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###
### Running command:
###
###   chmod a+r Rtreemix -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Rtreemix
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* checking for file 'Rtreemix/DESCRIPTION' ... OK
* preparing 'Rtreemix':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'Rtreemix' ...
** this is package 'Rtreemix' version '1.69.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -c Rtreemix.cc -o Rtreemix.o
Rtreemix.cc: In function 'replaceleda::array<std::__cxx11::basic_string<char> > C_get_profile(SEXP)':
Rtreemix.cc:145:11: error: 'length' was not declared in this scope
  145 |   int L = length(R_events);
      |           ^~~~~~
In file included from Rtreemix.cc:25:
Rtreemix.cc:155:22: error: 'coerceVector' was not declared in this scope; did you mean 'Rf_coerceVector'?
  155 |   PROTECT(R_events = coerceVector(R_events, STRSXP));
      |                      ^~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'replaceleda::integer_matrix C_get_pattern(SEXP)':
Rtreemix.cc:191:15: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'?
  191 |   SEXP Rdim = getAttrib(R_mat, R_DimSymbol);
      |               ^~~~~~~~~
      |               Rf_getAttrib
Rtreemix.cc:201:19: error: 'coerceVector' was not declared in this scope; did you mean 'Rf_coerceVector'?
  201 |   PROTECT(R_mat = coerceVector(R_mat,INTSXP));
      |                   ^~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_int_matrix(replaceleda::integer_matrix)':
Rtreemix.cc:245:19: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'?
  245 |   PROTECT(R_mat = allocMatrix(INTSXP, C_mat.dim1(), C_mat.dim2()));
      |                   ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_real_matrix(replaceleda::matrix)':
Rtreemix.cc:301:19: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'?
  301 |   PROTECT(R_mat = allocMatrix(REALSXP, C_mat.dim1(), C_mat.dim2()));
      |                   ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_real_vector(replaceleda::vector)':
Rtreemix.cc:333:19: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  333 |   PROTECT(R_vec = allocVector(REALSXP, v.size()));
      |                   ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_scalarString(const char*)':
Rtreemix.cc:359:17: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  359 |   PROTECT(ans = allocVector(STRSXP, 1));
      |                 ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:365:28: error: 'mkChar' was not declared in this scope; did you mean 'char'?
  365 |     SET_STRING_ELT(ans, 0, mkChar(v));
      |                            ^~~~~~
      |                            char
Rtreemix.cc: In function 'SEXPREC* R_fit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:475:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  475 |   PROTECT(result = allocVector(VECSXP, 4));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:481:33: error: 'mkChar' was not declared in this scope; did you mean 'char'?
  481 |   SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
      |                                 ^~~~~~
      |                                 char
Rtreemix.cc:491:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
  491 |   setAttrib(result, R_NamesSymbol, list_names);
      |   ^~~~~~~~~
      |   Rf_setAttrib
Rtreemix.cc:509:31: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'?
  509 |     SET_VECTOR_ELT(result, 2, allocMatrix(REALSXP, 0, 0));
      |                               ^~~~~~~~~~~
      |                               Rf_allocMatrix
In file included from include/replaceleda.hh:7,
                 from include/max_weight_branch.h:25,
                 from include/mtree.h:14,
                 from include/mtreemix.h:14,
                 from Rtreemix.cc:3:
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:596:7: note: in expansion of macro 'forall_nodes'
  596 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:596:7: note: in expansion of macro 'forall_nodes'
  596 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function 'SEXPREC* R_fit1(SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:828:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
  828 |   PROTECT(result = allocVector(VECSXP, 3));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:834:33: error: 'mkChar' was not declared in this scope; did you mean 'char'?
  834 |   SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight of the tree
      |                                 ^~~~~~
      |                                 char
Rtreemix.cc:842:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
  842 |   setAttrib(result, R_NamesSymbol, list_names);
      |   ^~~~~~~~~
      |   Rf_setAttrib
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:938:7: note: in expansion of macro 'forall_nodes'
  938 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:938:7: note: in expansion of macro 'forall_nodes'
  938 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function 'SEXPREC* R_fit0(SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:1170:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 1170 |   PROTECT(result = allocVector(VECSXP, 3));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:1176:33: error: 'mkChar' was not declared in this scope; did you mean 'char'?
 1176 |   SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight of the star tree
      |                                 ^~~~~~
      |                                 char
Rtreemix.cc:1184:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
 1184 |   setAttrib(result, R_NamesSymbol, list_names);
      |   ^~~~~~~~~
      |   Rf_setAttrib
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1281:7: note: in expansion of macro 'forall_nodes'
 1281 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1281:7: note: in expansion of macro 'forall_nodes'
 1281 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function 'SEXPREC* R_bootstrap(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:1559:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 1559 |   PROTECT(result = allocVector(VECSXP, 5));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:1565:33: error: 'mkChar' was not declared in this scope; did you mean 'char'?
 1565 |   SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
      |                                 ^~~~~~
      |                                 char
Rtreemix.cc:1577:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
 1577 |   setAttrib(result, R_NamesSymbol, list_names);
      |   ^~~~~~~~~
      |   Rf_setAttrib
Rtreemix.cc:1595:31: error: 'allocMatrix' was not declared in this scope; did you mean 'Rf_allocMatrix'?
