* installing *source* package ‘GSE’ ...
** this is package ‘GSE’ version ‘4.2-3’
** package ‘GSE’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-CXX20/GSE/src'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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 cov-em.cpp -o cov-em.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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 emve.cpp -o emve.o
In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from emve.h:5,
                 from emve.cpp:4:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
   27 |     #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emve.cpp: In function ‘arma::cube emve_resamp(arma::mat, arma::umat, arma::vec, int, int, arma::vec, arma::mat, int, arma::uvec, arma::umat, arma::uvec, arma::umat, arma::umat, arma::uvec, int, int, int, arma::uvec, arma::vec, arma::vec, int)’:
emve.cpp:193:20: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  193 |             if( rk == p){
      |                 ~~~^~~~
emve.cpp:216:24: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  216 |                 if( rk == p){
      |                     ~~~^~~~
emve.cpp: In function ‘arma::vec fast_pmd(arma::mat, arma::mat, arma::umat, arma::uvec)’:
emve.cpp:422:49: error: reference to ‘span’ is ambiguous
  422 |                         xi.col(mm) = x_mu_diff( span(rowid_start, rowid_end ), j );
      |                                                 ^~~~
In file included from /usr/include/c++/15/format:51,
                 from /usr/include/c++/15/bits/chrono_io.h:41,
                 from /usr/include/c++/15/chrono:3378,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:53,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:155:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: emve.o] Error 1
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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 gse-rocke.cpp -o gse-rocke.o
gse-rocke.cpp: In function ‘SEXPREC* GSE_Rocke(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
gse-rocke.cpp:46:13: warning: unused variable ‘print_step’ [-Wunused-variable]
   46 |         int print_step = as<int>(Print_step);
      |             ^~~~~~~~~~
gse-rocke.cpp:131:13: warning: unused variable ‘ximp_update’ [-Wunused-variable]
  131 |         int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, gamma_tune_group, wgts_mem, wgtsp_mem, ximp_mem);
      |             ^~~~~~~~~~~
gse-rocke.cpp: In function ‘arma::mat iterS(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double*, double*, double*, int*)’:
gse-rocke.cpp:206:65: error: reference to ‘span’ is ambiguous
  206 |                                                 xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                                                 ^~~~
In file included from /usr/include/c++/15/format:51,
                 from /usr/include/c++/15/bits/chrono_io.h:41,
                 from /usr/include/c++/15/chrono:3378,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:53,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from gse-rocke.h:5,
                 from gse-rocke.cpp:1:
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:155:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
gse-rocke.cpp:263:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  263 |                                 for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
      |                                               ~~~^~~
gse-rocke.cpp: In function ‘arma::mat gradient(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double, int, double)’:
gse-rocke.cpp:295:13: warning: unused variable ‘n’ [-Wunused-variable]
  295 |         int n = x.n_rows;
      |             ^
gse-rocke.cpp: In function ‘int update(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, arma::vec, double*, double*, double*)’:
gse-rocke.cpp:376:65: error: reference to ‘span’ is ambiguous
  376 |                                                 xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                                                 ^~~~
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
gse-rocke.cpp:426:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  426 |                                 for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
      |                                               ~~~^~~
gse-rocke.cpp:416:40: warning: unused variable ‘weight2’ [-Wunused-variable]
  416 |                                 double weight2 = weight1 * (md / ppi);
      |                                        ^~~~~~~
gse-rocke.cpp: In function ‘arma::mat pmd_adj(arma::mat, arma::mat, arma::mat, bool, arma::mat, arma::umat, arma::uvec, arma::vec, arma::vec)’:
gse-rocke.cpp:494:65: error: reference to ‘span’ is ambiguous
  494 |                                                 xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                                                 ^~~~
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: gse-rocke.o] Error 1
g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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 gse.cpp -o gse.o
gse.cpp: In function ‘SEXPREC* GSE_Rcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
gse.cpp:41:9: warning: unused variable ‘print_step’ [-Wunused-variable]
   41 |     int print_step = as<int>(Print_step);
      |         ^~~~~~~~~~
gse.cpp:102:9: warning: unused variable ‘ximp_update’ [-Wunused-variable]
  102 |     int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, wgts_mem, wgtsp_mem, ximp_mem);
      |         ^~~~~~~~~~~
gse.cpp: In function ‘arma::mat iterS(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, double*, double*, double*, int*)’:
gse.cpp:176:41: error: reference to ‘span’ is ambiguous
  176 |                         xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                         ^~~~
In file included from /usr/include/c++/15/format:51,
                 from /usr/include/c++/15/bits/chrono_io.h:41,
                 from /usr/include/c++/15/chrono:3378,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:53,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from gse.h:5,
                 from gse.cpp:1:
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:155:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
gse.cpp:233:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  233 |                 for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
      |                               ~~~^~~
gse.cpp: In function ‘int update(arma::mat, arma::mat, arma::mat, bool, arma::mat, double, arma::umat, arma::uvec, arma::vec, double*, double*, double*)’:
gse.cpp:299:41: error: reference to ‘span’ is ambiguous
  299 |                         xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                         ^~~~
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
gse.cpp:347:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  347 |                 for(int jj=0; jj < p; jj++) ximp(rowid_start + m, jj) = xpred(0, jj); // new July 28, 2014 for outputing the imputed data matrix
      |                               ~~~^~~
gse.cpp:337:24: warning: unused variable ‘weight2’ [-Wunused-variable]
  337 |                 double weight2 = weight1 * (md / ppi);
      |                        ^~~~~~~
gse.cpp: In function ‘arma::mat pmd_adj(arma::mat, arma::mat, arma::mat, bool, arma::mat, arma::umat, arma::uvec, arma::vec)’:
gse.cpp:414:41: error: reference to ‘span’ is ambiguous
  414 |                         xi.col(mm) = x( span(rowid_start, rowid_end ), j );
      |                                         ^~~~
/usr/include/c++/15/span:60:11: note: candidates are: ‘template<class _Type, long unsigned int _Extent> class std::span’
   60 |     class span;
      |           ^~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note:                 ‘struct arma::span’
   38 | struct span : public span_base<>
      |        ^~~~
make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: gse.o] Error 1
gcc -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include    -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
make[1]: Target 'all' not remade because of errors.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-CXX20/GSE/src'
ERROR: compilation failed for package ‘GSE’
* removing ‘/data/gannet/ripley/R/packages/tests-CXX20/GSE.Rcheck/GSE’