* 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:158: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  158 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:159: warning: ignoring '#pragma mark Functions' [-Wunknown-pragmas]
  159 | #pragma mark Functions for debugging
      | 
phylogenetics_cpp_routines.cpp:160: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  160 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:229: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  229 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:230: warning: ignoring '#pragma mark Auxiliary' [-Wunknown-pragmas]
  230 | #pragma mark Auxiliary functions
      | 
phylogenetics_cpp_routines.cpp:231: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
  231 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:1302: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1302 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:1303: warning: ignoring '#pragma mark Graphs' [-Wunknown-pragmas]
 1303 | #pragma mark Graphs
      | 
phylogenetics_cpp_routines.cpp:1304: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1304 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:1449: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1449 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:1450: warning: ignoring '#pragma mark Polynomials' [-Wunknown-pragmas]
 1450 | #pragma mark Polynomials
      | 
phylogenetics_cpp_routines.cpp:1451: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 1451 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:2788: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 2788 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:2789: warning: ignoring '#pragma mark Integration' [-Wunknown-pragmas]
 2789 | #pragma mark Integration, antiderivatives, derivatives
      | 
phylogenetics_cpp_routines.cpp:2790: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 2790 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3293: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3293 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3294: warning: ignoring '#pragma mark Vectorized' [-Wunknown-pragmas]
 3294 | #pragma mark Vectorized basic arithmetics
      | 
phylogenetics_cpp_routines.cpp:3295: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3295 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3444: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3444 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3445: warning: ignoring '#pragma mark Random' [-Wunknown-pragmas]
 3445 | #pragma mark Random numbers
      | 
phylogenetics_cpp_routines.cpp:3446: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3446 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:3840: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3840 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:3841: warning: ignoring '#pragma mark Matrix' [-Wunknown-pragmas]
 3841 | #pragma mark Matrix algebra
      | 
phylogenetics_cpp_routines.cpp:3842: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 3842 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:7050: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 7050 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:7051: warning: ignoring '#pragma mark Numerical' [-Wunknown-pragmas]
 7051 | #pragma mark Numerical solvers
      | 
phylogenetics_cpp_routines.cpp:7052: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 7052 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:8463: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 8463 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:8464: warning: ignoring '#pragma mark Time' [-Wunknown-pragmas]
 8464 | #pragma mark Time series analysis
      | 
phylogenetics_cpp_routines.cpp:8465: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 8465 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:9870: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 9870 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:9871: warning: ignoring '#pragma mark Class' [-Wunknown-pragmas]
 9871 | #pragma mark Class: LinearInterpolationFunctor
      | 
phylogenetics_cpp_routines.cpp:9872: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
 9872 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10350: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10350 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10351: warning: ignoring '#pragma mark Stochastic' [-Wunknown-pragmas]
10351 | #pragma mark Stochastic processes
      | 
phylogenetics_cpp_routines.cpp:10352: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10352 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:10545: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10545 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:10546: warning: ignoring '#pragma mark Deterministic' [-Wunknown-pragmas]
10546 | #pragma mark Deterministic diversity dynamics
      | 
phylogenetics_cpp_routines.cpp:10547: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10547 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:11646: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11646 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:11647: warning: ignoring '#pragma mark Building' [-Wunknown-pragmas]
11647 | #pragma mark Building auxiliary data structures
      | 
phylogenetics_cpp_routines.cpp:11648: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11648 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:12332: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12332 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:12333: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
12333 | #pragma mark Tree statistics
      | 
phylogenetics_cpp_routines.cpp:12334: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12334 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:14518: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14518 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:14519: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
14519 | #pragma mark Generating & manipulating trees
      | 
phylogenetics_cpp_routines.cpp:14520: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14520 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:17775: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17775 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:17776: warning: ignoring '#pragma mark Comparing' [-Wunknown-pragmas]
17776 | #pragma mark Comparing trees
      | 
phylogenetics_cpp_routines.cpp:17777: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17777 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18195: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18195 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18196: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
18196 | #pragma mark Tree dating
      | 
phylogenetics_cpp_routines.cpp:18197: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18197 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18296: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18296 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18297: warning: ignoring '#pragma mark Plotting' [-Wunknown-pragmas]
18297 | #pragma mark Plotting trees
      | 
phylogenetics_cpp_routines.cpp:18298: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18298 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18393: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18393 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18394: warning: ignoring '#pragma mark Writing' [-Wunknown-pragmas]
18394 | #pragma mark Writing/reading trees
      | 
phylogenetics_cpp_routines.cpp:18395: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18395 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:18884: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18884 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:18885: warning: ignoring '#pragma mark Statistics' [-Wunknown-pragmas]
18885 | #pragma mark Statistics of trait distribution
      | 
phylogenetics_cpp_routines.cpp:18886: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18886 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:20262: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20262 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:20263: warning: ignoring '#pragma mark Most' [-Wunknown-pragmas]
20263 | #pragma mark Most recent common ancestors
      | 
phylogenetics_cpp_routines.cpp:20264: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20264 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:20683: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20683 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:20684: warning: ignoring '#pragma mark Ancestral' [-Wunknown-pragmas]
20684 | #pragma mark Ancestral state reconstruction
      | 
phylogenetics_cpp_routines.cpp:20685: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20685 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:22396: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22396 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:22397: warning: ignoring '#pragma mark MuSSE' [-Wunknown-pragmas]
