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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rtreemix
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Rtreemix’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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));
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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));
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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()));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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()));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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()));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:365:28: error: ‘mkChar’ was not declared in this scope
365 | SET_STRING_ELT(ans, 0, mkChar(v));
| ^~~~~~
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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:481:33: error: ‘mkChar’ was not declared in this scope
481 | SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
| ^~~~~~
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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:834:33: error: ‘mkChar’ was not declared in this scope
834 | SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight of the tree
| ^~~~~~
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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:1176:33: error: ‘mkChar’ was not declared in this scope
1176 | SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight of the star tree
| ^~~~~~
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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:1565:33: error: ‘mkChar’ was not declared in this scope
1565 | SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
| ^~~~~~
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));
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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));
| ^~~~~~~~~
/home/biocbuild/bbs-3.20-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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:2178:32: error: ‘mkChar’ was not declared in this scope
2178 | SET_STRING_ELT(listNames, 0, mkChar("patterns"));
| ^~~~~~
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)));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #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));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
Rtreemix.cc:2530:33: error: ‘mkChar’ was not declared in this scope
2530 | SET_STRING_ELT(list_names, 0, mkChar("alpha")); // the weight vector of the model
| ^~~~~~
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()));
| ^~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
371 | #define PROTECT(s) Rf_protect(s)
| ^
make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:200: Rtreemix.o] Error 1
ERROR: compilation failed for package ‘Rtreemix’
* removing ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rtreemix’
* restoring previous ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rtreemix’
