* installing *source* package ‘gRim’ ...
** package ‘gRim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gRim/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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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
gcc-14 -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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c _utils_mat.c -o _utils_mat.o
In file included from ../inst/include/gRim.h:13,
                 from RcppExports.cpp:4:
../inst/include/gRim_RcppExports.h:16:14: warning: 'void gRim::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
   16 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
gcc-14 -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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c _utils_print.c -o _utils_print.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 fit2way.cpp -o fit2way.o
gcc-14 -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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c ggmfit.c -o ggmfit.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 grips_arma_utils.cpp -o grips_arma_utils.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 grips_fit_ips.cpp -o grips_fit_ips.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 grips_fit_ncd.cpp -o grips_fit_ncd.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 grips_utils.cpp -o grips_utils.o
gcc-14 -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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c init.c -o init.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'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gRbase/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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 parm_conversion.cpp -o parm_conversion.o
grips_fit_ips.cpp: In function 'Rcpp::List covips_ggm_(arma::mat&, Rcpp::List&, arma::umat&, int&, arma::mat&, int&, double&, int&, int&, Rcpp::List&)':
grips_fit_ips.cpp:295:16: warning: variable 'logLp' set but not used [-Wunused-but-set-variable]
  295 |   double logL, logLp, conv_check=9999, gap=-1.0, maxabs;
      |                ^~~~~
In file included from grips_fit_ips.cpp:2:
grips_fit_ips.cpp: In function 'Rcpp::List conips_ggm_(arma::mat&, Rcpp::List&, arma::umat&, int&, arma::mat, int&, double&, int&, int&, Rcpp::List&)':
grips_utils.h:85:26: warning: 'logLp' may be used uninitialized [-Wmaybe-uninitialized]
   85 |   conv_check = fabs(logL - logLp)  / nparm;     \
      |                     ~~~~~^~~~~~~
grips_fit_ips.cpp:168:7: note: in expansion of macro 'CONV_CHECK_LOGL_DIFF'
  168 |       CONV_CHECK_LOGL_DIFF;
      |       ^~~~~~~~~~~~~~~~~~~~
grips_fit_ips.cpp:119:16: note: 'logLp' was declared here
  119 |   double logL, logLp, conv_check=9999, gap=-1.0;
      |                ^~~~~
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 grips_fit_ncd.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 /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 = double]' 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 = double]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/wrap.h:744:34,
    inlined from 'SEXPREC* Rcpp::wrap(const T&) [with T = double]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
    inlined from 'static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/converter.h:80:23,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:532:13,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:525:46,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:514:34,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<double>; TArgs = {Rcpp::traits::named_object<int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:1168:32,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<arma::Mat<double> >; TArgs = {Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:1169:37,
    inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<arma::Mat<double> >; TArgs = {Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:1169:37,
    inlined from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:1148:37,
    inlined from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<int>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:1131:33,
    inlined from 'Rcpp::List ncd_ggm_(arma::mat&, Rcpp::List&, arma::umat&, int&, arma::mat, int, double&, int&, int, Rcpp::List&)' at grips_fit_ncd.cpp:363:33:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: 'logL' may be used uninitialized [-Wmaybe-uninitialized]
  442 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
grips_fit_ncd.cpp: In function 'Rcpp::List ncd_ggm_(arma::mat&, Rcpp::List&, arma::umat&, int&, arma::mat, int, double&, int&, int, Rcpp::List&)':
grips_fit_ncd.cpp:263:10: note: 'logL' was declared here
  263 |   double logL, gap=-1.0, conv_check, eps2, mno;
      |          ^~~~
grips_fit_ncd.cpp:352:21: warning: 'itcount' may be used uninitialized [-Wmaybe-uninitialized]
  352 |   itcount = itcount / n_vars;
      |             ~~~~~~~~^~~~~~~~
grips_fit_ncd.cpp:264:21: note: 'itcount' was declared here
  264 |   int iter1, iter2, itcount, n_upd=0;
      |                     ^~~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o gRim.so RcppExports.o _utils_mat.o _utils_print.o fit2way.o ggmfit.o grips_arma_utils.o grips_fit_ips.o grips_fit_ncd.o grips_utils.o init.o parm_conversion.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gRim/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/gRim/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/gRim/src'
installing to /data/gannet/ripley/R/packages/tests-devel/gRim.Rcheck/00LOCK-gRim/00new/gRim/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (gRim)