22397 | #pragma mark MuSSE model fitting
      | 
phylogenetics_cpp_routines.cpp:22398: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22398 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:23662: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
23662 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:23663: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
23663 | #pragma mark Homogenous Birth-Death models
      | 
phylogenetics_cpp_routines.cpp:23664: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
23664 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:25120: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25120 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:25121: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
25121 | #pragma mark Homogenous Birth-Death-Sampling model
      | 
phylogenetics_cpp_routines.cpp:25122: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25122 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:26231: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26231 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:26232: warning: ignoring '#pragma mark Simulate' [-Wunknown-pragmas]
26232 | #pragma mark Simulate models of trait evolution
      | 
phylogenetics_cpp_routines.cpp:26233: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26233 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:26745: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26745 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:26746: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
26746 | #pragma mark Generating random trees via cladogenic models
      | 
phylogenetics_cpp_routines.cpp:26747: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26747 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:29411: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29411 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:29412: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
29412 | #pragma mark Generating gene trees
      | 
phylogenetics_cpp_routines.cpp:29413: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29413 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:30660: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
30660 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:30661: warning: ignoring '#pragma mark Spherical' [-Wunknown-pragmas]
30661 | #pragma mark Spherical Brownian motion
      | 
phylogenetics_cpp_routines.cpp:30662: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
30662 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp:32205: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32205 | #pragma mark -
      | 
phylogenetics_cpp_routines.cpp:32206: warning: ignoring '#pragma mark Loading' [-Wunknown-pragmas]
32206 | #pragma mark Loading files
      | 
phylogenetics_cpp_routines.cpp:32207: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32207 | #pragma mark
      | 
phylogenetics_cpp_routines.cpp: In function 'long int count_occurrences(const std::string&, char, bool)':
phylogenetics_cpp_routines.cpp:321:24: 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]
  321 |         for(long i=0; i<haystack.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void split_string(const std::string&, const std::string&, long int, std::vector<std::__cxx11::basic_string<char> >&)':
phylogenetics_cpp_routines.cpp:344:46: 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]
  344 |         while((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                                  ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:346:23: 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]
  346 |                 if(pos==string::npos) break;
      |                    ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:350:43: 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]
  350 |         if((max_Nparts<0) || (parts.size()<max_Nparts)){
      |                               ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int find_first_non_nan(const std::vector<double>&, long int)':
phylogenetics_cpp_routines.cpp:447:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  447 |         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:694:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  694 |         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:709:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  709 |         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:727:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  727 |         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:734:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  734 |         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:763:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  763 |         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:794:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  794 |         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:799:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  799 |         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:806:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  806 |         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:816:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  816 |         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:869:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  869 |         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:919:33: 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]
  919 |         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:947:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  947 |         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:968:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  968 |                 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:1485:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1485 |         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:2706:30: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2706 |         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:3146:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3146 |         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:3173:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3173 |         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:4370:17: warning: variable 'info' set but not used [-Wunused-but-set-variable]
 4370 |         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:5721:40: 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]
 5721 |                         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:5801:19: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 5801 |         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:5833:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 5833 |         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:8746:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 8746 |         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:8783:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 8783 |         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:9827:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 9827 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9853:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 9853 |                                         for(long k=0; k<invalids.size(); ++k){
      |                                                       ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()':
phylogenetics_cpp_routines.cpp:10815:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
