* installing *source* package 'castor' ...
** package 'castor' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2026_02_04_01_50_01_15123/RtmpED2USy/R.INSTALL1a28c5e212057/castor/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/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-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/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-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/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:154: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
154 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:155: warning: ignoring '#pragma mark Declarations' [-Wunknown-pragmas]
155 | #pragma mark Declarations
|
phylogenetics_cpp_routines.cpp:156: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
156 | #pragma mark
|
phylogenetics_cpp_routines.cpp:168: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
168 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:169: warning: ignoring '#pragma mark Functions' [-Wunknown-pragmas]
169 | #pragma mark Functions for debugging
|
phylogenetics_cpp_routines.cpp:170: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
170 | #pragma mark
|
phylogenetics_cpp_routines.cpp:243: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
243 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:244: warning: ignoring '#pragma mark Auxiliary' [-Wunknown-pragmas]
244 | #pragma mark Auxiliary functions
|
phylogenetics_cpp_routines.cpp:245: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
245 | #pragma mark
|
phylogenetics_cpp_routines.cpp:1445: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
1445 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:1446: warning: ignoring '#pragma mark Graphs' [-Wunknown-pragmas]
1446 | #pragma mark Graphs
|
phylogenetics_cpp_routines.cpp:1447: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
1447 | #pragma mark
|
phylogenetics_cpp_routines.cpp:1592: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
1592 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:1593: warning: ignoring '#pragma mark Polynomials' [-Wunknown-pragmas]
1593 | #pragma mark Polynomials
|
phylogenetics_cpp_routines.cpp:1594: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
1594 | #pragma mark
|
phylogenetics_cpp_routines.cpp:2931: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
2931 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:2932: warning: ignoring '#pragma mark Integration' [-Wunknown-pragmas]
2932 | #pragma mark Integration, antiderivatives, derivatives
|
phylogenetics_cpp_routines.cpp:2933: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
2933 | #pragma mark
|
phylogenetics_cpp_routines.cpp:3436: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3436 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:3437: warning: ignoring '#pragma mark Vectorized' [-Wunknown-pragmas]
3437 | #pragma mark Vectorized basic arithmetics
|
phylogenetics_cpp_routines.cpp:3438: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3438 | #pragma mark
|
phylogenetics_cpp_routines.cpp:3587: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3587 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:3588: warning: ignoring '#pragma mark Random' [-Wunknown-pragmas]
3588 | #pragma mark Random numbers
|
phylogenetics_cpp_routines.cpp:3589: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3589 | #pragma mark
|
phylogenetics_cpp_routines.cpp:3983: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3983 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:3984: warning: ignoring '#pragma mark Matrix' [-Wunknown-pragmas]
3984 | #pragma mark Matrix algebra
|
phylogenetics_cpp_routines.cpp:3985: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
3985 | #pragma mark
|
phylogenetics_cpp_routines.cpp:7193: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
7193 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:7194: warning: ignoring '#pragma mark Numerical' [-Wunknown-pragmas]
7194 | #pragma mark Numerical solvers
|
phylogenetics_cpp_routines.cpp:7195: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
7195 | #pragma mark
|
phylogenetics_cpp_routines.cpp:8606: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
8606 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:8607: warning: ignoring '#pragma mark Time' [-Wunknown-pragmas]
8607 | #pragma mark Time series analysis
|
phylogenetics_cpp_routines.cpp:8608: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
8608 | #pragma mark
|
phylogenetics_cpp_routines.cpp:10013: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10013 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:10014: warning: ignoring '#pragma mark Class' [-Wunknown-pragmas]
10014 | #pragma mark Class: LinearInterpolationFunctor
|
phylogenetics_cpp_routines.cpp:10015: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10015 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:10493: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10493 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:10494: warning: ignoring '#pragma mark Stochastic' [-Wunknown-pragmas]
10494 | #pragma mark Stochastic processes
|
phylogenetics_cpp_routines.cpp:10495: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10495 | #pragma mark
|
phylogenetics_cpp_routines.cpp:10688: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10688 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:10689: warning: ignoring '#pragma mark Deterministic' [-Wunknown-pragmas]
10689 | #pragma mark Deterministic diversity dynamics
|
phylogenetics_cpp_routines.cpp:10690: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
10690 | #pragma mark
|
phylogenetics_cpp_routines.cpp:11789: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11789 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:11790: warning: ignoring '#pragma mark Building' [-Wunknown-pragmas]
11790 | #pragma mark Building auxiliary data structures
|
phylogenetics_cpp_routines.cpp:11791: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
11791 | #pragma mark
|
phylogenetics_cpp_routines.cpp:12477: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12477 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:12478: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
12478 | #pragma mark Tree statistics
|
phylogenetics_cpp_routines.cpp:12479: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
12479 | #pragma mark
|
phylogenetics_cpp_routines.cpp:14604: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14604 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:14605: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
