* installing *source* package 'castor' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'g++.exe (GCC) 12.2.0'
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 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 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 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 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 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 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 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 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 'std::vector<double>::size_type' {aka 'long 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 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 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 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 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 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 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
STMathExpression.cpp:1227:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1227 |         for(long i=0; i<components.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phylogenetics_cpp_routines.cpp -o phylogenetics_cpp_routines.o
phylogenetics_cpp_routines.cpp:157: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  157 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:158: warning: ignoring '#pragma mark Functions' [-Wunknown-pragmas]
  158 | #pragma mark Functions for debugging
      | 
phylogenetics_cpp_routines.cpp:159: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  159 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:228: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  228 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:229: warning: ignoring '#pragma mark Auxiliary' [-Wunknown-pragmas]
  229 | #pragma mark Auxiliary functions
      | 
phylogenetics_cpp_routines.cpp:230: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  230 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:1288: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1288 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:1289: warning: ignoring '#pragma mark Graphs' [-Wunknown-pragmas]
 1289 | #pragma mark Graphs
      | 
phylogenetics_cpp_routines.cpp:1290: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1290 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:1435: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1435 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:1436: warning: ignoring '#pragma mark Polynomials' [-Wunknown-pragmas]
 1436 | #pragma mark Polynomials
      | 
phylogenetics_cpp_routines.cpp:1437: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1437 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:2774: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 2774 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:2775: warning: ignoring '#pragma mark Integration' [-Wunknown-pragmas]
 2775 | #pragma mark Integration, antiderivatives, derivatives
      | 
phylogenetics_cpp_routines.cpp:2776: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 2776 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3279: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3279 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3280: warning: ignoring '#pragma mark Vectorized' [-Wunknown-pragmas]
 3280 | #pragma mark Vectorized basic arithmetics
      | 
phylogenetics_cpp_routines.cpp:3281: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3281 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3430: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3430 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3431: warning: ignoring '#pragma mark Random' [-Wunknown-pragmas]
 3431 | #pragma mark Random numbers
      | 
phylogenetics_cpp_routines.cpp:3432: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3432 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3826: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3826 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3827: warning: ignoring '#pragma mark Matrix' [-Wunknown-pragmas]
 3827 | #pragma mark Matrix algebra
      | 
phylogenetics_cpp_routines.cpp:3828: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3828 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:7036: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 7036 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:7037: warning: ignoring '#pragma mark Numerical' [-Wunknown-pragmas]
 7037 | #pragma mark Numerical solvers
      | 
phylogenetics_cpp_routines.cpp:7038: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 7038 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:8449: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 8449 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:8450: warning: ignoring '#pragma mark Time' [-Wunknown-pragmas]
 8450 | #pragma mark Time series analysis
      | 
phylogenetics_cpp_routines.cpp:8451: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 8451 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:9856: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 9856 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:9857: warning: ignoring '#pragma mark Class' [-Wunknown-pragmas]
 9857 | #pragma mark Class: LinearInterpolationFunctor
      | 
phylogenetics_cpp_routines.cpp:9858: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 9858 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10336: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10336 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10337: warning: ignoring '#pragma mark Stochastic' [-Wunknown-pragmas]
10337 | #pragma mark Stochastic processes
      | 
phylogenetics_cpp_routines.cpp:10338: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10338 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:10531: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10531 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10532: warning: ignoring '#pragma mark Deterministic' [-Wunknown-pragmas]
10532 | #pragma mark Deterministic diversity dynamics
      | 
phylogenetics_cpp_routines.cpp:10533: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10533 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:11632: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11632 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:11633: warning: ignoring '#pragma mark Building' [-Wunknown-pragmas]
11633 | #pragma mark Building auxiliary data structures
      | 
phylogenetics_cpp_routines.cpp:11634: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11634 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:12318: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12318 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:12319: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
12319 | #pragma mark Tree statistics
      | 
phylogenetics_cpp_routines.cpp:12320: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12320 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:14504: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14504 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:14505: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
14505 | #pragma mark Generating & manipulating trees
      | 
phylogenetics_cpp_routines.cpp:14506: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14506 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:17691: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17691 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:17692: warning: ignoring '#pragma mark Comparing' [-Wunknown-pragmas]
17692 | #pragma mark Comparing trees
      | 
phylogenetics_cpp_routines.cpp:17693: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17693 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18111: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18111 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18112: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
18112 | #pragma mark Tree dating
      | 
phylogenetics_cpp_routines.cpp:18113: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18113 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18212: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18212 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18213: warning: ignoring '#pragma mark Plotting' [-Wunknown-pragmas]
18213 | #pragma mark Plotting trees
      | 
phylogenetics_cpp_routines.cpp:18214: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18214 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18309: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18309 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18310: warning: ignoring '#pragma mark Writing' [-Wunknown-pragmas]
18310 | #pragma mark Writing/reading trees
      | 
phylogenetics_cpp_routines.cpp:18311: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18311 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18800: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18800 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18801: warning: ignoring '#pragma mark Statistics' [-Wunknown-pragmas]
18801 | #pragma mark Statistics of trait distribution
      | 
phylogenetics_cpp_routines.cpp:18802: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18802 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:20178: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20178 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:20179: warning: ignoring '#pragma mark Most' [-Wunknown-pragmas]
