp -o header.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:189, from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from /data/gannet/ripley/R/test-dev/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 /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/wrap.h:465:46, inlined from 'SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = int]' at /data/gannet/ripley/R/test-dev/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 /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/wrap.h:744:34, inlined from 'SEXPREC* Rcpp::wrap(const T&) [with T = int]' at /data/gannet/ripley/R/test-dev/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 /data/gannet/ripley/R/test-dev/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: /data/gannet/ripley/R/test-dev/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++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o surtvep.so PenalizeStopCpp.o RcppExports.o header.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/surtvep/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/surtvep/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/surtvep/src' installing to /data/gannet/ripley/R/packages/tests-devel/surtvep.Rcheck/00LOCK-surtvep/00new/surtvep/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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)