10815 |                 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:12549:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12549 |         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:12678:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12678 |         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:12784:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12784 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12815:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12815 |         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:12903:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12903 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12934:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12934 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12962:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12962 |         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:13031:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13031 |                 for(long t=0; t<onlyToTips.size(); ++t){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13061:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13061 |         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:13153:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13153 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13173:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13173 |         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:13284:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13284 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13304:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13304 |         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:13511:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13511 |         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:13619:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13619 |         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:13776:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13776 |         for(long q=0; q<queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13800:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13800 |         for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13801:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13801 |         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:13953:45: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13953 |         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:14211:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14211 |         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:14380:16: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14380 |         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:14437:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14437 |         while(queue_pointer<clades.size()){
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14454:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14454 |         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:14502:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14502 |         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:15061:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15061 |         for(long c=0; c<clades_to_keep.size(); ++c){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15078:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15078 |         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:15902:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15902 |         for(long t=0; t<target_tips.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15925:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15925 |         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:16032:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16032 |         for(long t=0, tip; t<target_tips.size(); ++t){
      |                            ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16046:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16046 |         for(long q=1; q<traversal_queue_root2tips.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16081:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16081 |                 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:16348:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16348 |         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:16458:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16458 |                 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:16798:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16798 |                 for(long n=0, node; n<nodes_to_merge.size(); ++n){
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16808:49: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16808 |                 for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
      |                                                ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16872:89: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16872 |         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:16969:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16969 |         for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
      |                                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16992:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16992 |                 for(long q=1, clade, node, inedge, e; q<traversal.queue.size(); ++q){
      |                                                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17026:47: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17026 |                 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:17362:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17362 |         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:17939:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17939 |         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:18169:60: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18169 |                                 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:18225:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18225 |         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:18249:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18249 |         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:18278:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18278 |         for(long a=0; a<anchor_nodes.size(); ++a){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18283:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18283 |         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:18345:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18345 |         for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
      |                                      ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18362:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18362 |         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:18959:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18959 |         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:19272:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
19272 |         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:20321:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20321 |         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:20392:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20392 |         for(long fc=0; fc<focal_clades.size(); ++fc){
      |                        ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20398:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20398 |         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:20526:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20526 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20545:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20545 |         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:20663:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20663 |         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:20893:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20893 |         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:21255:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21255 |                 for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21296:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21296 |         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:21700:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21700 |         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:21756:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21756 |         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:21930:42: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21930 |                 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:22191:30: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22191 |         if(node_states.size()>Nnodes) node_states.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22192:39: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22192 |         if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22193:29: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22193 |         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:22234:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22234 |         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:22269:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22269 |                 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:22288:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22288 |                 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:22308:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22308 |                 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:22513:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22513 |                 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:22527:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22527 |                 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:22619:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22619 |                         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:22632:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22632 |                         for(long i=0; i<candidateY.size(); ++i){