14605 | #pragma mark Generating & manipulating trees
|
phylogenetics_cpp_routines.cpp:14606: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
14606 | #pragma mark
|
phylogenetics_cpp_routines.cpp:17978: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17978 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:17979: warning: ignoring '#pragma mark Comparing' [-Wunknown-pragmas]
17979 | #pragma mark Comparing trees
|
phylogenetics_cpp_routines.cpp:17980: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
17980 | #pragma mark
|
phylogenetics_cpp_routines.cpp:18398: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18398 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:18399: warning: ignoring '#pragma mark Tree' [-Wunknown-pragmas]
18399 | #pragma mark Tree dating
|
phylogenetics_cpp_routines.cpp:18400: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18400 | #pragma mark
|
phylogenetics_cpp_routines.cpp:18499: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18499 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:18500: warning: ignoring '#pragma mark Plotting' [-Wunknown-pragmas]
18500 | #pragma mark Plotting trees
|
phylogenetics_cpp_routines.cpp:18501: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18501 | #pragma mark
|
phylogenetics_cpp_routines.cpp:18722: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18722 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:18723: warning: ignoring '#pragma mark Writing' [-Wunknown-pragmas]
18723 | #pragma mark Writing/reading trees
|
phylogenetics_cpp_routines.cpp:18724: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
18724 | #pragma mark
|
phylogenetics_cpp_routines.cpp:19213: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
19213 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:19214: warning: ignoring '#pragma mark Statistics' [-Wunknown-pragmas]
19214 | #pragma mark Statistics of trait distribution
|
phylogenetics_cpp_routines.cpp:19215: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
19215 | #pragma mark
|
phylogenetics_cpp_routines.cpp:20591: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20591 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:20592: warning: ignoring '#pragma mark Most' [-Wunknown-pragmas]
20592 | #pragma mark Most recent common ancestors
|
phylogenetics_cpp_routines.cpp:20593: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
20593 | #pragma mark
|
phylogenetics_cpp_routines.cpp:21030: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
21030 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:21031: warning: ignoring '#pragma mark Ancestral' [-Wunknown-pragmas]
21031 | #pragma mark Ancestral state reconstruction
|
phylogenetics_cpp_routines.cpp:21032: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
21032 | #pragma mark
|
phylogenetics_cpp_routines.cpp:22810: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22810 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:22811: warning: ignoring '#pragma mark MuSSE' [-Wunknown-pragmas]
22811 | #pragma mark MuSSE model fitting
|
phylogenetics_cpp_routines.cpp:22812: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
22812 | #pragma mark
|
phylogenetics_cpp_routines.cpp:24076: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
24076 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:24077: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
24077 | #pragma mark Homogenous Birth-Death models
|
phylogenetics_cpp_routines.cpp:24078: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
24078 | #pragma mark
|
phylogenetics_cpp_routines.cpp:25534: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25534 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:25535: warning: ignoring '#pragma mark Homogenous' [-Wunknown-pragmas]
25535 | #pragma mark Homogenous Birth-Death-Sampling model
|
phylogenetics_cpp_routines.cpp:25536: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
25536 | #pragma mark
|
phylogenetics_cpp_routines.cpp:26645: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26645 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:26646: warning: ignoring '#pragma mark Simulate' [-Wunknown-pragmas]
26646 | #pragma mark Simulate models of trait evolution
|
phylogenetics_cpp_routines.cpp:26647: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
26647 | #pragma mark
|
phylogenetics_cpp_routines.cpp:27159: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
27159 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:27160: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
27160 | #pragma mark Generating random trees via cladogenic models
|
phylogenetics_cpp_routines.cpp:27161: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
27161 | #pragma mark
|
phylogenetics_cpp_routines.cpp:29820: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29820 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:29821: warning: ignoring '#pragma mark Generating' [-Wunknown-pragmas]
29821 | #pragma mark Generating gene trees
|
phylogenetics_cpp_routines.cpp:29822: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
29822 | #pragma mark
|
phylogenetics_cpp_routines.cpp:31066: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
31066 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:31067: warning: ignoring '#pragma mark Spherical' [-Wunknown-pragmas]
31067 | #pragma mark Spherical Brownian motion
|
phylogenetics_cpp_routines.cpp:31068: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
31068 | #pragma mark
|
phylogenetics_cpp_routines.cpp:32600: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32600 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:32601: warning: ignoring '#pragma mark Loading' [-Wunknown-pragmas]
32601 | #pragma mark Loading files
|
phylogenetics_cpp_routines.cpp:32602: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32602 | #pragma mark
|
phylogenetics_cpp_routines.cpp:32790: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32790 | #pragma mark -
|
phylogenetics_cpp_routines.cpp:32791: warning: ignoring '#pragma mark Working' [-Wunknown-pragmas]
32791 | #pragma mark Working with raw sequences
|
phylogenetics_cpp_routines.cpp:32792: warning: ignoring '#pragma mark ' [-Wunknown-pragmas]
32792 | #pragma mark
|
phylogenetics_cpp_routines.cpp: In function 'void string_to_ascii(const std::string&, lvector&)':
phylogenetics_cpp_routines.cpp:252:20: warning: comparison of integer expressions of different signedness: 'long int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
252 | for(long i=0; i<input.length(); ++i){
| ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int count_occurrences(const std::string&, char, bool)':
phylogenetics_cpp_routines.cpp:344:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
344 | for(long i=0; i<haystack.size(); ++i){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void split_string(const std::string&, const std::string&, long int, std::vector<std::__cxx11::basic_string<char> >&)':
phylogenetics_cpp_routines.cpp:367:46: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
367 | while((max_Nparts<0) || (parts.size()<max_Nparts)){
| ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:369:23: warning: comparison of integer expressions of different signedness: 'long int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long long unsigned int'} [-Wsign-compare]
369 | if(pos==string::npos) break;
| ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:373:43: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
373 | if((max_Nparts<0) || (parts.size()<max_Nparts)){
| ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int find_first_non_nan(const std::vector<double>&, long int)':
phylogenetics_cpp_routines.cpp:470:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
470 | for(long n=start; n<haystack.size(); ++n){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int vector_sum(const std::vector<char>&)':
phylogenetics_cpp_routines.cpp:717:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
717 | for(long i=0; i<values.size(); ++i) S += values[i];
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double smallest_nonzero_step(const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:732:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
732 | for(long i=0; i<times.size(); ++i){
| ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double vector_mean(const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:750:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
750 | for(long i=0; i<values.size(); ++i) S += values[i];
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double vector_abs_mean(const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:757:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
757 | for(long i=0; i<values.size(); ++i) S += abs(values[i]);
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double vector_max_abs(const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:786:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
786 | for(long i=0; i<values.size(); ++i) A = max(A, abs(values[i]));
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void make_vector_positive(std::vector<double>&)':
phylogenetics_cpp_routines.cpp:817:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
817 | for(long i=0; i<values.size(); ++i) values[i] = max(0.0, values[i]);
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void replace_negatives(std::vector<double>&, double)':
phylogenetics_cpp_routines.cpp:822:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
822 | for(long i=0; i<values.size(); ++i){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void replace_non_positives(std::vector<double>&, double)':
phylogenetics_cpp_routines.cpp:829:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
829 | for(long i=0; i<values.size(); ++i){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void cap_values(double, double, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:839:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
839 | for(long i=0; i<values.size(); ++i){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int vector_count_zeros(const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:892:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
892 | for(long i=0; i<values.size(); ++i) S += (values[i]==0 ? 1 : 0);
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'int taxon_descends(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&)':
phylogenetics_cpp_routines.cpp:912:32: warning: comparison of integer expressions of different signedness: 'long int' and 'const long long unsigned int' [-Wsign-compare]
912 | for(long level=0; level<min(parent_taxonomy.size(), child_taxonomy.size()); ++level){
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void remove_item_from_mapped_list(lvector&, lvector&, long int)':
phylogenetics_cpp_routines.cpp:958:33: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type' {aka 'long int'} and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
958 | if(pool2list[pool_index]==list2pool.size()-1){
phylogenetics_cpp_routines.cpp: In function 'long int get_nearest_index(const std::vector<long int>&, long int)':
phylogenetics_cpp_routines.cpp:986:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
986 | for(long i=0; i<(haystack.size()-1); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List dense_binary_matrix_row2column_major_CPP(long int, long int, const Rcpp::List&, bool)':
phylogenetics_cpp_routines.cpp:1007:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1007 | for(long i=0; i<dense_row.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void filtered_indices_to_bool(long int, const lvector&, const lvector&, bvector&)':
phylogenetics_cpp_routines.cpp:1432:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1432 | for(long i=0; i<only_indices.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:1437:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1437 | for(long i=0; i<omit_indices.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double sum_piecewise_polynomials(const std::vector<std::vector<double> >&, const lvector&, const dvector&, double, long int)':
phylogenetics_cpp_routines.cpp:1628:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1628 | for(long i=0; i<Ydegrees.size(); ++i){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector evaluate_spline_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::string&, long int)':
phylogenetics_cpp_routines.cpp:2849:30: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
2849 | for(long t=0, g=-1; t<Xtarget.size(); ++t){
| ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector get_antiderivative_CPP(const std::vector<double>&, double, const std::vector<double>&, long int, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:3289:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3289 | for(long t=0, g=0; t<Xtarget.size(); ++t){
| ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector get_derivative_CPP(const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:3316:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3316 | for(long t=0, g=0, p; t<Xtarget.size(); ++t){
| ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void QR_linear_least_squares(double*, long int, long int, long int, long int, const double*, long int*, double*, double*, double*)':
phylogenetics_cpp_routines.cpp:4513:17: warning: variable 'info' set but not used [-Wunused-but-set-variable]
4513 | long i, info, j, k;
| ^~~~
phylogenetics_cpp_routines.cpp: In member function 'void matrix_exponentiator::initialize(long int, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, const std::vector<std::complex<double> >&, double)':
phylogenetics_cpp_routines.cpp:5864:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<std::complex<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
5864 | for(long r=0; r<eigenvalues.size(); ++r) eigenvalues[r] *= rescaling;
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void apply_approximate_RosenbrockEuler_exponential(long int, long int, const std::vector<double>&, const double&, const std::vector<double>&, const long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:5944:19: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
5944 | for(k=0; k<Y.size(); ++k) Y[k] = scaling*X[k];
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double dot_product(const dvector&, const dvector&)':
phylogenetics_cpp_routines.cpp:5976:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
5976 | for(long i=0; i<X.size(); ++i) S += X[i]*Y[i];
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void refine_piecewise_polynomial(long int, long int, const double*, const double*, bool, const dvector&, dvector&)':
phylogenetics_cpp_routines.cpp:8889:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
8889 | for(long ng=0, og=0; ng<newTimes.size(); ++ng){
| ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void refine_piecewise_polynomial(long int, const dvector&, const dvector&, bool, const dvector&, dvector&, dvector&)':
phylogenetics_cpp_routines.cpp:8926:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
8926 | for(long ng=0, og=0; ng<newTimes.size(); ++ng){
| ~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List monotonize_series_via_interpolation_CPP(const std::vector<double>&, std::vector<double>, bool, bool)':
phylogenetics_cpp_routines.cpp:9970:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
9970 | for(long k=0; k<invalids.size(); ++k){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9996:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
9996 | for(long k=0; k<invalids.size(); ++k){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()':
phylogenetics_cpp_routines.cpp:10958:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
10958 | for(long t=0; t<times.size(); ++t){
| ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void get_cumulative_edge_lengths_per_node(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:12686:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12686 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void get_clade_ages(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const tree_context&, dvector&)':
phylogenetics_cpp_routines.cpp:12808:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12808 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_closest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:12914:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12914 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12945:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12945 | for(long q=0; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_farthest_tip_per_clade_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:13033:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13033 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13064:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13064 | for(long q=1; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13092:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13092 | for(long q=0; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_farthest_tips_per_edge_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:13154:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13154 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13184:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13184 | for(long q=0; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:13276:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13276 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13296:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13296 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector get_distances_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:13407:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13407 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13427:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13427 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List count_clades_at_regular_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int, double, double, bool, long int, bool)':
phylogenetics_cpp_routines.cpp:13620:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13620 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::IntegerVector count_clades_at_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, long int)':
phylogenetics_cpp_routines.cpp:13721:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13721 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_speciation_extinction_events_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:13878:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13878 | for(long q=0; q<queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13902:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13902 | for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13903:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
13903 | for(long c=0; c<omit_clades.size(); ++c) include_clade[omit_clades[c]] = false;
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void get_relative_evolutionary_divergences(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:14048:45: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14048 | for(long q=1, clade, pnode, cnode; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double get_gamma_statistic_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:14304:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14304 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::IntegerVector extract_tip_neighborhood_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int)':
phylogenetics_cpp_routines.cpp:14469:16: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14469 | while(k<clade_queue.size()){
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::IntegerVector extract_deep_frame_CPP(long int, long int, long int, const std::vector<long int>&, long int)':
