* installing *source* package ‘bigalgebra’ ... ** package ‘bigalgebra’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/bigalgebra/src' gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../include -DUSE_FC_LEN_T -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/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 R_init_bigalgebra.c -o R_init_bigalgebra.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../include -DUSE_FC_LEN_T -I'/data/gannet/ripley/R/test-dev/bigmemory/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/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 -DR_NO_REMAP -c bigalgebra.cpp -o bigalgebra.o bigalgebra.cpp:5: warning: "USE_FC_LEN_T" redefined 5 | #define USE_FC_LEN_T | : note: this is the location of the previous definition In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17, from /data/gannet/ripley/R/test-dev/bigmemory/include/bigmemory/BigMatrix.h:10, from bigalgebra.cpp:2: /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/local/gcc13/include/c++/13.2.0/memory:78, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:27: /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)': /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/local/gcc13/include/c++/13.2.0/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from bigalgebra.cpp:8: bigalgebra.cpp: In function 'double* make_double_ptr(SEXP, SEXP)': bigalgebra.cpp:38:40: error: 'install' was not declared in this scope 38 | SEXP address = GET_SLOT (matrix, install ("address")); | ^~~~~~~ /data/gannet/ripley/R/R-devel/include/Rdefines.h:151:46: note: in definition of macro 'GET_SLOT' 151 | #define GET_SLOT(x, what) R_do_slot(x, what) | ^~~~ In file included from bigalgebra.cpp:7: bigalgebra.cpp: In function 'SEXPREC* dgemm_wrapper(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': bigalgebra.cpp:94:19: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'? 94 | PROTECT(ans = allocMatrix(REALSXP, (int)MM, (int)NN)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ bigalgebra.cpp:110:3: error: 'unprotect' was not declared in this scope; did you mean 'mprotect'? 110 | unprotect(1); | ^~~~~~~~~ | mprotect bigalgebra.cpp: In function 'SEXPREC* daxpy_wrapper(SEXP, SEXP, SEXP, SEXP, SEXP)': bigalgebra.cpp:132:16: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'? 132 | PROTECT(Tr = allocVector(LGLSXP, 1)); | ^~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT' 371 | #define PROTECT(s) Rf_protect(s) | ^ bigalgebra.cpp:142:3: error: 'unprotect' was not declared in this scope; did you mean 'mprotect'? 142 | unprotect(2); | ^~~~~~~~~ | mprotect make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: bigalgebra.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/bigalgebra/src' ERROR: compilation failed for package ‘bigalgebra’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/bigalgebra-lib/bigalgebra’ Command exited with non-zero status 1 Time 0:03.86, 2.88 + 0.40