20179 | #pragma mark Most recent common ancestors
      | 
phylogenetics_cpp_routines.cpp:20180: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20180 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:20599: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20599 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:20600: warning: ignoring '#pragma mark Ancestral' [-Wunknown-pragmas]
20600 | #pragma mark Ancestral state reconstruction
      | 
phylogenetics_cpp_routines.cpp:20601: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20601 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:22312: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22312 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:22313: warning: ignoring '#pragma mark MuSSE' [-Wunknown-pragmas]
22313 | #pragma mark MuSSE model fitting
      | 
phylogenetics_cpp_routines.cpp:22314: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22314 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:23578: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
23578 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:23579: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
23579 | #pragma mark Homogenous Birth-Death models
      | 
phylogenetics_cpp_routines.cpp:23580: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
23580 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:25036: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25036 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:25037: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
25037 | #pragma mark Homogenous Birth-Death-Sampling model
      | 
phylogenetics_cpp_routines.cpp:25038: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25038 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:26147: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26147 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:26148: warning: ignoring '#pragma mark Simulate' [-Wunknown-pragmas]
26148 | #pragma mark Simulate models of trait evolution
      | 
phylogenetics_cpp_routines.cpp:26149: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26149 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:26661: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26661 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:26662: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
26662 | #pragma mark Generating random trees via cladogenic models
      | 
phylogenetics_cpp_routines.cpp:26663: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26663 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:29327: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29327 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:29328: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
29328 | #pragma mark Generating gene trees
      | 
phylogenetics_cpp_routines.cpp:29329: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29329 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:30576: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
30576 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:30577: warning: ignoring '#pragma mark Spherical' [-Wunknown-pragmas]
30577 | #pragma mark Spherical Brownian motion
      | 
phylogenetics_cpp_routines.cpp:30578: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
30578 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:32121: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32121 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:32122: warning: ignoring '#pragma mark Loading' [-Wunknown-pragmas]
32122 | #pragma mark Loading files
      | 
phylogenetics_cpp_routines.cpp:32123: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32123 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp: In function 'long int count_occurrences(const std::string&, char, bool)':
phylogenetics_cpp_routines.cpp:320:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  320 |         for(long i=0; i<haystack.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool extract_string_parts(const std::string&, const std::string&, long int, std::vector<std::__cxx11::basic_string<char> >&)':
phylogenetics_cpp_routines.cpp:342:27: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
  342 |         while(parts.size()<max_Nparts){
      |               ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:344:23: warning: comparison of integer expressions of different signedness: 'long int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long long unsigned int'} [-Wsign-compare]
  344 |                 if(pos==string::npos) break;
      |                    ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:348:24: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
  348 |         if(parts.size()<max_Nparts){
      |            ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:351:29: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
  351 |         return (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:433:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  433 |         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:680:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  680 |         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:695:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  695 |         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:713:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  713 |         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:720:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  720 |         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:749:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  749 |         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:780:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  780 |         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:785:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  785 |         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:792:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  792 |         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:802:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  802 |         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:855:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  855 |         for(long i=0; i<values.size(); ++i) S += (values[i]==0 ? 1 : 0);
      |                       ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void remove_item_from_mapped_list(lvector&, lvector&, long int)':
phylogenetics_cpp_routines.cpp:905:33: 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 long unsigned int'} [-Wsign-compare]
  905 |         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:933:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  933 |         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:954:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  954 |                 for(long i=0; i<dense_row.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:1471:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1471 |         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:2692:30: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2692 |         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:3132:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3132 |         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:3159:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3159 |         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:4356:17: warning: variable 'info' set but not used [-Wunused-but-set-variable]
 4356 |         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:5707:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<std::complex<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 5707 |                         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:5787:19: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 5787 |         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:5819:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 5819 |         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:8732:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 8732 |         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:8769:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 8769 |         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:9813:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 9813 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9839:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 9839 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()':
phylogenetics_cpp_routines.cpp:10801:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
10801 |                 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:12535:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12535 |         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_traversal&, dvector&)':
