* installing *source* package ‘ASMap’ ...
** package ‘ASMap’ 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/ASMap/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -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 MSTOpt.cpp -o MSTOpt.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -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 genetic_map_DH.cpp -o genetic_map_DH.o
In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41,
                 from linkage_group_DH.h:25,
                 from genetic_map_DH.h:18,
                 from genetic_map_DH.cpp:11:
genetic_map_DH.cpp: In member function 'int genetic_map::read_raw_mapping_data(SEXPREC*&, SEXPREC*&)':
genetic_map_DH.cpp:39:24: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'?
   39 |   SEXP names = PROTECT(getAttrib(data, R_NamesSymbol));
      |                        ^~~~~~~~~
/data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
genetic_map_DH.cpp:40:44: error: 'install' was not declared in this scope
   40 |   SEXP row_names = PROTECT(getAttrib(data, install("row.names")));
      |                                            ^~~~~~~
/data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
genetic_map_DH.cpp:108:11: error: 'isNumeric' was not declared in this scope; did you mean 'Rf_isNumeric'?
  108 |       if(!isNumeric(ielem(data,jj))) {
      |           ^~~~~~~~~
      |           Rf_isNumeric
genetic_map_DH.cpp:132:22: error: 'coerceVector' was not declared in this scope; did you mean 'Rf_coerceVector'?
  132 |         sstr << REAL(coerceVector(ielem(data,jj),REALSXP))[ii];
      |                      ^~~~~~~~~~~~
      |                      Rf_coerceVector
genetic_map_DH.cpp: In member function 'void genetic_map::write_output(SEXPREC*&)':
genetic_map_DH.cpp:462:18: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  462 |   PROTECT(iNames=allocVector(STRSXP,individual_names.size()));
      |                  ^~~~~~~~~~~
/data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
genetic_map_DH.cpp:464:32: error: 'mkChar' was not declared in this scope
  464 |     SET_STRING_ELT(iNames, jj, mkChar(individual_names[jj].c_str()));
      |                                ^~~~~~
genetic_map_DH.cpp:510:39: error: 'mkChar' was not declared in this scope
  510 |         SET_STRING_ELT(mNames, kount, mkChar(marker_names[*iter2].c_str()));
      |                                       ^~~~~~
genetic_map_DH.cpp:528:41: error: 'mkChar' was not declared in this scope
  528 |           SET_STRING_ELT(mNames, kount, mkChar(marker_names[*iter2].c_str()));
      |                                         ^~~~~~
genetic_map_DH.cpp:539:7: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
  539 |       setAttrib(dist, R_NamesSymbol, mNames);
      |       ^~~~~~~~~
      |       Rf_setAttrib
genetic_map_DH.cpp:543:36: error: 'mkChar' was not declared in this scope
  543 |         SET_STRING_ELT(cNames, jj, mkChar(rownames[jj].c_str()));
      |                                    ^~~~~~
genetic_map_DH.cpp: In member function 'virtual void genetic_map_DH::generate_map(SEXPREC*&)':
genetic_map_DH.cpp:777:17: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  777 |   PROTECT(map = allocVector(VECSXP,number_of_connected_components));
      |                 ^~~~~~~~~~~
/data/gannet/ripley/R/R-devel/include/Rinternals.h:371:36: note: in definition of macro 'PROTECT'
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
genetic_map_DH.cpp:784:36: error: 'mkChar' was not declared in this scope
  784 |         SET_STRING_ELT(lNames, nn, mkChar(comp[nn]));
      |                                    ^~~~~~
genetic_map_DH.cpp:785:7: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
  785 |       setAttrib(newnode, R_NamesSymbol, lNames);
      |       ^~~~~~~~~
      |       Rf_setAttrib
make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: genetic_map_DH.o] Error 1
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/ASMap/src'
ERROR: compilation failed for package ‘ASMap’
* removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/ASMap-lib/ASMap’
Command exited with non-zero status 1
Time 0:09.82, 8.20 + 0.57