      |                                       ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22637:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22637 |                         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:22657:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22657 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22679:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22679 |                         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:22702:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22702 |                 for(long s=0; s<candidateY.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22726:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22726 |                         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:22909:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22909 |                 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:22922:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22922 |                 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:22939:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22939 |                 for(long s=0; s<candidate_state.size(); ++s){
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22961:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22961 |                         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:23210:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23210 |         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:24035:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
24035 |                         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:26291:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26291 |         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:26371:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26371 |                 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:26453:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26453 |                 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:26524:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26524 |                 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:26604:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26604 |                 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:26696:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26696 |                 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:26808:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26808 |         for(long i=0; i<sampled_tips.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26811:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26811 |         for(long i=0; i<sampled_node_clades.size(); ++i){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26817:53: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
26817 |         if(only_sampled_tips && (sampled_tips.size()<Ntips)){
      |                                  ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:26854:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26854 |                 for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
      |                                       ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26860:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26860 |                 for(long i=0; i<sampled_tips.size(); ++i){
      |                               ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:26863:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26863 |                 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:26949:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
26949 |         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:26949:133: 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]
26949 |         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:27164:100: 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]
27164 |         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:27164:167: 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]
27164 |         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:27164:235: 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]
27164 |         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:27350:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27350 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27357:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27357 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27364:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27364 |         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:28018:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
28018 |         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:28212:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
28212 |         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:28673:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28673 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28679:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28679 |                 for(long nc=0; nc<new2old_clade.size(); ++nc){
      |                                ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28684:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
28684 |         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:29352:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29352 |                 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:29596:44: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29596 |                 if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29598:42: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29598 |                 if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29607:41: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29607 |         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:29660:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
29660 |                 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:29710:64: 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]
29710 |         const bool got_allele_counts    = (allele_counts.size()==NStips);
      |                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:29711:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29711 |         const bool got_population_sizes = (population_sizes.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29712:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29712 |         const bool got_generation_times = (generation_times.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29713:65: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29713 |         const bool got_mutation_rates   = (mutation_rates.size()==NSclades);
      |                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29739:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29739 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29756:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29756 |                 for(allele=0; allele<gene_orphans[stip].size(); ++allele){
      |                               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29841:50: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29841 |                         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:29995:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29995 |         const bool got_population_sizes                 = (population_sizes.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29996:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29996 |         const bool got_generation_times                 = (generation_times.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29997:81: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29997 |         const bool got_mutation_rates                   = (mutation_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:29998:80: 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]
29998 |         const bool got_allele_counts                    = (allele_counts.size()==NStips);
      |                                                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:29999:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
29999 |         const bool got_HGT_rates                                = (HGT_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30000:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30000 |         const bool got_duplication_rates                = (duplication_rates.size()==NSclades);
      |                                                            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30001:85: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30001 |         const bool got_loss_rates                               = (loss_rates.size()==NSclades);
