* installing *source* package ‘MAGEE’ ... ** this is package ‘MAGEE’ version ‘1.4.4’ ** package ‘MAGEE’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++20 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++20 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for ZSTD_decompress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for libdeflate_zlib_decompress in -ldeflate... yes checking libdeflate.h usability... yes checking libdeflate.h presence... yes checking for libdeflate.h... yes configure: Will use system-wide libdeflate library configure: creating ./config.status config.status: creating src/Makevars ** 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/MAGEE/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -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 fitglmm.cpp -o fitglmm.o fitglmm.cpp: In function ‘SEXPREC* glmm_gei_bgen13(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: fitglmm.cpp:488:61: error: reference to ‘span’ is ambiguous 488 | bool is_non_singular_IV_V1 = inv(IV_E_i,IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:155, 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 fitglmm.cpp:26: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ 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: /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:488:78: error: reference to ‘span’ is ambiguous 488 | bool is_non_singular_IV_V1 = inv(IV_E_i,IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:490:35: error: reference to ‘span’ is ambiguous 490 | IV_E_i=pinv(IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:490:52: error: reference to ‘span’ is ambiguous 490 | IV_E_i=pinv(IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:499:37: error: reference to ‘span’ is ambiguous 499 | IV_GE_i=inv(IV_V_i1(span(0,ngei1-1),span(0,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:499:53: error: reference to ‘span’ is ambiguous 499 | IV_GE_i=inv(IV_V_i1(span(0,ngei1-1),span(0,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:595:37: error: reference to ‘span’ is ambiguous 595 | split_mat=split_mat(span(1,ei),span(1,ei)); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:595:48: error: reference to ‘span’ is ambiguous 595 | split_mat=split_mat(span(1,ei),span(1,ei)); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp: In function ‘SEXPREC* glmm_gei_bgen11(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: fitglmm.cpp:1019:32: error: reference to ‘span’ is ambiguous 1019 | IV_E_i=inv(IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:1019:49: error: reference to ‘span’ is ambiguous 1019 | IV_E_i=inv(IV_V_i1(span(ng,ngei1-1),span(ng,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:1022:33: error: reference to ‘span’ is ambiguous 1022 | IV_GE_i=inv(IV_V_i1(span(0,ngei1-1),span(0,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:1022:49: error: reference to ‘span’ is ambiguous 1022 | IV_GE_i=inv(IV_V_i1(span(0,ngei1-1),span(0,ngei1-1))); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:1095:37: error: reference to ‘span’ is ambiguous 1095 | split_mat=split_mat(span(1,ei),span(1,ei)); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ fitglmm.cpp:1095:48: error: reference to ‘span’ is ambiguous 1095 | split_mat=split_mat(span(1,ei),span(1,ei)); | ^~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’ 38 | struct span : public span_base<> | ^~~~ /usr/include/c++/15/span:60:11: note: ‘template class std::span’ 60 | class span; | ^~~~ make[1]: *** [/data/gannet/ripley/R/cxx20/etc/Makeconf:201: fitglmm.o] Error 1 g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -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 fitmagee.cpp -o fitmagee.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DARMA_64BIT_WORD -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 read_bgen.cpp -o read_bgen.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from read_bgen.cpp:2: /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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /data/gannet/ripley/R/cxx20/include/R.h:73, from read_bgen.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]’: /data/gannet/ripley/R/cxx20/include/R_ext/Error.h:89:17: warning: infinite recursion detected [-Winfinite-recursion] 89 | #define warning Rf_warning | ^~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro ‘warning’ 190 | inline void warning(const char* fmt, Args&&... args ) { | ^~~~~~~ In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:132: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call 191 | Rf_warning("%s", tfm::format(fmt, std::forward(args)... ).c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/cxx20/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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 registerDynamicSymbol.c -o registerDynamicSymbol.o make[1]: Target 'MAGEE.so' not remade because of errors. make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-CXX20/MAGEE/src' ERROR: compilation failed for package ‘MAGEE’ * removing ‘/data/gannet/ripley/R/packages/tests-CXX20/MAGEE.Rcheck/MAGEE’