phylogenetics_cpp_routines.cpp:14526:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14526 | while(queue_pointer<clades.size()){
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14543:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14543 | for(long c=0, clade; c<clades.size(); ++c){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector get_all_distances_to_tip_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, long int)':
phylogenetics_cpp_routines.cpp:14588:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14588 | for(long q=0; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_subtree_with_specific_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:15147:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15147 | for(long c=0; c<clades_to_keep.size(); ++c){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15164:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15164 | for(long q=0; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'long int find_root_for_monophyletic_clade_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)':
phylogenetics_cpp_routines.cpp:15988:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15988 | for(long t=0; t<target_tips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16011:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16011 | for(long q=1, cnode, pnode; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)':
phylogenetics_cpp_routines.cpp:16118:29: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16118 | for(long t=0, tip; t<target_tips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16132:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16132 | for(long q=1; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16167:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16167 | for(long q=1; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List trim_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double)':
phylogenetics_cpp_routines.cpp:16434:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16434 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List split_tree_at_height_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double)':
phylogenetics_cpp_routines.cpp:16544:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16544 | for(long q=0; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List merge_nodes_to_multifurcations_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, bool)':
phylogenetics_cpp_routines.cpp:16884:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16884 | for(long n=0, node; n<nodes_to_merge.size(); ++n){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16894:49: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16894 | for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16958:89: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
16958 | for(long q=0, clade, node, absorbing_ancestor, parent, child, e, edge, inedge; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List shift_clade_times_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:17055:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17055 | for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17078:56: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17078 | for(long q=1, clade, node, inedge, e; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17112:47: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17112 | for(long q=1, clade, inedge; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void assign_clades_to_taxa(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:17448:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17448 | for(long q=0, clade; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List place_tips_taxonomically_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, bool)':
phylogenetics_cpp_routines.cpp:17907:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17907 | for(long f=0; f<fits.size(); ++f){
| ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17908:66: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
17908 | if(clade_taxonomies_split[fits[f]].size()==max_precision) precise_fits.push_back(fits[f]);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List tree_from_placements_CPP(long int, long int, long int, std::vector<long int>, std::vector<double>, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:17944:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
17944 | for(long i=0; i<tree_edge.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List congruify_trees_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:18142:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18142 | for(long m=0, Tnode, Rnode; m<mapped_Tnodes.size(); ++m){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_Robinson_Foulds_distance_CPP(long int, long int, long int, const std::vector<long int>&, long int, long int, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:18372:60: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18372 | for(long fb=0, fa=-1, f; fb<membershipsB[nodeB].size(); ++fb){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'std::vector<double> relative_to_absolute_node_ages_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:18428:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18428 | for(long q=1, clade, node, pnode; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'std::vector<double> propagate_min_ages_upstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:18452:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18452 | for(long a=0; a<anchor_nodes.size(); ++a){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'std::vector<double> propagate_max_ages_downstream_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:18481:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18481 | for(long a=0; a<anchor_nodes.size(); ++a){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18486:44: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18486 | for(long q=0, clade, node, pnode; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_phylogram_geometry_CPP(long int, long int, long int, std::vector<long int>, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:18548:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18548 | for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18565:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18565 | for(long q=0, clade, node; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_radial_tree_geometry_CPP(long int, long int, long int, std::vector<long int>, const std::vector<double>&, double, bool, double)':