      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30022:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30022 |         for(long q=0; q<traversal.queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30029:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30029 |         for(long q=0, clade; q<traversal.queue.size(); ++q){
      |                              ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30132:66: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30132 |                                 for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
      |                                                                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30158:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30158 |                 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:30977:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30977 |         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:31093:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31093 |         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:31566:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31566 |                 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:31608:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31608 |         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:31646:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31646 |         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:31808:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31808 |         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:32291:32: 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]
32291 |                 if(parts.size()<=distances_column){
      |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32319:56: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
32319 |                 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:5212:29:   required from here
phylogenetics_cpp_routines.cpp:567:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  567 |         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:5407:34:   required from here
phylogenetics_cpp_routines.cpp:4813:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 4813 |         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:5407:77:   required from here
phylogenetics_cpp_routines.cpp:4821:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 4821 |         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:8620:48:   required from here
phylogenetics_cpp_routines.cpp:679:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  679 |         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:8842:25:   required from here
phylogenetics_cpp_routines.cpp:4663:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4663 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4664:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4664 |                 for(j=0; j<N; ++j){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4679:87: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
 4679 |                 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:9212:40:   required from here
phylogenetics_cpp_routines.cpp:9074:21: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
 9074 |         if((x.size()<=end) || (y.size()<=end)) return false;
      |            ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9074:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
 9074 |         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:9646:24:   required from here
phylogenetics_cpp_routines.cpp:3336:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3336 |         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:12030:33:   required from here
phylogenetics_cpp_routines.cpp:11999:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
11999 |         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:12688:36:   required from here
phylogenetics_cpp_routines.cpp:757:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  757 |         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:13785:14:   required from here
phylogenetics_cpp_routines.cpp:1042:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1042 |         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:14084:33:   required from here
phylogenetics_cpp_routines.cpp:757:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  757 |         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:14753:30:   required from here
phylogenetics_cpp_routines.cpp:14725:36: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14725 |                 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:14989:40:   required from here
phylogenetics_cpp_routines.cpp:14885:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14885 |         for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
      |                              ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14899:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14899 |         for(long q=0; q<traversal_queue.size(); ++q){
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14922:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14922 |         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:15601:32:   required from here
phylogenetics_cpp_routines.cpp:15459:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15459 |         for(long t=0; t<tips_to_keep.size(); ++t){
      |                       ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15462:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15462 |         for(long fn=0; fn<force_keep_nodes.size(); ++fn){
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15535:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15535 |         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:16828:26:   required from here
phylogenetics_cpp_routines.cpp:12629:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12629 |         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:18171:33:   required from here
phylogenetics_cpp_routines.cpp:473:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  473 |         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:22502:19:   required from here
phylogenetics_cpp_routines.cpp:3418:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3418 |         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:22565:27:   required from here
phylogenetics_cpp_routines.cpp:3318:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3318 |         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:22565:27:   required from here
phylogenetics_cpp_routines.cpp:3372:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3372 |         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:22674:66:   required from here
phylogenetics_cpp_routines.cpp:3345:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3345 |         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:22738:22:   required from here
phylogenetics_cpp_routines.cpp:852:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  852 |         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:23098:32:   required from here
phylogenetics_cpp_routines.cpp:3309:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3309 |         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:23119:30:   required from here
phylogenetics_cpp_routines.cpp:679:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  679 |         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:23120:23:   required from here
phylogenetics_cpp_routines.cpp:3427:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3427 |         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:23128:56:   required from here
phylogenetics_cpp_routines.cpp:3300:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3300 |         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:23638:38:   required from here
phylogenetics_cpp_routines.cpp:702:24: warning: comparison of integer expressions of different signedness: 'long int' and 'const long long unsigned int' [-Wsign-compare]
  702 |         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:24037:83:   required from here
phylogenetics_cpp_routines.cpp:3390:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3390 |         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:24657:48:   required from here
phylogenetics_cpp_routines.cpp:3436:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3436 |         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:25149:26:   required from here
phylogenetics_cpp_routines.cpp:2532:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2532 |                 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:25154:26:   required from here
phylogenetics_cpp_routines.cpp:2543:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 2543 |                 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:25577:20:   required from here
