* installing *source* package ‘castor’ ...
** this is package ‘castor’ version ‘1.8.5’
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c STMathExpression.cpp -o STMathExpression.o
STMathExpression.cpp:10: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   10 | #pragma mark -
STMathExpression.cpp:11: warning: ignoring ‘#pragma mark String’ [-Wunknown-pragmas]
   11 | #pragma mark String manipulations
STMathExpression.cpp:12: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   12 | #pragma mark
STMathExpression.cpp:65: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   65 | #pragma mark -
STMathExpression.cpp:66: warning: ignoring ‘#pragma mark MathExpression’ [-Wunknown-pragmas]
   66 | #pragma mark MathExpression
STMathExpression.cpp:67: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
   67 | #pragma mark
STMathExpression.cpp: In static member function ‘static long int MathExpression::splitBinaryOperatorInverseOrder(const std::string&, long int, long int, const std::vector<long int>&)’:
STMathExpression.cpp:256:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  256 |                                 else if(j==string::npos){ if(!STMath_isReal(expression.substr(0,i-1))) return getLeftMostOfPlusMinusOperatorChain(expression,start,i); }
      |                                         ~^~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘std::string MathExpression::parseBlock(const std::string&, long int, long int, const std::vector<long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, long int, bool)’:
STMathExpression.cpp:313:105: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  313 |         if(isWhiteSpace(expression,start,end)) return "Missing "+(start==0 ? "leading expression" : (end==expression.size()-1 ? "trailing expression" : "expression between '"+expression.substr(0,start)+"' and '"+expression.substr(end+1)+"'"));
      |                                                                                                      ~~~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:359:37: warning: comparison of integer expressions of different signedness: ‘const long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  359 |                 if((rightMostBracket==string::npos) || (rightMostBracket<start)){
      |                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:463:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  463 |         for(long i=0; i<expression.length(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findRoundBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:500:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  500 |         for(long i=0; i<expression.length(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘void MathExpression::printDebug(std::ostream&) const’:
STMathExpression.cpp:953:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  953 |         for(long i=0; i<variableValues.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:957:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  957 |         for(long i=0; i<stackValues.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&) const’:
STMathExpression.cpp:981:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  981 |                 if(variableIDs[i]>=x.size()){ variableValues[i]=0; }
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&, long int, ...) const’:
STMathExpression.cpp:1044:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘long unsigned int’ [-Wsign-compare]
 1044 |                 if(variableIDs[i]>=x.size()+numberOfAdditionalVariables){ variableValues[i]=0; }
STMathExpression.cpp:1045:39: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1045 |                 else if(variableIDs[i]<x.size()){ variableValues[i]=x[variableIDs[i]]; }
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariable(const std::string&) const’:
STMathExpression.cpp:1195:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1195 |         for(long i=0; i<variableNames.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariableWithPrefix(const std::string&) const’:
STMathExpression.cpp:1202:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1202 |         for(long i=0; i<variableNames.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::isValidName(const std::string&, std::string&)’:
STMathExpression.cpp:1258:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1258 |         for(long i=0; i<s.size(); ++i){
      |                       ~^~~~~~~~~
STMathExpression.cpp: In static member function ‘static std::string MathExpression::lowercase(std::string)’:
STMathExpression.cpp:1269:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1269 |         for(long n=0; n<s.length(); ++n){ s[n] = tolower(s[n]); }
      |                       ~^~~~~~~~~~~
STMathExpression.cpp: In function ‘Rcpp::List evaluate_univariate_expression_CPP(const std::string&, const std::string&, const std::vector<double>&)’:
STMathExpression.cpp:1378:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1378 |         for(long i=0; i<X.size(); ++i){
      |                       ~^~~~~~~~~
STMathExpression.cpp: In instantiation of ‘void MathExpression::printTuple(std::ostream&, const std::vector<T>&) const [with TYPE = long int; std::ostream = std::basic_ostream<char>]’:
STMathExpression.cpp:961:14:   required from here
  961 |                         printTuple(stream, stackArguments[i]);
      |                         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:1227:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1227 |         for(long i=0; i<components.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c phylogenetics_cpp_routines.cpp -o phylogenetics_cpp_routines.o
phylogenetics_cpp_routines.cpp:154: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  154 | #pragma mark -
phylogenetics_cpp_routines.cpp:155: warning: ignoring ‘#pragma mark Declarations’ [-Wunknown-pragmas]
  155 | #pragma mark Declarations
phylogenetics_cpp_routines.cpp:156: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  156 | #pragma mark
phylogenetics_cpp_routines.cpp:168: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  168 | #pragma mark -
phylogenetics_cpp_routines.cpp:169: warning: ignoring ‘#pragma mark Functions’ [-Wunknown-pragmas]
  169 | #pragma mark Functions for debugging
phylogenetics_cpp_routines.cpp:170: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  170 | #pragma mark
phylogenetics_cpp_routines.cpp:243: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  243 | #pragma mark -
phylogenetics_cpp_routines.cpp:244: warning: ignoring ‘#pragma mark Auxiliary’ [-Wunknown-pragmas]
  244 | #pragma mark Auxiliary functions
phylogenetics_cpp_routines.cpp:245: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
  245 | #pragma mark
phylogenetics_cpp_routines.cpp:1445: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1445 | #pragma mark -
phylogenetics_cpp_routines.cpp:1446: warning: ignoring ‘#pragma mark Graphs’ [-Wunknown-pragmas]
 1446 | #pragma mark Graphs
phylogenetics_cpp_routines.cpp:1447: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1447 | #pragma mark
phylogenetics_cpp_routines.cpp:1592: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1592 | #pragma mark -
phylogenetics_cpp_routines.cpp:1593: warning: ignoring ‘#pragma mark Polynomials’ [-Wunknown-pragmas]
 1593 | #pragma mark Polynomials
phylogenetics_cpp_routines.cpp:1594: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 1594 | #pragma mark
phylogenetics_cpp_routines.cpp:2931: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 2931 | #pragma mark -
phylogenetics_cpp_routines.cpp:2932: warning: ignoring ‘#pragma mark Integration’ [-Wunknown-pragmas]
 2932 | #pragma mark Integration, antiderivatives, derivatives
phylogenetics_cpp_routines.cpp:2933: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 2933 | #pragma mark
phylogenetics_cpp_routines.cpp:3436: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3436 | #pragma mark -
phylogenetics_cpp_routines.cpp:3437: warning: ignoring ‘#pragma mark Vectorized’ [-Wunknown-pragmas]
 3437 | #pragma mark Vectorized basic arithmetics
phylogenetics_cpp_routines.cpp:3438: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3438 | #pragma mark
phylogenetics_cpp_routines.cpp:3587: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3587 | #pragma mark -
phylogenetics_cpp_routines.cpp:3588: warning: ignoring ‘#pragma mark Random’ [-Wunknown-pragmas]
 3588 | #pragma mark Random numbers
phylogenetics_cpp_routines.cpp:3589: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3589 | #pragma mark
phylogenetics_cpp_routines.cpp:3983: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3983 | #pragma mark -
phylogenetics_cpp_routines.cpp:3984: warning: ignoring ‘#pragma mark Matrix’ [-Wunknown-pragmas]
 3984 | #pragma mark Matrix algebra
phylogenetics_cpp_routines.cpp:3985: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 3985 | #pragma mark
phylogenetics_cpp_routines.cpp:7193: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 7193 | #pragma mark -
phylogenetics_cpp_routines.cpp:7194: warning: ignoring ‘#pragma mark Numerical’ [-Wunknown-pragmas]
 7194 | #pragma mark Numerical solvers
phylogenetics_cpp_routines.cpp:7195: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 7195 | #pragma mark
phylogenetics_cpp_routines.cpp:8606: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 8606 | #pragma mark -
phylogenetics_cpp_routines.cpp:8607: warning: ignoring ‘#pragma mark Time’ [-Wunknown-pragmas]
 8607 | #pragma mark Time series analysis
phylogenetics_cpp_routines.cpp:8608: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
 8608 | #pragma mark
phylogenetics_cpp_routines.cpp:10013: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10013 | #pragma mark -
phylogenetics_cpp_routines.cpp:10014: warning: ignoring ‘#pragma mark Class’ [-Wunknown-pragmas]
10014 | #pragma mark Class: LinearInterpolationFunctor
phylogenetics_cpp_routines.cpp:10015: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10015 | #pragma mark -
phylogenetics_cpp_routines.cpp:10493: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10493 | #pragma mark -
phylogenetics_cpp_routines.cpp:10494: warning: ignoring ‘#pragma mark Stochastic’ [-Wunknown-pragmas]
10494 | #pragma mark Stochastic processes
phylogenetics_cpp_routines.cpp:10495: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10495 | #pragma mark
phylogenetics_cpp_routines.cpp:10688: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10688 | #pragma mark -
phylogenetics_cpp_routines.cpp:10689: warning: ignoring ‘#pragma mark Deterministic’ [-Wunknown-pragmas]
10689 | #pragma mark Deterministic diversity dynamics
phylogenetics_cpp_routines.cpp:10690: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10690 | #pragma mark
phylogenetics_cpp_routines.cpp:11789: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11789 | #pragma mark -
phylogenetics_cpp_routines.cpp:11790: warning: ignoring ‘#pragma mark Building’ [-Wunknown-pragmas]
11790 | #pragma mark Building auxiliary data structures
phylogenetics_cpp_routines.cpp:11791: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11791 | #pragma mark
phylogenetics_cpp_routines.cpp:12477: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12477 | #pragma mark -
phylogenetics_cpp_routines.cpp:12478: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
12478 | #pragma mark Tree statistics
phylogenetics_cpp_routines.cpp:12479: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12479 | #pragma mark
phylogenetics_cpp_routines.cpp:14604: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14604 | #pragma mark -
phylogenetics_cpp_routines.cpp:14605: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
14605 | #pragma mark Generating & manipulating trees
phylogenetics_cpp_routines.cpp:14606: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14606 | #pragma mark
phylogenetics_cpp_routines.cpp:17978: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
17978 | #pragma mark -
phylogenetics_cpp_routines.cpp:17979: warning: ignoring ‘#pragma mark Comparing’ [-Wunknown-pragmas]
17979 | #pragma mark Comparing trees
phylogenetics_cpp_routines.cpp:17980: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
17980 | #pragma mark
phylogenetics_cpp_routines.cpp:18398: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18398 | #pragma mark -
phylogenetics_cpp_routines.cpp:18399: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
18399 | #pragma mark Tree dating
phylogenetics_cpp_routines.cpp:18400: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18400 | #pragma mark
phylogenetics_cpp_routines.cpp:18499: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18499 | #pragma mark -
phylogenetics_cpp_routines.cpp:18500: warning: ignoring ‘#pragma mark Plotting’ [-Wunknown-pragmas]
18500 | #pragma mark Plotting trees
phylogenetics_cpp_routines.cpp:18501: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18501 | #pragma mark
phylogenetics_cpp_routines.cpp:18722: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18722 | #pragma mark -
phylogenetics_cpp_routines.cpp:18723: warning: ignoring ‘#pragma mark Writing’ [-Wunknown-pragmas]
18723 | #pragma mark Writing/reading trees
phylogenetics_cpp_routines.cpp:18724: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18724 | #pragma mark
phylogenetics_cpp_routines.cpp:19213: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19213 | #pragma mark -
phylogenetics_cpp_routines.cpp:19214: warning: ignoring ‘#pragma mark Statistics’ [-Wunknown-pragmas]
19214 | #pragma mark Statistics of trait distribution
phylogenetics_cpp_routines.cpp:19215: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19215 | #pragma mark
phylogenetics_cpp_routines.cpp:20591: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20591 | #pragma mark -
phylogenetics_cpp_routines.cpp:20592: warning: ignoring ‘#pragma mark Most’ [-Wunknown-pragmas]
20592 | #pragma mark Most recent common ancestors
phylogenetics_cpp_routines.cpp:20593: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20593 | #pragma mark
phylogenetics_cpp_routines.cpp:21030: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
21030 | #pragma mark -
phylogenetics_cpp_routines.cpp:21031: warning: ignoring ‘#pragma mark Ancestral’ [-Wunknown-pragmas]