phylogenetics_cpp_routines.cpp:18631:50: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18631 | for(long q=0, clade, node, edge, child; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18673:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
18673 | for(long q=1, clade, parent; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void aux_get_trait_depth_consenTRAIT(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, bool, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, double&, double&, double&, double&, long int&, std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:19288:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
19288 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void aux_get_discrete_trait_depths(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<double>&, double, std::vector<long int>&, double&, double&, double&, double&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:19601:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
19601 | for(long q=0, dominant_state; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List get_mrca_defining_tips_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:20650:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20650 | for(long q=0, parent; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::IntegerVector get_pairwise_ancestries_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:20721:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20721 | for(long fc=0; fc<focal_clades.size(); ++fc){
| ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20727:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20727 | for(long fc=0; fc<focal_clades.size(); ++fc){
| ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::IntegerVector get_most_recent_common_ancestors_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:20855:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20855 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20874:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20874 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool is_monophyletic_tip_set_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<long int>&)':
phylogenetics_cpp_routines.cpp:21010:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21010 | for(long t=0; t<focal_tips.size(); ++t) tip_is_focal[focal_tips[t]] = true;
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List WMPR_ASR_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<double>&, double, bool, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:21240:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21240 | for(long q=0; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List ASR_with_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const std::vector<double>&, const std::string&, const std::vector<double>&, bool, bool, double, double, long int, bool)':
phylogenetics_cpp_routines.cpp:21602:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21602 | for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21643:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
21643 | for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List apply_fixed_rate_Markov_model_to_missing_clades_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, long int, Rcpp::LogicalVector, std::vector<double>, bool)':
phylogenetics_cpp_routines.cpp:22053:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22053 | for(long q=0, node, clade; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector apply_attributes_to_descendants_CPP(long int, long int, long int, long int, const std::vector<long int>&, std::vector<long int>, std::vector<double>)':
phylogenetics_cpp_routines.cpp:22111:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22111 | for(long q=0, node, clade; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List ASR_via_squared_change_parsimony_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)':
phylogenetics_cpp_routines.cpp:22285:42: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22285 | for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List ASR_via_independent_contrasts_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, bool)':
phylogenetics_cpp_routines.cpp:22546:30: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22546 | if(node_states.size()>Nnodes) node_states.resize(Nnodes);
| ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22547:39: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22547 | if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22548:29: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
22548 | if(node_CI95s.size()>Nnodes) node_CI95s.resize(Nnodes);
| ~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericVector apply_BM_parsimony_to_missing_clades_CPP(long int, long int, long int, const std::vector<long int>&, Rcpp::LogicalVector, std::vector<double>)':
phylogenetics_cpp_routines.cpp:22589:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22589 | for(long q=0, node, clade; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'double BinaryTraitLogLikelihood::operator()(double) const':
phylogenetics_cpp_routines.cpp:22625:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22625 | for(long i=0, tip; i<only_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'double BinaryTraitLogLikelihood::gradient(double) const':
phylogenetics_cpp_routines.cpp:22653:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22653 | for(long i=0, tip; i<only_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'double BinaryTraitLogLikelihood::Hessian(double) const':
phylogenetics_cpp_routines.cpp:22682:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22682 | for(long i=0, tip; i<only_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'void MuSSEmodelD::registerState(double, const MuSSEstateD&)':
phylogenetics_cpp_routines.cpp:22927:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22927 | for(long s=0; s<trajectory[i].size(); ++s) trajectory[i][s] = max(0.0, min(1.0, trajectory[i][s]));
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'void MuSSEmodelD::registerScaledState(double, const MuSSEstateD&, double)':
phylogenetics_cpp_routines.cpp:22941:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
22941 | for(long s=0; s<trajectory_shape[i].size(); ++s) trajectory_shape[i][s] = max(0.0, trajectory_shape[i][s]);
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, const MuSSEstateD&) const':
phylogenetics_cpp_routines.cpp:23033:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23033 | for(long i=0; i<candidate_state.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'bool MuSSEmodelD::checkShouldRefineTimeStep(double, const MuSSEstateD&, double, double, const MuSSEstateD&, double) const':