phylogenetics_cpp_routines.cpp:12664:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12664 |         for(long q=0, clade; q<traversal.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:12770:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12770 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12801:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12801 |         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:12889:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12889 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12920:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12920 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12948:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12948 |         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:13017:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13017 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13047:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13047 |         for(long q=0; q<traversal.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:13139:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13139 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13159:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13159 |         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:13270:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13270 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13290:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13290 |         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:13497:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13497 |         for(long q=0, clade; q<traversal.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:13605:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13605 |         for(long q=0, clade; q<traversal.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:13762:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13762 |         for(long q=0; q<queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13786:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13786 |         for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13787:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13787 |         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:13939:45: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13939 |         for(long q=1, clade, pnode, cnode; q<traversal.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:14197:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14197 |         for(long q=0, clade; q<traversal.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:14366:16: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14366 |         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:14423:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14423 |         while(queue_pointer<clades.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14440:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14440 |         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:14488:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14488 |         for(long q=0; q<traversal.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:15048:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15048 |         for(long c=0; c<clades_to_keep.size(); ++c){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15065:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15065 |         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:15889:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15889 |         for(long t=0; t<target_tips.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15912:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15912 |         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:16019:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16019 |         for(long t=0, tip; t<target_tips.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16033:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16033 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16068:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16068 |                 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:16335:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16335 |         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:16445:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16445 |                 for(long q=0; q<traversal.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:16785:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16785 |                 for(long n=0, node; n<nodes_to_merge.size(); ++n){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16795:49: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16795 |                 for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
      |                                                ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16859:89: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16859 |         for(long q=0, clade, node, absorbing_ancestor, parent, child, e, edge, inedge; q<traversal.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:16956:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16956 |         for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16979:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16979 |                 for(long q=1, clade, node, inedge, e; q<traversal.queue.size(); ++q){
      |                                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17013:47: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17013 |                 for(long q=1, clade, inedge; q<traversal.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:17349:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17349 |         for(long q=0, clade; q<traversal_queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
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:17855:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17855 |         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:18085:60: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18085 |                                 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:18141:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18141 |         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:18165:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18165 |         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:18194:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18194 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18199:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18199 |         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:18261:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18261 |         for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18278:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18278 |         for(long q=0, clade, node; q<traversal_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:18875:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18875 |         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:19188:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
19188 |         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:20237:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20237 |         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:20308:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20308 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20314:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20314 |         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:20442:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20442 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20461:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20461 |         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:20579:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20579 |         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:20809:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20809 |         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:21171:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21171 |                 for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21212:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21212 |         for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
      |                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector 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:21616:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21616 |         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:21672:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21672 |         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:21846:42: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21846 |                 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:22107:30: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22107 |         if(node_states.size()>Nnodes) node_states.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22108:39: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22108 |         if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22109:29: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22109 |         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:22150:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22150 |         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:22185:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22185 |                 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:22204:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22204 |                 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:22224:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22224 |                 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:22429:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22429 |                 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:22443:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22443 |                 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:22535:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22535 |                         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:22548:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22548 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22553:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22553 |                         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:22573:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22573 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22595:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22595 |                         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:22618:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22618 |                 for(long s=0; s<candidateY.