21031 | #pragma mark Ancestral state reconstruction
phylogenetics_cpp_routines.cpp:21032: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
21032 | #pragma mark
phylogenetics_cpp_routines.cpp:22810: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22810 | #pragma mark -
phylogenetics_cpp_routines.cpp:22811: warning: ignoring ‘#pragma mark MuSSE’ [-Wunknown-pragmas]
22811 | #pragma mark MuSSE model fitting
phylogenetics_cpp_routines.cpp:22812: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22812 | #pragma mark
phylogenetics_cpp_routines.cpp:24076: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
24076 | #pragma mark -
phylogenetics_cpp_routines.cpp:24077: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
24077 | #pragma mark Homogenous Birth-Death models
phylogenetics_cpp_routines.cpp:24078: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
24078 | #pragma mark
phylogenetics_cpp_routines.cpp:25534: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25534 | #pragma mark -
phylogenetics_cpp_routines.cpp:25535: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
25535 | #pragma mark Homogenous Birth-Death-Sampling model
phylogenetics_cpp_routines.cpp:25536: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25536 | #pragma mark
phylogenetics_cpp_routines.cpp:26645: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26645 | #pragma mark -
phylogenetics_cpp_routines.cpp:26646: warning: ignoring ‘#pragma mark Simulate’ [-Wunknown-pragmas]
26646 | #pragma mark Simulate models of trait evolution
phylogenetics_cpp_routines.cpp:26647: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26647 | #pragma mark
phylogenetics_cpp_routines.cpp:27159: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27159 | #pragma mark -
phylogenetics_cpp_routines.cpp:27160: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
27160 | #pragma mark Generating random trees via cladogenic models
phylogenetics_cpp_routines.cpp:27161: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27161 | #pragma mark
phylogenetics_cpp_routines.cpp:29820: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29820 | #pragma mark -
phylogenetics_cpp_routines.cpp:29821: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
29821 | #pragma mark Generating gene trees
phylogenetics_cpp_routines.cpp:29822: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29822 | #pragma mark
phylogenetics_cpp_routines.cpp:31066: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
31066 | #pragma mark -
phylogenetics_cpp_routines.cpp:31067: warning: ignoring ‘#pragma mark Spherical’ [-Wunknown-pragmas]
31067 | #pragma mark Spherical Brownian motion
phylogenetics_cpp_routines.cpp:31068: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
31068 | #pragma mark
phylogenetics_cpp_routines.cpp:32600: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32600 | #pragma mark -
phylogenetics_cpp_routines.cpp:32601: warning: ignoring ‘#pragma mark Loading’ [-Wunknown-pragmas]
32601 | #pragma mark Loading files
phylogenetics_cpp_routines.cpp:32602: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32602 | #pragma mark
phylogenetics_cpp_routines.cpp:32790: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32790 | #pragma mark -
phylogenetics_cpp_routines.cpp:32791: warning: ignoring ‘#pragma mark Working’ [-Wunknown-pragmas]
32791 | #pragma mark Working with raw sequences
phylogenetics_cpp_routines.cpp:32792: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32792 | #pragma mark
phylogenetics_cpp_routines.cpp: In function ‘void string_to_ascii(const std::string&, lvector&)’:
phylogenetics_cpp_routines.cpp:252:20: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |     for(long i=0; i<input.length(); ++i){
      |                   ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int count_occurrences(const std::string&, char, bool)’:
phylogenetics_cpp_routines.cpp:344:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |         for(long i=0; i<haystack.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void split_string(const std::string&, const std::string&, long int, std::vector<std::__cxx11::basic_string<char> >&)’:
phylogenetics_cpp_routines.cpp:367:46: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
  367 |         while((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                                  ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:369:23: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  369 |                 if(pos==string::npos) break;
      |                    ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:373:43: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
  373 |         if((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                               ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int find_first_non_nan(const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:470:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  470 |         for(long n=start; n<haystack.size(); ++n){
      |                           ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int vector_sum(const std::vector<char>&)’:
phylogenetics_cpp_routines.cpp:717:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  717 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double smallest_nonzero_step(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:732:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  732 |         for(long i=0; i<times.size(); ++i){
      |                       ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_mean(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:750:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  750 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_abs_mean(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:757:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  757 |         for(long i=0; i<values.size(); ++i) S += abs(values[i]);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double vector_max_abs(const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:786:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  786 |         for(long i=0; i<values.size(); ++i) A = max(A, abs(values[i]));
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void make_vector_positive(std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:817:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  817 |         for(long i=0; i<values.size(); ++i) values[i] = max(0.0, values[i]);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void replace_negatives(std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:822:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  822 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void replace_non_positives(std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:829:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  829 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void cap_values(double, double, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:839:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  839 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int vector_count_zeros(const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:892:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  892 |         for(long i=0; i<values.size(); ++i) S += (values[i]==0 ? 1 : 0);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘int taxon_descends(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&)’:
phylogenetics_cpp_routines.cpp:912:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
  912 |         for(long level=0; level<min(parent_taxonomy.size(),     child_taxonomy.size()); ++level){
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void remove_item_from_mapped_list(lvector&, lvector&, long int)’:
phylogenetics_cpp_routines.cpp:958:33: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘long int’} and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  958 |         if(pool2list[pool_index]==list2pool.size()-1){
phylogenetics_cpp_routines.cpp: In function ‘long int get_nearest_index(const std::vector<long int>&, long int)’:
phylogenetics_cpp_routines.cpp:986:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  986 |         for(long i=0; i<(haystack.size()-1); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List dense_binary_matrix_row2column_major_CPP(long int, long int, const Rcpp::List&, bool)’:
phylogenetics_cpp_routines.cpp:1007:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1007 |                 for(long i=0; i<dense_row.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void filtered_indices_to_bool(long int, const lvector&, const lvector&, bvector&)’:
phylogenetics_cpp_routines.cpp:1432:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1432 |                 for(long i=0; i<only_indices.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:1437:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1437 |                 for(long i=0; i<omit_indices.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double sum_piecewise_polynomials(const std::vector<std::vector<double> >&, const lvector&, const dvector&, double, long int)’:
phylogenetics_cpp_routines.cpp:1628:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1628 |         for(long i=0; i<Ydegrees.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector evaluate_spline_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::string&, long int)’:
phylogenetics_cpp_routines.cpp:2849:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2849 |         for(long t=0, g=-1; t<Xtarget.size(); ++t){
      |                             ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_antiderivative_CPP(const std::vector<double>&, double, const std::vector<double>&, long int, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:3289:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3289 |         for(long t=0, g=0; t<Xtarget.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_derivative_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:3316:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3316 |         for(long t=0, g=0, p; t<Xtarget.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void QR_linear_least_squares(double*, long int, long int, long int, long int, const double*, long int*, double*, double*, double*)’:
phylogenetics_cpp_routines.cpp:4513:17: warning: variable ‘info’ set but not used [-Wunused-but-set-variable]
 4513 |         long i, info, j, k;
      |                 ^~~~
phylogenetics_cpp_routines.cpp: In member function ‘void matrix_exponentiator::initialize(long int, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, double)’:
phylogenetics_cpp_routines.cpp:5864:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5864 |                         for(long r=0; r<eigenvalues.size(); ++r) eigenvalues[r] *= rescaling;
      |                                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void apply_approximate_RosenbrockEuler_exponential(long int, long int, const std::vector<double>&, const double&, const std::vector<double>&, const long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:5944:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5944 |         for(k=0; k<Y.size(); ++k) Y[k] = scaling*X[k];
      |                  ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double dot_product(const dvector&, const dvector&)’:
phylogenetics_cpp_routines.cpp:5976:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 5976 |         for(long i=0; i<X.size(); ++i) S += X[i]*Y[i];
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void refine_piecewise_polynomial(long int, long int, const double*, const double*, bool, const dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:8889:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 8889 |         for(long ng=0, og=0; ng<newTimes.size(); ++ng){
      |                              ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void refine_piecewise_polynomial(long int, const dvector&, const dvector&, bool, const dvector&, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:8926:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 8926 |         for(long ng=0, og=0; ng<newTimes.size(); ++ng){
      |                              ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List monotonize_series_via_interpolation_CPP(const std::vector<double>&, std::vector<double>, bool, bool)’:
phylogenetics_cpp_routines.cpp:9970:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 9970 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9996:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 9996 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()’:
phylogenetics_cpp_routines.cpp:10958:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
10958 |                 for(long t=0; t<times.size(); ++t){
      |                               ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_cumulative_edge_lengths_per_node(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:12686:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12686 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_clade_ages(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const tree_context&, dvector&)’:
phylogenetics_cpp_routines.cpp:12808:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12808 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_closest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:12914:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12914 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12945:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12945 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_farthest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13033:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13033 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13064:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13064 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13092:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13092 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_farthest_tips_per_edge_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:13154:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13154 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13184:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13184 |         for(long q=0; q<context.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13276:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13276 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13296:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13296 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_distances_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13407:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13407 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13427:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13427 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List count_clades_at_regular_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int, double, double, bool, long int, bool)’:
phylogenetics_cpp_routines.cpp:13620:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13620 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector count_clades_at_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:13721:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13721 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_speciation_extinction_events_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:13878:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13878 |         for(long q=0; q<queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13902:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13902 |         for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13903:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13903 |         for(long c=0; c<omit_clades.size(); ++c) include_clade[omit_clades[c]] = false;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void get_relative_evolutionary_divergences(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:14048:45: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14048 |         for(long q=1, clade, pnode, cnode; q<context.queue.size(); ++q){
      |                                            ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double get_gamma_statistic_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:14304:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14304 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector extract_tip_neighborhood_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int)’:
phylogenetics_cpp_routines.cpp:14469:16: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14469 |         while(k<clade_queue.size()){
      |               ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector extract_deep_frame_CPP(long int, long int, long int, const std::vector<long int>&, long int)’:
phylogenetics_cpp_routines.cpp:14526:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14526 |         while(queue_pointer<clades.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14543:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14543 |         for(long c=0, clade; c<clades.size(); ++c){
      |                              ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector get_all_distances_to_tip_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int)’:
phylogenetics_cpp_routines.cpp:14588:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14588 |         for(long q=0; q<context.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_subtree_with_specific_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:15147:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15147 |         for(long c=0; c<clades_to_keep.size(); ++c){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15164:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15164 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘long int find_root_for_monophyletic_clade_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:15988:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15988 |         for(long t=0; t<target_tips.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16011:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16011 |         for(long q=1, cnode, pnode; q<traversal_queue_root2tips.size(); ++q){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:16118:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16118 |         for(long t=0, tip; t<target_tips.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16132:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16132 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16167:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16167 |                 for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List trim_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double)’:
phylogenetics_cpp_routines.cpp:16434:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16434 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List split_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double)’:
phylogenetics_cpp_routines.cpp:16544:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16544 |                 for(long q=0; q<context.queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List merge_nodes_to_multifurcations_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool)’:
phylogenetics_cpp_routines.cpp:16884:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16884 |                 for(long n=0, node; n<nodes_to_merge.size(); ++n){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16894:49: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16894 |                 for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
      |                                                ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16958:89: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16958 |         for(long q=0, clade, node, absorbing_ancestor, parent, child, e, edge, inedge; q<context.queue.size(); ++q){
      |                                                                                        ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List shift_clade_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:17055:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17055 |         for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17078:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17078 |                 for(long q=1, clade, node, inedge, e; q<context.queue.size(); ++q){
      |                                                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17112:47: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17112 |                 for(long q=1, clade, inedge; q<context.queue.size(); ++q){
      |                                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void assign_clades_to_taxa(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:17448:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17448 |         for(long q=0, clade; q<traversal_queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List place_tips_taxonomically_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, bool)’:
phylogenetics_cpp_routines.cpp:17907:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17907 |                 for(long f=0; f<fits.size(); ++f){
      |                               ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17908:66: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
17908 |                         if(clade_taxonomies_split[fits[f]].size()==max_precision) precise_fits.push_back(fits[f]);
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List tree_from_placements_CPP(long int, long int, long int, std::vector<long int>, std::vector<double>, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:17944:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17944 |         for(long i=0; i<tree_edge.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List congruify_trees_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18142:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18142 |         for(long m=0, Tnode, Rnode; m<mapped_Tnodes.size(); ++m){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_Robinson_Foulds_distance_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18372:60: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18372 |                                 for(long fb=0, fa=-1, f; fb<membershipsB[nodeB].size(); ++fb){
      |                                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> relative_to_absolute_node_ages_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:18428:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18428 |         for(long q=1, clade, node, pnode; q<traversal_queue.size(); ++q){
      |                                           ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> propagate_min_ages_upstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18452:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18452 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘std::vector<double> propagate_max_ages_downstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:18481:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18481 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18486:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18486 |         for(long q=0, clade, node, pnode; q<traversal_queue.size(); ++q){
      |                                           ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_phylogram_geometry_CPP(long int, long int, long int, std::vector<long int>, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:18548:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18548 |         for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18565:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18565 |         for(long q=0, clade, node; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_radial_tree_geometry_CPP(long int, long int, long int, std::vector<long int>, const std::vector<double>&, double, bool, double)’:
phylogenetics_cpp_routines.cpp:18631:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18631 |         for(long q=0, clade, node, edge, child; q<context.queue.size(); ++q){
      |                                                 ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18673:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18673 |         for(long q=1, clade, parent; q<context.queue.size(); ++q){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_get_trait_depth_consenTRAIT(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, bool, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, double&, double&, double&, double&, long int&, std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:19288:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19288 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_get_discrete_trait_depths(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, std::vector<long int>&, double&, double&, double&, double&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:19601:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19601 |         for(long q=0, dominant_state; q<traversal_queue.size(); ++q){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_mrca_defining_tips_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:20650:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20650 |         for(long q=0, parent; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector get_pairwise_ancestries_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:20721:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20721 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20727:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20727 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::IntegerVector get_most_recent_common_ancestors_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:20855:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20855 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20874:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20874 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool is_monophyletic_tip_set_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)’:
phylogenetics_cpp_routines.cpp:21010:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21010 |         for(long t=0; t<focal_tips.size(); ++t) tip_is_focal[focal_tips[t]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List WMPR_ASR_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, double, bool, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:21240:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21240 |         for(long q=0; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_with_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const std::vector<double>&, const std::string&, const std::vector<double>&, bool, bool, double, double, long int, bool)’:
phylogenetics_cpp_routines.cpp:21602:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21602 |                 for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21643:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21643 |         for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
      |                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List apply_fixed_rate_Markov_model_to_missing_clades_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, long int, Rcpp::LogicalVector, std::vector<double>, bool)’:
phylogenetics_cpp_routines.cpp:22053:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22053 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_attributes_to_descendants_CPP(long int, long int, long int, long int, const std::vector<long int>&, std::vector<long int>, std::vector<double>)’:
phylogenetics_cpp_routines.cpp:22111:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22111 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_via_squared_change_parsimony_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)’:
phylogenetics_cpp_routines.cpp:22285:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22285 |                 for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
      |                                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List ASR_via_independent_contrasts_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)’:
phylogenetics_cpp_routines.cpp:22546:30: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22546 |         if(node_states.size()>Nnodes) node_states.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22547:39: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22547 |         if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22548:29: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22548 |         if(node_CI95s.size()>Nnodes) node_CI95s.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_BM_parsimony_to_missing_clades_CPP(long int, long int, long int, const std::vector<long int>&, Rcpp::LogicalVector, std::vector<double>)’:
phylogenetics_cpp_routines.cpp:22589:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22589 |         for(long q=0, node, clade; q<traversal_queue.size(); ++q){
      |                                    ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::operator()(double) const’:
phylogenetics_cpp_routines.cpp:22625:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22625 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::gradient(double) const’:
phylogenetics_cpp_routines.cpp:22653:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22653 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double BinaryTraitLogLikelihood::Hessian(double) const’:
phylogenetics_cpp_routines.cpp:22682:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22682 |                 for(long i=0, tip; i<only_tips.size(); ++i){
      |                                    ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void MuSSEmodelD::registerState(double, const MuSSEstateD&)’:
phylogenetics_cpp_routines.cpp:22927:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22927 |                 for(long s=0; s<trajectory[i].size(); ++s) trajectory[i][s] = max(0.0, min(1.0, trajectory[i][s]));
      |                               ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void MuSSEmodelD::registerScaledState(double, const MuSSEstateD&, double)’:
phylogenetics_cpp_routines.cpp:22941:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22941 |                 for(long s=0; s<trajectory_shape[i].size(); ++s) trajectory_shape[i][s] = max(0.0, trajectory_shape[i][s]);
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, const MuSSEstateD&) const’:
phylogenetics_cpp_routines.cpp:23033:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23033 |                         for(long i=0; i<candidate_state.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, double, const MuSSEstateD&, double) const’:
phylogenetics_cpp_routines.cpp:23046:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23046 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23051:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23051 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double&, MuSSEstateD&, bool) const’:
phylogenetics_cpp_routines.cpp:23071:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23071 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23093:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23093 |                         for(long s=0; s<candidate_state.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double, double&, MuSSEstateD&, double&, bool) const’:
phylogenetics_cpp_routines.cpp:23116:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23116 |                 for(long s=0; s<candidateY.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23140:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23140 |                         for(long s=0; s<candidateY.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘bool MuSSEmodelE::checkShouldRefineTimeStep(double, const MuSSEstateE&, double, const MuSSEstateE&) const’:
phylogenetics_cpp_routines.cpp:23323:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23323 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double MuSSEmodelE::getRelativeChange(const MuSSEstateE&, const MuSSEstateE&) const’:
phylogenetics_cpp_routines.cpp:23336:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23336 |                 for(long s=0; s<stateA.size(); ++s){
      |                               ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘CrossedBoundary MuSSEmodelE::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateE&, double&, MuSSEstateE&, bool) const’:
phylogenetics_cpp_routines.cpp:23353:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23353 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23375:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23375 |                         for(long s=0; s<candidate_state.size(); ++s){
      |                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool get_MuSSE_flow(long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, double, double, double, double, bool, std::vector<std::__cxx11::basic_string<char> >&, std::string&, double&, long int&, MuSSEmodelE&, MuSSEmodelD&, std::vector<LinearInterpolationFunctor<std::vector<double> > >&, std::vector<LinearInterpolationFunctor<double> >&)’:
phylogenetics_cpp_routines.cpp:23624:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23624 |         for(long a=0; a<ages.size(); ++a){
      |                       ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_deterministic_HBD_model_CPP(double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, std::vector<double>, const std::vector<double>&, double, double, double, double, long int, double, bool)’:
phylogenetics_cpp_routines.cpp:24449:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
24449 |                         for(long i=0; i<lambdas.size(); ++i) coarse_mus[i] = lambdas[i] * mu_over_lambda[i];
      |                                       ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26705:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26705 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26785:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26785 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_reflected_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26867:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26867 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_scalar_Brownian_motion_model_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:26938:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26938 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_multivariate_Brownian_motion_model_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:27018:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27018 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_neutral_gene_evolution_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, bool, long int)’:
phylogenetics_cpp_routines.cpp:27110:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27110 |                 for(long q=0; q<traversal_queue.size(); ++q){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_finalize_generated_random_tree(double, bool, bool, bool, const dvector&, const dvector&, const dvector&, long int&, long int&, long int&, long int&, double&, lvector&, dvector&, lvector&, lvector&, lvector&, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:27222:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27222 |         for(long i=0; i<sampled_tips.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27225:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27225 |         for(long i=0; i<sampled_node_clades.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27231:53: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
27231 |         if(only_sampled_tips && (sampled_tips.size()<Ntips)){
      |                                  ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:27268:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27268 |                 for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
      |                                       ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27274:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27274 |                 for(long i=0; i<sampled_tips.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27277:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27277 |                 for(long i=0; i<sampled_node_clades.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_CPP(long int, long int, double, double, double, double, double, double, double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:27362:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
27362 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp:27362:133: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27362 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                                                                                                   ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_HBDS_CPP(long int, long int, long int, long int, long int, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, double, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:27575:100: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27575 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                 ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27575:167: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27575 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                                                                                     ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27575:235: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27575 |         while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
      |                                                                                                                                                                                                                        ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27759:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27759 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27766:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27766 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27773:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27773 |         for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_BM_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:28427:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28427 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_OU_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:28621:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28621 |         while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_Mk_rates_CPP(long int, long int, long int, double, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:29082:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29082 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29088:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29088 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29093:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29093 |         for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_random_tree_tdSSE_CPP(long int, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, bool, long int, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:29761:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29761 |                 for(long stip=0; stip<extant_tips[state].size(); ++stip){
      |                                  ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void aux_coalesce_genes(const std::vector<double>&, double, EdgeLengthUnit, double, double, long int, std::vector<long int>&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:30005:44: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
30005 |                 if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30007:42: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
30007 |                 if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30016:41: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30016 |         for(long orphan=0, clade; orphan<orphan_clades.size(); ++orphan){
      |                                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void add_edges_from_branching_heights(const std::vector<double>&, std::vector<long int>&, long int&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:30069:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
30069 |                 if(clade_heights.size()<=next_clade) clade_heights.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool generate_gene_tree_in_species_tree_MSC(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, long int&, long int&, long int&, long int&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, std::string&)’:
phylogenetics_cpp_routines.cpp:30119:64: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30119 |         const bool got_allele_counts    = (allele_counts.size()==NStips);
      |                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30120:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30120 |         const bool got_population_sizes = (population_sizes.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30121:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30121 |         const bool got_generation_times = (generation_times.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30122:65: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30122 |         const bool got_mutation_rates   = (mutation_rates.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30145:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30145 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30162:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30162 |                 for(allele=0; allele<gene_orphans[stip].size(); ++allele){
      |                               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30247:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30247 |                         for(long orphan=0; orphan<gene_orphans[context.root].size()-1; ++orphan){
      |                                            ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List generate_gene_tree_in_species_tree_MSC_HGT_DL_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, bool, bool, double, double, bool)’:
phylogenetics_cpp_routines.cpp:30401:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30401 |         const bool got_population_sizes                 = (population_sizes.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30402:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30402 |         const bool got_generation_times                 = (generation_times.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30403:81: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30403 |         const bool got_mutation_rates                   = (mutation_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30404:80: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30404 |         const bool got_allele_counts                    = (allele_counts.size()==NStips);
      |                                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30405:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30405 |         const bool got_HGT_rates                                = (HGT_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30406:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30406 |         const bool got_duplication_rates                = (duplication_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30407:85: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30407 |         const bool got_loss_rates                               = (loss_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30428:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30428 |         for(long q=0; q<context.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30435:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30435 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30538:66: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30538 |                                 for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
      |                                                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30564:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30564 |                 for(long l=0, locus; l<clade_current_loci[mclade].size(); ++l){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, double, dvector&, dvector&)’:
phylogenetics_cpp_routines.cpp:31376:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31376 |         for(long q=0, parent, child, e, edge; q<context.queue.size(); ++q){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_SBM_trajectory_CPP(const std::vector<double>&, double, double, double, double)’:
phylogenetics_cpp_routines.cpp:31489:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31489 |         for(long t=1; t<times.size(); ++t){
      |                       ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘double Spherical_Brownian_Motion_LL::operator()(double) const’:
phylogenetics_cpp_routines.cpp:31962:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31962 |                 for(long p=0; p<time_steps.size(); ++p){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List SBM_LLs_of_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, long int)’:
phylogenetics_cpp_routines.cpp:32004:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32004 |         for(long d=0; d<diffusivities.size(); ++d){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List SBM_LLs_of_sampled_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, long int, const std::vector<double>&, double, long int)’:
phylogenetics_cpp_routines.cpp:32042:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32042 |         for(long d=0; d<diffusivities.size(); ++d){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double SBM_planar_diffusivity_estimate(const dvector&, const dvector&, const std::vector<char>&)’:
phylogenetics_cpp_routines.cpp:32204:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32204 |         for(long p=0; p<time_steps.size(); ++p){
      |                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List read_distances_list_CPP(const std::string&, const std::string&, const std::string&, bool, long int, double, double, long int, long int, const std::string&)’:
phylogenetics_cpp_routines.cpp:32752:32: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32752 |                 if(parts.size()<=distances_column){
      |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32780:56: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32780 |                 if((max_Nedges>=0) && (distances.size()>=max_Nedges)) break;
      |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool char_in_string(char, const std::string&, bool)’:
phylogenetics_cpp_routines.cpp:32830:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32830 |                 for(long i=0; i<haystack.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32835:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32835 |                 for(long i=0; i<haystack.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List place_paired_end_reads_CPP(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, long int, long int)’:
phylogenetics_cpp_routines.cpp:32915:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32915 |         for(long s=0; s<forward_reads.size(); ++s){
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void multiply_array_with_scalar(ARRAY_TYPE&, double) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5355:29:   required from here
 5355 |                 multiply_array_with_scalar(A,factor);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:590:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  590 |         for(long i=0; i<X.size(); ++i) X[i] *= scalar;
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘double get_norm_L2_of_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5550:34:   required from here
 5550 |         epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
      |                    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4956:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 4956 |         for(long i=0; i<X.size(); ++i) S += SQR(X[i]);
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘double get_norm_L2_of_inverted_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:5550:77:   required from here
 5550 |         epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
      |                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4964:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 4964 |         for(long i=0; i<X.size(); ++i) S += SQR(1.0/X[i]);
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_sum(const std::vector<T>&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:8763:48:   required from here
 8763 |         const long NR = (end_c-start_c+1) + vector_sum(dN);
      |                                             ~~~~~~~~~~^~~~
phylogenetics_cpp_routines.cpp:702:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  702 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:8985:25:   required from here
 8985 |         if(!LUsolveLinearSystem(        &matrix[0],
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
 8986 |                                                         &scratchSpace[0],
      |                                                         ~~~~~~~~~~~~~~~~~
 8987 |                                                         3,
      |                                                         ~~
 8988 |                                                         &b[0],
      |                                                         ~~~~~~
 8989 |                                                         epsilon*3,
      |                                                         ~~~~~~~~~~
 8990 |                                                         5,
      |                                                         ~~
 8991 |                                                         &sol[0])){
      |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4806:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4806 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4807:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4807 |                 for(j=0; j<N; ++j){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4822:87: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
 4822 |                 while((errorInLinearSolution(matrix, N, b, x) > maxError) && (impCount<maxImprovements)){
      |                                                                              ~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool fitLeastSquares_affine_real_scalar(const std::vector<T>&, const std::vector<T>&, long int, long int, double, bool, bool, REAL_TYPE&, REAL_TYPE&, REAL_TYPE&, long int&) [with REAL_TYPE = double]’:
phylogenetics_cpp_routines.cpp:9355:40:   required from here
 9355 |                 if(fitLeastSquares_affine_real_scalar(X, logY, start, end, Xshift[n], false, false, A[n], rate[n], RSS, count[n])){
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9217:21: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
 9217 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |            ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9217:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
 9217 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |                               ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator*=(std::vector<T>&, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:9789:24:   required from here
 9789 |         Acoeff *= (Ngrid-1.0)/Aend;
      |                               ^~~~
phylogenetics_cpp_routines.cpp:3479:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3479 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_tree_traversal_root_to_tips(long int, long int, long int, long int, const ARRAY_TYPE&, bool, bool, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, bool, const std::string&) [with ARRAY_TYPE = std::vector<long int>; std::string = std::__cxx11::basic_string<char>]’:
phylogenetics_cpp_routines.cpp:12172:33:   required from here
12172 |         get_tree_traversal_root_to_tips(Ntips,
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
12173 |                                                                         Nnodes,
      |                                                                         ~~~~~~~
12174 |                                                                         Nedges,
      |                                                                         ~~~~~~~
12175 |                                                                         -1,
      |                                                                         ~~~
12176 |                                                                         tree_edge,
      |                                                                         ~~~~~~~~~~
12177 |                                                                         include_tips,
      |                                                                         ~~~~~~~~~~~~~
12178 |                                                                         false,
      |                                                                         ~~~~~~
12179 |                                                                         queue,
      |                                                                         ~~~~~~
12180 |                                                                         node2first_edge,
      |                                                                         ~~~~~~~~~~~~~~~~
12181 |                                                                         node2last_edge,
      |                                                                         ~~~~~~~~~~~~~~~
12182 |                                                                         edges,
      |                                                                         ~~~~~~
12183 |                                                                         false,
      |                                                                         ~~~~~~
12184 |                                                                         "");
      |                                                                         ~~~
phylogenetics_cpp_routines.cpp:12145:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12145 |         while(queue_pointer<queue.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_max(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:12818:36:   required from here
12818 |         const double root_age = vector_max(ages);
      |                                 ~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:780:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  780 |         for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void qsortIndices(const std::vector<T>&, std::vector<long int>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:13887:14:   required from here
13887 |         qsortIndices(distances_from_root, chronological_clade_order);
      |         ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:1081:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1081 |         for(long n=0; n<sortedIndices.size(); ++n) sortedIndices[n] = n;
      |                       ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_max(const std::vector<T>&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:14186:33:   required from here
14186 |         const long Nsplits = vector_max(node2child_count);
      |                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:780:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  780 |         for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void sort_tree_edges_root_to_tips(long int, long int, long int, bool, bool, const ARRAY_TYPE&, std::vector<long int>&) [with ARRAY_TYPE = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:14839:30:   required from here
14839 |         sort_tree_edges_root_to_tips(   Ntips,
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
14840 |                                                                         Nnodes,
      |                                                                         ~~~~~~~
14841 |                                                                         Nedges,
      |                                                                         ~~~~~~~
14842 |                                                                         depth_first_search,
