* installing *source* package ‘phangorn’ ...
** package ‘phangorn’ 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’
using C++11
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/phangorn/src'
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -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 RcppExports.cpp -o RcppExports.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 RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:26: warning: "R_NO_REMAP" redefined
   26 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -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 dist.c -o dist.o
g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -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 dupAtomMat.cpp -o dupAtomMat.o
In file included from rcSet.h:2,
                 from dupAtomMat.cpp:1:
lessAndEqual.h: In constructor 'CharSEXP::CharSEXP(SEXP)':
lessAndEqual.h:27:14: error: 'error' was not declared in this scope; did you mean 'perror'?
   27 |         else error("CharSEXP should be initialized with a CHARSXP type object");
      |              ^~~~~
      |              perror
dupAtomMat.cpp: In function 'SEXPREC* grpDupAtomMat(SEXP, SEXP, SEXP)':
dupAtomMat.cpp:16:21: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'?
   16 |         dim=INTEGER(getAttrib(x, R_DimSymbol));
      |                     ^~~~~~~~~
      |                     Rf_getAttrib
In file included from lessAndEqual.h:6:
dupAtomMat.cpp:17:23: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
   17 |         out = PROTECT(allocVector(INTSXP, dim[*INTEGER(MARGIN)-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)
      |                                    ^
dupAtomMat.cpp:45:25: error: 'error' was not declared in this scope; did you mean 'perror'?
   45 |                         error("C function 'grpDupAtomMat' only accepts REALSXP, LGLSXP, INTSXP and STRSXP");
      |                         ^~~~~
      |                         perror
dupAtomMat.cpp:51:20: error: 'install' was not declared in this scope
   51 |     setAttrib(out, install("nlevels"), nLevels);
      |                    ^~~~~~~
dupAtomMat.cpp:51:5: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
   51 |     setAttrib(out, install("nlevels"), nLevels);
      |     ^~~~~~~~~
      |     Rf_setAttrib
make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:202: dupAtomMat.o] Error 1
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/phangorn/src'
ERROR: compilation failed for package ‘phangorn’
* removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/phangorn-lib/phangorn’
Command exited with non-zero status 1
Time 0:17.02, 15.75 + 1.00