* 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-13 13.2.0
zlib 1.2.11 is available ok
R CMD SHLIB supports OpenMP without any extra hint
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/surtvep/src'
g++-13 -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   -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   -c PenalizeStopCpp.cpp -o PenalizeStopCpp.o
g++-13 -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   -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   -c RcppExports.cpp -o RcppExports.o
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:188,
                 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++-13 -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   -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   -c header.cpp -o header.o
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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)