* installing *source* package ‘distory’ ...
** using staged installation
** libs
using C compiler: ‘Debian clang version 18.1.8 (9)’
using C++ compiler: ‘Debian clang version 18.1.8 (9)’
clang-18  -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O3 -Wall -pedantic -c distory.c -o distory.o
clang++-18  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c newick.cpp -o newick.o
newick.cpp:100:18: warning: variable 'ctr' set but not used [-Wunused-but-set-variable]
  100 |     unsigned int ctr = 0; // nesting level
      |                  ^
1 warning generated.
clang++-18  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1  -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c phydist_r.cpp -o phydist_r.o
phydist_r.cpp:69:27: error: use of undeclared identifier 'asLogical'; did you mean 'Rf_asLogical'?
   69 |         bool be_verbose = asLogical(verbose);
      |                           ^~~~~~~~~
      |                           Rf_asLogical
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:486:5: note: 'Rf_asLogical' declared here
  486 | int Rf_asLogical(SEXP x);
      |     ^
phydist_r.cpp:72:19: error: use of undeclared identifier 'length'
   72 |         int len = length(trees);
      |                   ^
phydist_r.cpp:80:30: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
   80 |         PROTECT(distmatrix = allocMatrix(REALSXP,len, len));
      |                              ^~~~~~~~~~~
      |                              Rf_allocMatrix
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
  504 | SEXP Rf_allocMatrix(SEXPTYPE, int, int);
      |      ^
phydist_r.cpp:96:25: error: use of undeclared identifier 'length'
   96 |         unsigned len1 = length(set1);
      |                         ^
phydist_r.cpp:98:25: error: use of undeclared identifier 'length'
   98 |         unsigned len2 = length(set2);
      |                         ^
phydist_r.cpp:102:26: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  102 |         PROTECT(newset = allocVector(INTSXP, len1));
      |                          ^~~~~~~~~~~
      |                          Rf_allocVector
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
 1078 | SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
      |          ^
phydist_r.cpp:136:19: error: use of undeclared identifier 'length'
  136 |         int len = length(treelist);
      |                   ^
phydist_r.cpp:148:30: error: use of undeclared identifier 'allocMatrix'; did you mean 'Rf_allocMatrix'?
  148 |         PROTECT(distmatrix = allocMatrix(REALSXP,len,len));
      |                              ^~~~~~~~~~~
      |                              Rf_allocMatrix
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:504:6: note: 'Rf_allocMatrix' declared here
  504 | SEXP Rf_allocMatrix(SEXPTYPE, int, int);
      |      ^
phydist_r.cpp:174:28: error: use of undeclared identifier 'asLogical'; did you mean 'Rf_asLogical'?
  174 |         bool list_deltas = asLogical(bDeltas);
      |                            ^~~~~~~~~
      |                            Rf_asLogical
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:486:5: note: 'Rf_asLogical' declared here
  486 | int Rf_asLogical(SEXP x);
      |     ^
phydist_r.cpp:175:22: error: use of undeclared identifier 'asInteger'; did you mean 'Rf_asInteger'?
  175 |         int scaleM = asInteger(scale_method);
      |                      ^~~~~~~~~
      |                      Rf_asInteger
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:487:5: note: 'Rf_asInteger' declared here
  487 | int Rf_asInteger(SEXP x);
      |     ^
phydist_r.cpp:177:24: error: use of undeclared identifier 'length'
  177 |         unsigned len = length(distmatrix);
      |                        ^
phydist_r.cpp:185:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  185 |             PROTECT(g = allocVector(REALSXP, (n*(n-1)*(n-2)*(n-3))/(4*3*2)));
      |                         ^~~~~~~~~~~
      |                         Rf_allocVector
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
 1078 | SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
      |          ^
phydist_r.cpp:191:25: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
  191 |             PROTECT(g = allocVector(REALSXP, 1));
      |                         ^~~~~~~~~~~
      |                         Rf_allocVector
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
/home/hornik/tmp/R-d-clang-18/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
 1078 | SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
      |          ^
13 errors generated.
make: *** [/home/hornik/tmp/R-d-clang-18/etc/Makeconf:202: phydist_r.o] Error 1
ERROR: compilation failed for package ‘distory’
* removing ‘/srv/hornik/tmp/CRAN_pretest/distory.Rcheck/distory’