 1595 |     SET_VECTOR_ELT(result, 2, allocMatrix(REALSXP, 0, 0));
      |                               ^~~~~~~~~~~
      |                               Rf_allocMatrix
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1728:7: note: in expansion of macro 'forall_nodes'
 1728 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:1728:7: note: in expansion of macro 'forall_nodes'
 1728 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function 'int get_index(SEXP, const char*)':
Rtreemix.cc:1910:23: error: 'length' was not declared in this scope
 1910 |   for (int i = 0; i < length(listNames); i++) {
      |                       ^~~~~~
Rtreemix.cc: In function 'void R_get_graph(SEXP, SEXP, replaceleda::vector&, replaceleda::array<replaceleda::graph>&, replaceleda::array<replaceleda::map<replaceleda::RefCountPtr<replaceleda::Node>, std::__cxx11::basic_string<char> > >&, replaceleda::array<replaceleda::map<replaceleda::RefCountPtr<replaceleda::Edge>, double> >&, replaceleda::array<replaceleda::map<int, replaceleda::RefCountPtr<replaceleda::Node> > >&)':
Rtreemix.cc:1942:21: error: 'coerceVector' was not declared in this scope; did you mean 'Rf_coerceVector'?
 1942 |   PROTECT(R_alpha = coerceVector(R_alpha, REALSXP));
      |                     ^~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:1950:12: error: 'length' was not declared in this scope
 1950 |   G.resize(length(listG));
      |            ^~~~~~
In file included from Rtreemix.cc:27:
Rtreemix.cc:2006:30: error: 'getAttrib' was not declared in this scope; did you mean 'Rf_getAttrib'?
 2006 |         names = AS_CHARACTER(getAttrib(ew, R_NamesSymbol));
      |                              ^~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:66:49: note: in definition of macro 'AS_CHARACTER'
   66 | #define AS_CHARACTER(x)         Rf_coerceVector(x,STRSXP)
      |                                                 ^
Rtreemix.cc: In function 'SEXPREC* R_draw(SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2068:16: error: 'length' was not declared in this scope
 2068 |   vector alpha(length(R_trees));      // mixture parameter
      |                ^~~~~~
Rtreemix.cc: In function 'SEXPREC* R_simulate(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2132:16: error: 'length' was not declared in this scope
 2132 |   vector alpha(length(R_trees));      // mixture parameter
      |                ^~~~~~
Rtreemix.cc:2176:23: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 2176 |   PROTECT(listNames = allocVector(STRSXP, 3));
      |                       ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:2178:32: error: 'mkChar' was not declared in this scope; did you mean 'char'?
 2178 |   SET_STRING_ELT(listNames, 0, mkChar("patterns"));
      |                                ^~~~~~
      |                                char
Rtreemix.cc:2188:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
 2188 |   setAttrib(result, R_NamesSymbol, listNames);
      |   ^~~~~~~~~
      |   Rf_setAttrib
Rtreemix.cc: In function 'SEXPREC* R_time(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2246:16: error: 'length' was not declared in this scope
 2246 |   vector alpha(length(R_trees));      // mixture parameter
      |                ^~~~~~
Rtreemix.cc:2284:21: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 2284 |   PROTECT(R_wtime = allocVector(VECSXP, length(R_trees)));
      |                     ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_likelihood(SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2370:16: error: 'length' was not declared in this scope
 2370 |   vector alpha(length(R_trees));      // mixture parameter
      |                ^~~~~~
Rtreemix.cc:2424:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 2424 |   PROTECT(result = allocVector(VECSXP, 2));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc: In function 'SEXPREC* R_random(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2524:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 2524 |   PROTECT(result = allocVector(VECSXP, 2));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
Rtreemix.cc:2530:33: error: 'mkChar' was not declared in this scope; did you mean 'char'?
 2530 |   SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
      |                                 ^~~~~~
      |                                 char
Rtreemix.cc:2536:3: error: 'setAttrib' was not declared in this scope; did you mean 'Rf_setAttrib'?
 2536 |   setAttrib(result, R_NamesSymbol, list_names);
      |   ^~~~~~~~~
      |   Rf_setAttrib
include/Graph.hh:16:55: warning: value computed is not used [-Wunused-value]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:2629:7: note: in expansion of macro 'forall_nodes'
 2629 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
include/Graph.hh:16:77: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   16 | #define forall_nodes(n,G) for(uint icount = 0; icount < G.number_of_nodes() ,  n = G.getNode(icount);++icount)
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Rtreemix.cc:2629:7: note: in expansion of macro 'forall_nodes'
 2629 |       forall_nodes (n, G[k]) {
      |       ^~~~~~~~~~~~
Rtreemix.cc: In function 'SEXPREC* R_distr(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Rtreemix.cc:2801:36: error: 'length' was not declared in this scope
 2801 |   vector                     alpha(length(R_trees));      // mixture parameter
      |                                    ^~~~~~
Rtreemix.cc:2837:20: error: 'allocVector' was not declared in this scope; did you mean 'Rf_allocVector'?
 2837 |   PROTECT(R_prob = allocVector(REALSXP, prob.dim()));
      |                    ^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro 'PROTECT'
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:294: Rtreemix.o] Error 1
ERROR: compilation failed for package 'Rtreemix'
* removing 'E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpIL8KHt/Rinst12318b6e3c/Rtreemix'
      -----------------------------------
ERROR: package installation failed