      |                                                                         ~~~~~~~~~~~~~~~~~~~
14843 |                                                                         root_to_tips,
      |                                                                         ~~~~~~~~~~~~~
14844 |                                                                         tree_edge,
      |                                                                         ~~~~~~~~~~
14845 |                                                                         new2old_edge);
      |                                                                         ~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14811:36: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14811 |                 while(queue_pointer<scratch_queue.size()){
      |                       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_tree_with_collapsed_monofurcations(long int, long int, long int, long int, bool, const lvector&, const ARRAY_INT&, const ARRAY_DOUBLE&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:15075:40:   required from here
15075 |         get_tree_with_collapsed_monofurcations( Ntips,
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
15076 |                                                                                         Nnodes,
      |                                                                                         ~~~~~~~
15077 |                                                                                         Nedges,
      |                                                                                         ~~~~~~~
15078 |                                                                                         root,
      |                                                                                         ~~~~~
15079 |                                                                                         force_keep_root,
      |                                                                                         ~~~~~~~~~~~~~~~~
15080 |                                                                                         force_keep_nodes,
      |                                                                                         ~~~~~~~~~~~~~~~~~
15081 |                                                                                         tree_edge,
      |                                                                                         ~~~~~~~~~~
15082 |                                                                                         edge_length,
      |                                                                                         ~~~~~~~~~~~~
15083 |                                                                                         new_tree_edge,
      |                                                                                         ~~~~~~~~~~~~~~
15084 |                                                                                         new_edge_length,
      |                                                                                         ~~~~~~~~~~~~~~~~
15085 |                                                                                         new2old_node,
      |                                                                                         ~~~~~~~~~~~~~
15086 |                                                                                         new_root,
      |                                                                                         ~~~~~~~~~
15087 |                                                                                         root_shift);
      |                                                                                         ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14971:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14971 |         for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
      |                              ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14985:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14985 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15008:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15008 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_subtree_with_specific_tips(long int, long int, long int, const ARRAY_INT&, const ARRAY_DOUBLE&, const ARRAY_INT&, bool, bool, const lvector&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, long int&, long int&, long int&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]’:
phylogenetics_cpp_routines.cpp:15687:32:   required from here
15687 |         get_subtree_with_specific_tips( Ntips,
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
15688 |                                                                         Nnodes,
      |                                                                         ~~~~~~~
15689 |                                                                         Nedges,
      |                                                                         ~~~~~~~
15690 |                                                                         tree_edge,
      |                                                                         ~~~~~~~~~~
15691 |                                                                         edge_length,
      |                                                                         ~~~~~~~~~~~~
15692 |                                                                         tips_to_keep,
      |                                                                         ~~~~~~~~~~~~~
15693 |                                                                         collapse_monofurcations,
      |                                                                         ~~~~~~~~~~~~~~~~~~~~~~~~
15694 |                                                                         force_keep_root,
      |                                                                         ~~~~~~~~~~~~~~~~
15695 |                                                                         lvector(),
      |                                                                         ~~~~~~~~~~
15696 |                                                                         new_tree_edge,
      |                                                                         ~~~~~~~~~~~~~~
15697 |                                                                         new_edge_length,
      |                                                                         ~~~~~~~~~~~~~~~~
15698 |                                                                         new2old_clade,
      |                                                                         ~~~~~~~~~~~~~~
15699 |                                                                         new_root,
      |                                                                         ~~~~~~~~~
15700 |                                                                         old_stem_edge,
      |                                                                         ~~~~~~~~~~~~~~
15701 |                                                                         Ntips_kept,
      |                                                                         ~~~~~~~~~~~
15702 |                                                                         Nnodes_kept,
      |                                                                         ~~~~~~~~~~~~
15703 |                                                                         Nedges_kept,
      |                                                                         ~~~~~~~~~~~~
15704 |                                                                         root_shift);
      |                                                                         ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15545:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15545 |         for(long t=0; t<tips_to_keep.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15548:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15548 |         for(long fn=0; fn<force_keep_nodes.size(); ++fn){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15621:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15621 |         for(long fn=0, new_clade; fn<force_keep_nodes.size(); ++fn){
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void get_distances_from_root(long int, long int, long int, const ARRAY_TYPE_INT&, const ARRAY_TYPE_D&, const tree_context&, dvector&) [with ARRAY_TYPE_INT = std::vector<long int>; ARRAY_TYPE_D = std::vector<double>; dvector = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:16914:26:   required from here
16914 |                 get_distances_from_root(Ntips, Nnodes, Nedges, tree_edge, edge_length, context, clade_times);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12766:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12766 |         for(long q=0, clade; q<context.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘long int find_in_ascending_list(const std::vector<T>&, TYPE2, long int) [with TYPE1 = long int; TYPE2 = long int]’:
phylogenetics_cpp_routines.cpp:18374:33:   required from here
18374 |                                         fa = find_in_ascending_list(membershipsA[nodeA],f,fa+1);
      |                                              ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:496:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  496 |         for(long n=start; n<haystack.size(); ++n){
      |                           ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator/(std::vector<T>, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22916:19:   required from here
22916 |                 shape = initial/initial_mean;
      |                                 ^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3561:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3561 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(std::vector<T>, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22979:27:   required from here
22979 |                                 rateY = YA - currentY*rateS;
      |                                                       ^~~~~
phylogenetics_cpp_routines.cpp:3461:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3461 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator-(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:22979:27:   required from here
22979 |                                 rateY = YA - currentY*rateS;
      |                                                       ^~~~~
phylogenetics_cpp_routines.cpp:3515:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3515 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator+(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23088:66:   required from here
23088 |                         candidate_state = previous_state*(1-lambda) + candidate_state*lambda;
      |                                                                                       ^~~~~~
phylogenetics_cpp_routines.cpp:3488:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3488 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool contains_nan(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23152:22:   required from here
23152 |                 return contains_nan(state);
      |                        ~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:875:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  875 |         for(long i=0; i<values.size(); ++i){
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator*=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23512:32:   required from here
23512 |                                 posteriors[node] *= modelD.initial;
      |                                                            ^~~~~~~
phylogenetics_cpp_routines.cpp:3452:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3452 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE vector_sum(const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23533:30:   required from here
23533 |                 const double S = vector_sum(posteriors[node]);
      |                                  ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:702:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  702 |         for(long i=0; i<values.size(); ++i) S += values[i];
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator/=(std::vector<T>&, double) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23534:23:   required from here
23534 |                 posteriors[node] /= S;
      |                                     ^
phylogenetics_cpp_routines.cpp:3570:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3570 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(std::vector<T>, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:23542:56:   required from here
23542 |         loglikelihood += log(vector_sum(posteriors[root_node]*root_prior));
      |                                                               ^~~~~~~~~~
phylogenetics_cpp_routines.cpp:3443:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3443 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘TYPE scalar_product(const std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:24052:38:   required from here
24052 |                 loglikelihood += log(scalar_product(substem_D,substem_prior));
      |                                      ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:725:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
  725 |         for(long i=0; i<min(A.size(),B.size()); ++i) S += A[i] * B[i];
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator-=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:24451:83:   required from here
24451 |                 dvector coarse_diversification_rates = lambdas; coarse_diversification_rates -= mus;
      |                                                                                                 ^~~
phylogenetics_cpp_routines.cpp:3533:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3533 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> abs(std::vector<T>) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:25071:48:   required from here