phylogenetics_cpp_routines.cpp:3363:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3363 |         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:26820:52:   required from here
phylogenetics_cpp_routines.cpp:3381:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3381 |         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:27286:27:   required from here
phylogenetics_cpp_routines.cpp:889:17: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  889 |         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:31126:22:   required from here
phylogenetics_cpp_routines.cpp:31028:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31028 |         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:4670:21:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8842:25:   required from here
phylogenetics_cpp_routines.cpp:4518:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4518 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4519:34: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4519 |                 for(j=0, big=0; j<N; ++j){
      |                                 ~^~
phylogenetics_cpp_routines.cpp:4528:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4528 |         for(j=0; j<N; ++j){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4535:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4535 |                 for(i=j; i<N; ++i){
      |                          ~^~
phylogenetics_cpp_routines.cpp:4545:35: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4545 |                         for(k=0; k<N; ++k){
      |                                  ~^~
phylogenetics_cpp_routines.cpp:4557:22: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4557 |                 if(j < N-1){
      |                    ~~^~~~~
phylogenetics_cpp_routines.cpp:4559:37: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4559 |                         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:4675:21:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8842:25:   required from here
phylogenetics_cpp_routines.cpp:4580:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4580 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4593:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4593 |                 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:4680:35:   required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8842:25:   required from here
phylogenetics_cpp_routines.cpp:4631:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4631 |         for(i=0; i<N; ++i){
      |                  ~^~
phylogenetics_cpp_routines.cpp:4633:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4633 |                 for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
      |                          ~^~
phylogenetics_cpp_routines.cpp:4637:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
 4637 |         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:5286:27:   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:21197:94:   required from here
phylogenetics_cpp_routines.cpp:455:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  455 |         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:10080:64:   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:23071:141:   required from here
phylogenetics_cpp_routines.cpp:3327:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 3327 |         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:7344:21:   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:23173:9:   required from here
phylogenetics_cpp_routines.cpp:418:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  418 |         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:1293:25: warning: 't1' may be used uninitialized [-Wmaybe-uninitialized]
 1293 |                 W += (t2-t1) * abs(CDFY-CDFX);
      |                      ~~~^~~~
phylogenetics_cpp_routines.cpp:1277:32: note: 't1' was declared here
 1277 |         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:2092:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2092 |         double a = Xmin, b = Xmax, c;
      |                                    ^
phylogenetics_cpp_routines.cpp: In function 'double legendre_polynomial(long int, double)':
phylogenetics_cpp_routines.cpp:30674:16: warning: 'Pn' may be used uninitialized [-Wmaybe-uninitialized]
30674 |         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:2167:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2167 |         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:2259:36: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
 2259 |         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:1624:17:
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:1622:28: note: 'Yvertex' was declared here
 1622 |                 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:4553:39: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
 4553 |                 pivoting_indices[j] = imax;
      |                                       ^~~~
phylogenetics_cpp_routines.cpp:4512:16: note: 'imax' was declared here
 4512 |         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:10804:96: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
10804 |                                 coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
      |                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10781:59: note: 'coalescent_diversity_at_resolution_age' was declared here
10781 |                 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:13213:155: warning: 'mrca' may be used uninitialized [-Wmaybe-uninitialized]
13213 |                         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:13186:30: note: 'mrca' was declared here
13186 |         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:26290:27: warning: 'parent' may be used uninitialized [-Wmaybe-uninitialized]
26290 |         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:19852:41:
phylogenetics_cpp_routines.cpp:3460:72: warning: 'count_tips_remaining' may be used uninitialized [-Wmaybe-uninitialized]
 3460 |         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:19755:26: note: 'count_tips_remaining' was declared here
19755 |         long tip, clade, count_tips_remaining;
      |                          ^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:19892:49: warning: 'tip' may be used uninitialized [-Wmaybe-uninitialized]
19892 |                                 tip_included[tip] = true;
      |                                                 ^
phylogenetics_cpp_routines.cpp:19755:14: note: 'tip' was declared here
19755 |         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:11033:88: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11033 |                                 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:11000:87: note: 'coalescent_diversity_at_resolution_age' was declared here
11000 |                 double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11025:86: warning: 'Pmissing_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11025 |                                 const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
      |                                                                                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11000:24: note: 'Pmissing_at_resolution_age' was declared here
11000 |                 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:24919:63: warning: 'Wdegree' may be used uninitialized [-Wmaybe-uninitialized]
24919 |                                 branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
      |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:24884:33: note: 'Wdegree' was declared here
24884 |         long Zdegree, EZdegree, Wdegree;
      |                                 ^~~~~~~
phylogenetics_cpp_routines.cpp:24918:63: warning: 'Zdegree' may be used uninitialized [-Wmaybe-uninitialized]
24918 |                                 branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
      |                                               ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:24884:14: note: 'Zdegree' was declared here
24884 |         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:25678:61: warning: 'logPhi_degree' may be used uninitialized [-Wmaybe-uninitialized]
25678 |         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:25526:42: note: 'logPhi_degree' was declared here
25526 |         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:25091:51: warning: 'W_degree' may be used uninitialized [-Wmaybe-uninitialized]
25091 |         const double origin_W   = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
      |                                   ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25019:24: note: 'W_degree' was declared here
25019 |         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)