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22642:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22642 |                         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:22825:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22825 |                 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:22838:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22838 |                 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:22855:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22855 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22877:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22877 |                         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:23126:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23126 |         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:23951:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23951 |                         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:26207:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26207 |         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:26287:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26287 |                 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:26369:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26369 |                 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:26440:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26440 |                 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:26520:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26520 |                 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:26612:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26612 |                 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:26724:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26724 |         for(long i=0; i<sampled_tips.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26727:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26727 |         for(long i=0; i<sampled_node_clades.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26733:53: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
26733 |         if(only_sampled_tips && (sampled_tips.size()<Ntips)){
      |                                  ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:26770:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26770 |                 for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
      |                                       ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26776:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26776 |                 for(long i=0; i<sampled_tips.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26779:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26779 |                 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:26865:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
26865 |         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:26865:133: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
26865 |         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:27080:100: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27080 |         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:27080:167: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27080 |         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:27080:235: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27080 |         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:27266:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27266 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27273:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27273 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27280:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27280 |         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:27934:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
27934 |         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:28128:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
28128 |         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:28589:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28589 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28595:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28595 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28600:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28600 |         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:29268:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29268 |                 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:29512:44: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29512 |                 if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29514:42: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29514 |                 if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29523:41: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29523 |         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:29576:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29576 |                 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:29626:64: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29626 |         const bool got_allele_counts    = (allele_counts.size()==NStips);
      |                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:29627:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29627 |         const bool got_population_sizes = (population_sizes.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29628:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29628 |         const bool got_generation_times = (generation_times.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29629:65: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29629 |         const bool got_mutation_rates   = (mutation_rates.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29655:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29655 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29672:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29672 |                 for(allele=0; allele<gene_orphans[stip].size(); ++allele){
      |                               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29757:50: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29757 |                         for(long orphan=0; orphan<gene_orphans[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:29911:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29911 |         const bool got_population_sizes                 = (population_sizes.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29912:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29912 |         const bool got_generation_times                 = (generation_times.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29913:81: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29913 |         const bool got_mutation_rates                   = (mutation_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29914:80: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29914 |         const bool got_allele_counts                    = (allele_counts.size()==NStips);
      |                                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:29915:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29915 |         const bool got_HGT_rates                                = (HGT_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29916:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29916 |         const bool got_duplication_rates                = (duplication_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29917:85: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29917 |         const bool got_loss_rates                               = (loss_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29938:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29938 |         for(long q=0; q<traversal.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29945:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29945 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30048:66: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30048 |                                 for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