25071 |         dvector coarse_abs_diversification_rates = abs(coarse_diversification_rates);
      |                                                    ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3579:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3579 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs() const [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:25563:26:   required from here
25563 |                 return lambda.getMaxAbs() + mu.getMaxAbs() + psi.getMaxAbs();
      |                        ~~~~~~~~~~~~~~~~^~
phylogenetics_cpp_routines.cpp:2675:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2675 |                 for(long i=0; i<X.size()-1; ++i){
      |                               ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs(double, double) const [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:25568:26:   required from here
25568 |                 return lambda.getMaxAbs(start_time,end_time) + mu.getMaxAbs(start_time,end_time) + psi.getMaxAbs(start_time,end_time);
      |                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:2686:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2686 |                 for(long i=0; i<X.size()-1; ++i){
      |                               ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T>& operator+=(std::vector<T>&, const TYPE&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:25991:20:   required from here
25991 |                 NCSAcrossings += 1l;
      |                                  ^~
phylogenetics_cpp_routines.cpp:3506:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3506 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator-(std::vector<T>, const TYPE&) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:27234:52:   required from here
27234 |                 lvector force_keep_nodes = sampled_node_clades - Ntips;
      |                                                                  ^~~~~
phylogenetics_cpp_routines.cpp:3524:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3524 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void remove_item_from_vector(std::vector<T>&, long int) [with TYPE = long int]’:
phylogenetics_cpp_routines.cpp:27695:27:   required from here
27695 |                         remove_item_from_vector(extant_tips, tip);
      |                         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:928:17: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  928 |         if(index==list.size()-1){
      |            ~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, const DFUNCTOR&, double, double, dvector&, dvector&) [with DFUNCTOR = PiecewisePolynomial<double>; dvector = std::vector<double>]’:
phylogenetics_cpp_routines.cpp:31522:22:   required from here
31522 |         simulate_SBM_on_tree(   Ntips,
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
31523 |                                                         Nnodes,
      |                                                         ~~~~~~~
31524 |                                                         Nedges,
      |                                                         ~~~~~~~
31525 |                                                         tree_edge,
      |                                                         ~~~~~~~~~~
31526 |                                                         edge_length,
      |                                                         ~~~~~~~~~~~~
31527 |                                                         radius,
      |                                                         ~~~~~~~
31528 |                                                         diffusivity_integral,
      |                                                         ~~~~~~~~~~~~~~~~~~~~~
31529 |                                                         root_theta,
      |                                                         ~~~~~~~~~~~
31530 |                                                         root_phi,
      |                                                         ~~~~~~~~~
31531 |                                                         clade_theta,
      |                                                         ~~~~~~~~~~~~
31532 |                                                         clade_phi);
      |                                                         ~~~~~~~~~~
phylogenetics_cpp_routines.cpp:31424:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31424 |         for(long q=0, parent, child, e, edge; q<context.queue.size(); ++q){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4813:21:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
 4813 |         if(!LUDecomposition(scratchSpace, N, pivoting_indices, Psign)){
      |             ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8985:25:   required from here
 8985 |         if(!LUsolveLinearSystem(        &matrix[0],
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
 8986 |                                                         &scratchSpace[0],
      |                                                         ~~~~~~~~~~~~~~~~~
 8987 |                                                         3,
      |                                                         ~~
 8988 |                                                         &b[0],
      |                                                         ~~~~~~
 8989 |                                                         epsilon*3,
      |                                                         ~~~~~~~~~~
 8990 |                                                         5,
      |                                                         ~~
 8991 |                                                         &sol[0])){
      |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4661:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4661 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4662:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4662 |                 for(j=0, big=0; j<N; ++j){
      |                                 ~^~
phylogenetics_cpp_routines.cpp:4671:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4671 |         for(j=0; j<N; ++j){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4678:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4678 |                 for(i=j; i<N; ++i){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4688:35: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4688 |                         for(k=0; k<N; ++k){
      |                                  ~^~
phylogenetics_cpp_routines.cpp:4700:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4700 |                 if(j < N-1){
      |                    ~~^~~~~
phylogenetics_cpp_routines.cpp:4702:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4702 |                         for(i=j+1; i<N; ++i){ matrix[i*N+j] *= dummyT; }
      |                                    ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void LUSolveLinearSystem(const TYPE*, long unsigned int, const long unsigned int*, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4818:21:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
 4818 |         LUSolveLinearSystem(scratchSpace, N, pivoting_indices, x);
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8985:25:   required from here
 8985 |         if(!LUsolveLinearSystem(        &matrix[0],
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
 8986 |                                                         &scratchSpace[0],
      |                                                         ~~~~~~~~~~~~~~~~~
 8987 |                                                         3,
      |                                                         ~~
 8988 |                                                         &b[0],
      |                                                         ~~~~~~
 8989 |                                                         epsilon*3,
      |                                                         ~~~~~~~~~~
 8990 |                                                         5,
      |                                                         ~~
 8991 |                                                         &sol[0])){
      |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4723:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4723 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4736:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4736 |                 for(j=i+1; j<N; ++j){ sum -= LUmatrix[i*N+j]*b[j]; }
      |                            ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void LUImproveSolutionToLinearSystem(const TYPE*, const TYPE*, long unsigned int, const long unsigned int*, const TYPE*, TYPE*) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4823:35:   required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
 4823 |                         LUImproveSolutionToLinearSystem(matrix, scratchSpace, N, pivoting_indices, b, x);
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8985:25:   required from here
 8985 |         if(!LUsolveLinearSystem(        &matrix[0],
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
 8986 |                                                         &scratchSpace[0],
      |                                                         ~~~~~~~~~~~~~~~~~
 8987 |                                                         3,
      |                                                         ~~
 8988 |                                                         &b[0],
      |                                                         ~~~~~~
 8989 |                                                         epsilon*3,
      |                                                         ~~~~~~~~~~
 8990 |                                                         5,
      |                                                         ~~
 8991 |                                                         &sol[0])){
      |                                                         ~~~~~~~~
phylogenetics_cpp_routines.cpp:4774:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4774 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4776:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4776 |                 for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
      |                          ~^~
phylogenetics_cpp_routines.cpp:4780:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
 4780 |         for(i=0; i<N; ++i){ x[i] -= r[i]; }
      |                  ~^~
phylogenetics_cpp_routines.cpp: In instantiation of ‘long int find_first_occurrence(const std::vector<T>&, TYPE2) [with TYPE1 = double; TYPE2 = double]’:
phylogenetics_cpp_routines.cpp:5429:27:   required from ‘long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’
 5429 |                 if(find_first_occurrence(sum_of_powers, 0.0)<0) return (p+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21544:94:   required from here
21544 |                 const long min_polynomials = min_polynomials_for_positive_exponential_of_irreducible_matrix(Nstates, transition_matrix);
      |                                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:478:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  478 |         for(long n=0; n<haystack.size(); ++n){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector<T> operator*(double, std::vector<T>) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:10223:64:   required from ‘LinearInterpolationFunctor<VALUE_TYPE>::LinearInterpolationFunctor(const std::vector<double>&, const std::vector<T>&, bool, const VALUE_TYPE&, const VALUE_TYPE&, bool, double) [with VALUE_TYPE = std::vector<double>]’
10223 |                         referenceValues[0] = referenceValues[referenceCount-1] = 0.5*(referenceValues[0] + referenceValues[referenceCount-1]);
      |                                                                                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23485:141:   required from here
23485 |         modelD.E = LinearInterpolationFunctor<MuSSEstateE>(modelE.ages,modelE.trajectory,false,modelE.trajectory[0],modelE.trajectory.back(),true,0);
      |                                                                                                                                                    ^
phylogenetics_cpp_routines.cpp:3470:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 3470 |         for(long i=0; i<x.size(); ++i){
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of ‘void linear_combination(double, const std::vector<T>&, double, const std::vector<T>&, std::vector<T>&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:7487:21:   required from ‘bool RungeKutta2(double, double, double, MODEL&, double, double, double, double, long int, double, const PROGRESS_REPORTER&, double, std::string&) [with COORDINATE = std::vector<double>; MODEL = MuSSEmodelE; PROGRESS_REPORTER = ProgressReporter; std::string = std::__cxx11::basic_string<char>]’
 7487 |                 linear_combination(1.0,currentPoint,current_dt1,k1,point2); // point2 = currentPoint + k1*current_dt1;
      |                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23587:9:   required from here
23586 |         bool success = RungeKutta2<MuSSEstateE,MuSSEmodelE,ProgressReporter>
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23587 |                                                                 (0, // start_time
      |                                                                 ^~~~~~~~~~~~~~~~~
23588 |                                                                 oldest_age, // end_time
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~
23589 |                                                                 max(0.000001*oldest_age,min(0.2*oldest_age,relative_ODE_step/maxErate)), // default integration time step
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23590 |                                                                 modelE,
      |                                                                 ~~~~~~~