      |                                                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30074:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30074 |                 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:30893:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30893 |         for(long q=0, parent, child, e, edge; q<traversal.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:31009:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31009 |         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:31482:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31482 |                 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:31524:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31524 |         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:31562:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31562 |         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:31724:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31724 |         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&, long int, double, double, long int, long int, const std::string&)':
phylogenetics_cpp_routines.cpp:32207:32: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
32207 |                 if(parts.size()<=distances_column){
      |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32235:56: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
32235 |                 if((max_Nedges>=0) && (distances.size()>=max_Nedges)) break;
      |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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:5198:29:   required from here
phylogenetics_cpp_routines.cpp:553:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  553 |         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:5393:34:   required from here
phylogenetics_cpp_routines.cpp:4799:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 4799 |         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:5393:77:   required from here
phylogenetics_cpp_routines.cpp:4807:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 4807 |         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:8606:48:   required from here
phylogenetics_cpp_routines.cpp:665:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  665 |         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:8828:25:   required from here
phylogenetics_cpp_routines.cpp:4649:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4649 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4650:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4650 |                 for(j=0; j<N; ++j){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4665:87: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
 4665 |                 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:9198:40:   required from here
phylogenetics_cpp_routines.cpp:9060:21: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
 9060 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |            ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9060:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
 9060 |         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:9632:24:   required from here
phylogenetics_cpp_routines.cpp:3322:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3322 |         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:12016:33:   required from here
phylogenetics_cpp_routines.cpp:11985:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
11985 |         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:12674:36:   required from here
phylogenetics_cpp_routines.cpp:743:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  743 |         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:13771:14:   required from here
phylogenetics_cpp_routines.cpp:1028:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1028 |         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:14070:33:   required from here
phylogenetics_cpp_routines.cpp:743:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  743 |         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:14739:30:   required from here
phylogenetics_cpp_routines.cpp:14711:36: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14711 |                 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:14975:40:   required from here
phylogenetics_cpp_routines.cpp:14871:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14871 |         for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
      |                              ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14885:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14885 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14908:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14908 |         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:15588:32:   required from here
phylogenetics_cpp_routines.cpp:15446:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15446 |         for(long t=0; t<tips_to_keep.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15449:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15449 |         for(long fn=0; fn<force_keep_nodes.size(); ++fn){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15522:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15522 |         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_traversal&, dvector&) [with ARRAY_TYPE_INT = std::vector<long int>; ARRAY_TYPE_D = std::vector<double>; dvector = std::vector<double>]':
phylogenetics_cpp_routines.cpp:16815:26:   required from here
phylogenetics_cpp_routines.cpp:12615:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12615 |         for(long q=0, clade; q<traversal.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:18087:33:   required from here
phylogenetics_cpp_routines.cpp:459:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  459 |         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:22418:19:   required from here
phylogenetics_cpp_routines.cpp:3404:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3404 |         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:22481:27:   required from here
phylogenetics_cpp_routines.cpp:3304:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3304 |         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:22481:27:   required from here
phylogenetics_cpp_routines.cpp:3358:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3358 |         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:22590:66:   required from here
phylogenetics_cpp_routines.cpp:3331:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3331 |         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:22654:22:   required from here
phylogenetics_cpp_routines.cpp:838:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  838 |         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:23014:32:   required from here
phylogenetics_cpp_routines.cpp:3295:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3295 |         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:23035:30:   required from here
phylogenetics_cpp_routines.cpp:665:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  665 |         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:23036:23:   required from here
phylogenetics_cpp_routines.cpp:3413:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3413 |         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:23044:56:   required from here
phylogenetics_cpp_routines.cpp:3286:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3286 |         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:23554:38:   required from here
phylogenetics_cpp_routines.cpp:688:24: warning: comparison of integer expressions of different signedness: 'long int' and 'const long long unsigned int' [-Wsign-compare]
  688 |         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:23953:83:   required from here
phylogenetics_cpp_routines.cpp:3376:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3376 |         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:24573:48:   required from here
phylogenetics_cpp_routines.cpp:3422:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3422 |         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:25065:26:   required from here
phylogenetics_cpp_routines.cpp:2518:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2518 |                 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:25070:26:   required from here
phylogenetics_cpp_routines.cpp:2529:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2529 |                 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:25493:20:   required from here
phylogenetics_cpp_routines.cpp:3349:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3349 |         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:26736:52:   required from here
phylogenetics_cpp_routines.cpp:3367:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3367 |         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:27202:27:   required from here
phylogenetics_cpp_routines.cpp:875:17: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  875 |         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:31042:22:   required from here
phylogenetics_cpp_routines.cpp:30944:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30944 |         for(long q=0, parent, child, e, edge; q<traversal.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:4656:21:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8828:25:   required from here
phylogenetics_cpp_routines.cpp:4504:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4504 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4505:34: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4505 |                 for(j=0, big=0; j<N; ++j){