23591 |                                                                 minRecordingTimeStep,
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~
23592 |                                                                 maxRecordingTimeStep,
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~
23593 |                                                                 guessNrecordings,
      |                                                                 ~~~~~~~~~~~~~~~~~
23594 |                                                                 E_value_step,   // recordingRelValueStep
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23595 |                                                                 5,                              // maxTimeStepRefinements
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23596 |                                                                 4,                              // refinement_factor
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23597 |                                                                 ProgressReporter(true),
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~
23598 |                                                                 (runtime_out_seconds>0 ? max(runtime_out_seconds*0.01, runtime_out_seconds+start_runtime-get_thread_monotonic_walltime_seconds()) : 0.0),
      |                                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23599 |                                                                 warningMessage);
      |                                                                 ~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:441:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  441 |         for(long i=0; i<X.size(); ++i) result[i] = a*X[i] + b*Y[i];
      |                       ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double first_Wasserstein_distance_CPP(const std::vector<double>&, const std::vector<double>&)’:
phylogenetics_cpp_routines.cpp:1332:25: warning: ‘t1’ may be used uninitialized [-Wmaybe-uninitialized]
 1332 |                 W += (t2-t1) * abs(CDFY-CDFX);
      |                      ~~~^~~~
phylogenetics_cpp_routines.cpp:1316:32: note: ‘t1’ was declared here
 1316 |         double CDFX=0, CDFY=0, t1, t2;
      |                                ^~
phylogenetics_cpp_routines.cpp: In function ‘double solve_polynomial_via_bisection(const double*, long int, double, double, double, double, double, double, long int)’:
phylogenetics_cpp_routines.cpp:2289:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2289 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2235:36: note: ‘c’ was declared here
 2235 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘double legendre_polynomial(long int, double)’:
phylogenetics_cpp_routines.cpp:31086:16: warning: ‘Pn’ may be used uninitialized [-Wmaybe-uninitialized]
31086 |         return Pn;
      |                ^~
phylogenetics_cpp_routines.cpp:31080:16: note: ‘Pn’ was declared here
31080 |         double Pn;
      |                ^~
phylogenetics_cpp_routines.cpp: In function ‘double solve_piecewise_polynomial_bisection(const dvector&, const dvector&, long int, bool, double, double, double, bool, double, double, long int, long int&, long int&)’:
phylogenetics_cpp_routines.cpp:2372:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2372 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2310:36: note: ‘c’ was declared here
 2310 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘double solve_piecewise_polynomial_sum_bisection(const dvector&, const std::vector<std::vector<double> >&, const lvector&, bool, const dvector&, double, double, double, bool, double, double, long int, long int&, long int&)’:
phylogenetics_cpp_routines.cpp:2469:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
 2469 |         return c; // did not converge, but the last c is the best estimate
      |                ^
phylogenetics_cpp_routines.cpp:2402:36: note: ‘c’ was declared here
 2402 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function ‘bool get_dominant_eigenvalue(long int, const dvector&, long int, double, dvector&, double&)’:
phylogenetics_cpp_routines.cpp:6060:37: warning: ‘error’ may be used uninitialized [-Wmaybe-uninitialized]
 6060 |         return (best_error<tolerance);
      |                                     ^
phylogenetics_cpp_routines.cpp:5990:21: note: ‘error’ was declared here
 5990 |         double XAX, error, best_lambda=0, best_error=INFTY_D;
      |                     ^~~~~
In file included from /usr/include/c++/15/cmath:59,
                 from phylogenetics_cpp_routines.cpp:31:
In function ‘constexpr double std::abs(double)’,
    inlined from ‘VALUE_TYPE polynomial_bound_abs(long int, const VALUE_TYPE*, double, double) [with VALUE_TYPE = double]’ at phylogenetics_cpp_routines.cpp:1767:17:
/usr/include/c++/15/bits/std_abs.h:78:30: warning: ‘Yvertex’ may be used uninitialized [-Wmaybe-uninitialized]
   78 |   { return __builtin_fabs(__x); }
      |                              ^
phylogenetics_cpp_routines.cpp: In function ‘VALUE_TYPE polynomial_bound_abs(long int, const VALUE_TYPE*, double, double) [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:1765:28: note: ‘Yvertex’ was declared here
 1765 |                 VALUE_TYPE Yvertex;
      |                            ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List HBD_PSR_loglikelihood_CPP(const std::vector<double>&, double, const std::vector<double>&, const std::vector<double>&, long int, const std::string&, double, double)’:
phylogenetics_cpp_routines.cpp:25505:51: warning: ‘W_degree’ may be used uninitialized [-Wmaybe-uninitialized]
25505 |         const double origin_W   = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
      |                                   ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25433:24: note: ‘W_degree’ was declared here
25433 |         long I_degree, W_degree, NRG;
      |                        ^~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List HBD_PDR_loglikelihood_CPP(const std::vector<double>&, double, double, const std::vector<double>&, const std::vector<double>&, long int, const std::string&, double, double, std::vector<double>, long int)’:
phylogenetics_cpp_routines.cpp:25332:102: warning: ‘Zdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25332 |                                 branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
      |                                                                                              ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25298:14: note: ‘Zdegree’ was declared here
25298 |         long Zdegree, EZdegree, Wdegree;
      |              ^~~~~~~
phylogenetics_cpp_routines.cpp:25333:102: warning: ‘Wdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25333 |                                 branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
      |                                                                                              ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25298:33: note: ‘Wdegree’ was declared here
25298 |         long Zdegree, EZdegree, Wdegree;
      |                                 ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4696:39: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized]
 4696 |                 pivoting_indices[j] = imax;
      |                                       ^~~~
phylogenetics_cpp_routines.cpp:4655:16: note: ‘imax’ was declared here
 4655 |         long i,imax,j,k;
      |                ^~~~
phylogenetics_cpp_routines.cpp: In member function ‘void TreeSpeciationExtinctionModel::get_coalescent_trajectory(double, double, std::vector<TreeStateHistory>&) const’:
phylogenetics_cpp_routines.cpp:10947:96: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
10947 |                                 coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
      |                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10924:59: note: ‘coalescent_diversity_at_resolution_age’ was declared here
10924 |                 double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_deterministic_diversity_growth_CPP(double, double, double, double, double, double, double, double, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, const std::vector<double>&, double, double, double, double, bool, bool, bool, bool, bool, bool, double)’:
phylogenetics_cpp_routines.cpp:11168:86: warning: ‘Pmissing_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11168 |                                 const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
      |                                                                                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11143:24: note: ‘Pmissing_at_resolution_age’ was declared here
11143 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11176:88: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11176 |                                 Pmissing = 1.0 - coalescent_diversity_at_resolution_age/total_diversities[t]; // effective Pmissing, based on coalescent and total diversity after collapsing and rarefaction
phylogenetics_cpp_routines.cpp:11143:87: note: ‘coalescent_diversity_at_resolution_age’ was declared here
11143 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_trait_richness_collectors_curve_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, long int, const std::string&, bool)’:
phylogenetics_cpp_routines.cpp:20221:49: warning: ‘tip’ may be used uninitialized [-Wmaybe-uninitialized]
20221 |                                 tip_included[tip] = true;
      |                                                 ^
phylogenetics_cpp_routines.cpp:20084:14: note: ‘tip’ was declared here
20084 |         long tip, clade, count_tips_remaining;
      |              ^~~
phylogenetics_cpp_routines.cpp:20181:76: warning: ‘count_tips_remaining’ may be used uninitialized [-Wmaybe-uninitialized]
20181 |                                         long tip_counter = uniformIntWithin(0,count_tips_remaining-1);
      |                                                            ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20084:26: note: ‘count_tips_remaining’ was declared here
20084 |         long tip, clade, count_tips_remaining;
      |                          ^~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:188,
                 from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27,
                 from phylogenetics_cpp_routines.cpp:39:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:471:46,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:495:40,
    inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:744:34,
    inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
    inlined from ‘static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/converter.h:80:23,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:530:13,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:523:46,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:512:34,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<double>; TArgs = {Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:24,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1146:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1128:50,
    inlined from ‘Rcpp::List read_Newick_string_CPP(std::string, bool, bool, bool, bool)’ at phylogenetics_cpp_routines.cpp:19205:39:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: ‘root_edge’ may be used uninitialized [-Wmaybe-uninitialized]
  448 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List read_Newick_string_CPP(std::string, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:19121:29: note: ‘root_edge’ was declared here
19121 |         double edge_length, root_edge;
      |                             ^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:16179:111: warning: ‘best_Ntargets_upstream’ may be used uninitialized [-Wmaybe-uninitialized]
16179 |                         else if((!descends_from_best_edge[tip]) && (Nnontargets_downstream_per_clade[tip]==1) && targets_should_be_upstream) misplaced_nontargets.push_back(tip);       // misplaced upstream non-target
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16140:30: note: ‘best_Ntargets_upstream’ was declared here
16140 |         long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
      |                              ^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16161:42: warning: ‘best_Nmisplaced_targets’ may be used uninitialized [-Wmaybe-uninitialized]
16161 |                 misplaced_targets.reserve(best_Nmisplaced_targets);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16140:80: note: ‘best_Nmisplaced_targets’ was declared here
16140 |         long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
      |                                                                                ^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16162:45: warning: ‘best_Nmisplaced_nontargets’ may be used uninitialized [-Wmaybe-uninitialized]
16162 |                 misplaced_nontargets.reserve(best_Nmisplaced_nontargets);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16140:105: note: ‘best_Nmisplaced_nontargets’ was declared here
16140 |         long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
      |                                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13336:155: warning: ‘mrca’ may be used uninitialized [-Wmaybe-uninitialized]
13336 |                         distances(i,j) = distance_from_root_per_clade[cladeA] + distance_from_root_per_clade[cladeB] - 2*distance_from_root_per_clade[mrca];
      |                                                                                                                                                           ^
phylogenetics_cpp_routines.cpp:13309:30: note: ‘mrca’ was declared here
13309 |         long cladeA, cladeB, mrca;
      |                              ^~~~
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o castor.so RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o -L/home/hornik/tmp/R/lib -lR
installing to /home/hornik/tmp/CRAN_recheck/castor.Rcheck/00LOCK-castor/00new/castor/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (castor)