      |                                 ~^~
phylogenetics_cpp_routines.cpp:4514:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4514 |         for(j=0; j<N; ++j){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4521:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4521 |                 for(i=j; i<N; ++i){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4531:35: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4531 |                         for(k=0; k<N; ++k){
      |                                  ~^~
phylogenetics_cpp_routines.cpp:4543:22: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4543 |                 if(j < N-1){
      |                    ~~^~~~~
phylogenetics_cpp_routines.cpp:4545:37: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4545 |                         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:4661:21:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8828:25:   required from here
phylogenetics_cpp_routines.cpp:4566:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4566 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4579:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4579 |                 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:4666:35:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8828:25:   required from here
phylogenetics_cpp_routines.cpp:4617:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4617 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4619:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4619 |                 for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
      |                          ~^~
phylogenetics_cpp_routines.cpp:4623:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4623 |         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:5272:27:   required from 'long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]'
phylogenetics_cpp_routines.cpp:21113:94:   required from here
phylogenetics_cpp_routines.cpp:441:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  441 |         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:10066:64:   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>]'
phylogenetics_cpp_routines.cpp:22987:141:   required from here
phylogenetics_cpp_routines.cpp:3313:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3313 |         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:7330:21:   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>]'
phylogenetics_cpp_routines.cpp:23089:9:   required from here
phylogenetics_cpp_routines.cpp:404:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  404 |         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:1279:25: warning: 't1' may be used uninitialized [-Wmaybe-uninitialized]
 1279 |                 W += (t2-t1) * abs(CDFY-CDFX);
      |                      ~~~^~~~
phylogenetics_cpp_routines.cpp:1263:32: note: 't1' was declared here
 1263 |         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:2078:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2078 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function 'double legendre_polynomial(long int, double)':
phylogenetics_cpp_routines.cpp:30590:16: warning: 'Pn' may be used uninitialized [-Wmaybe-uninitialized]
30590 |         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:2153:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2153 |         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:2245:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2245 |         double a = Xmin, b = Xmax, c;
      |                                    ^
In file included from d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\cmath:47,
                 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:1610:17:
d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\std_abs.h:72:30: warning: 'Yvertex' may be used uninitialized [-Wmaybe-uninitialized]
   72 |   { 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:1608:28: note: 'Yvertex' was declared here
 1608 |                 VALUE_TYPE Yvertex;
      |                            ^~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:4539:39: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
 4539 |                 pivoting_indices[j] = imax;
      |                                       ^~~~
phylogenetics_cpp_routines.cpp:4498:16: note: 'imax' was declared here
 4498 |         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:10790:96: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
10790 |                                 coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
      |                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10767:59: note: 'coalescent_diversity_at_resolution_age' was declared here
10767 |                 double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:13199:155: warning: 'mrca' may be used uninitialized [-Wmaybe-uninitialized]
13199 |                         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:13172:30: note: 'mrca' was declared here
13172 |         long cladeA, cladeB, mrca;
      |                              ^~~~
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:26206:27: warning: 'parent' may be used uninitialized [-Wmaybe-uninitialized]
26206 |         long clade, edge, parent, parent_state, state=0;
      |                           ^~~~~~
In function 'long int uniformIntWithin(long int, long int)',
    inlined from '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)' at phylogenetics_cpp_routines.cpp:19768:41:
phylogenetics_cpp_routines.cpp:3446:72: warning: 'count_tips_remaining' may be used uninitialized [-Wmaybe-uninitialized]
 3446 |         return min(maximum, (long) floor(minimum + (maximum-minimum+1) * R::runif(0.0,1.0)));
      |                                                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
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:19671:26: note: 'count_tips_remaining' was declared here
19671 |         long tip, clade, count_tips_remaining;
      |                          ^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:19808:49: warning: 'tip' may be used uninitialized [-Wmaybe-uninitialized]
19808 |                                 tip_included[tip] = true;
      |                                                 ^
phylogenetics_cpp_routines.cpp:19671:14: note: 'tip' was declared here
19671 |         long tip, clade, count_tips_remaining;
      |              ^~~
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:11019:88: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11019 |                                 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:10986:87: note: 'coalescent_diversity_at_resolution_age' was declared here
10986 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11011:86: warning: 'Pmissing_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11011 |                                 const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
      |                                                                                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10986:24: note: 'Pmissing_at_resolution_age' was declared here
10986 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
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:24835:63: warning: 'Wdegree' may be used uninitialized [-Wmaybe-uninitialized]
24835 |                                 branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
      |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:24800:33: note: 'Wdegree' was declared here
24800 |         long Zdegree, EZdegree, Wdegree;
      |                                 ^~~~~~~
phylogenetics_cpp_routines.cpp:24834:63: warning: 'Zdegree' may be used uninitialized [-Wmaybe-uninitialized]
24834 |                                 branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
      |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:24800:14: note: 'Zdegree' was declared here
24800 |         long Zdegree, EZdegree, Wdegree;
      |              ^~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_HBDS_model_loglikelihood_CPP(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<double>&, 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::string&, double, double, double)':
phylogenetics_cpp_routines.cpp:25594:61: warning: 'logPhi_degree' may be used uninitialized [-Wmaybe-uninitialized]
25594 |         double oldest_logPhi    = piecewise_polynomial_value(Phi_ages[oldest_s], logPhi_coeff[oldest_s], logPhi_degree, splines_slideX, oldest_sg, oldest_age);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25442:42: note: 'logPhi_degree' was declared here
25442 |         long dummyL1, dummyL2, I_degree, logPhi_degree, E_degree;
      |                                          ^~~~~~~~~~~~~
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:25007:51: warning: 'W_degree' may be used uninitialized [-Wmaybe-uninitialized]
25007 |         const double origin_W   = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
      |                                   ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:24935:24: note: 'W_degree' was declared here
24935 |         long I_degree, W_degree, NRG;
      |                        ^~~~~~~~
gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -s -static-libgcc -o castor.dll tmp.def RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-castor/00new/castor/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (castor)