phylogenetics_cpp_routines.cpp:23046:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23046 | for(long i=0; i<candidateY.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23051:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23051 | for(long i=0; i<candidateY.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double&, MuSSEstateD&, bool) const':
phylogenetics_cpp_routines.cpp:23071:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23071 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23093:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23093 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'CrossedBoundary MuSSEmodelD::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateD&, double, double&, MuSSEstateD&, double&, bool) const':
phylogenetics_cpp_routines.cpp:23116:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23116 | for(long s=0; s<candidateY.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23140:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23140 | for(long s=0; s<candidateY.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'bool MuSSEmodelE::checkShouldRefineTimeStep(double, const MuSSEstateE&, double, const MuSSEstateE&) const':
phylogenetics_cpp_routines.cpp:23323:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23323 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'double MuSSEmodelE::getRelativeChange(const MuSSEstateE&, const MuSSEstateE&) const':
phylogenetics_cpp_routines.cpp:23336:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23336 | for(long s=0; s<stateA.size(); ++s){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'CrossedBoundary MuSSEmodelE::checkCrossedDomainBoundaryAndFix(double, const MuSSEstateE&, double&, MuSSEstateE&, bool) const':
phylogenetics_cpp_routines.cpp:23353:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23353 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23375:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23375 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool get_MuSSE_flow(long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, double, double, double, double, bool, std::vector<std::__cxx11::basic_string<char> >&, std::string&, double&, long int&, MuSSEmodelE&, MuSSEmodelD&, std::vector<LinearInterpolationFunctor<std::vector<double> > >&, std::vector<LinearInterpolationFunctor<double> >&)':
phylogenetics_cpp_routines.cpp:23624:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
23624 | for(long a=0; a<ages.size(); ++a){
| ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_deterministic_HBD_model_CPP(double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, std::vector<double>, const std::vector<double>&, double, double, double, double, long int, double, bool)':
phylogenetics_cpp_routines.cpp:24449:40: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
24449 | for(long i=0; i<lambdas.size(); ++i) coarse_mus[i] = lambdas[i] * mu_over_lambda[i];
| ~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_fixed_rates_Markov_model_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:26705:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26705 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:26785:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26785 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_reflected_Ornstein_Uhlenbeck_on_tree_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:26867:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26867 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_scalar_Brownian_motion_model_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:26938:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
26938 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_multivariate_Brownian_motion_model_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:27018:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27018 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_neutral_gene_evolution_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, double, bool, bool, bool, long int)':
phylogenetics_cpp_routines.cpp:27110:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27110 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void aux_finalize_generated_random_tree(double, bool, bool, bool, const dvector&, const dvector&, const dvector&, long int&, long int&, long int&, long int&, double&, lvector&, dvector&, lvector&, lvector&, lvector&, dvector&, dvector&)':
phylogenetics_cpp_routines.cpp:27222:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27222 | for(long i=0; i<sampled_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27225:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27225 | for(long i=0; i<sampled_node_clades.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27231:53: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
27231 | if(only_sampled_tips && (sampled_tips.size()<Ntips)){
| ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:27268:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27268 | for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27274:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27274 | for(long i=0; i<sampled_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27277:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27277 | for(long i=0; i<sampled_node_clades.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_CPP(long int, long int, double, double, double, double, double, double, double, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, long int, bool, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:27362:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
27362 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp:27362:133: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27362 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_extant_tips<=0) || extant_tips.size()<max_extant_tips) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_HBDS_CPP(long int, long int, long int, long int, long int, double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, double, bool, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:27575:100: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27575 | while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27575:167: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27575 | while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27575:235: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
27575 | while(((max_tips<=0) || (Ntips<max_tips)) && ((max_sampled_tips<=0) || (sampled_tips.size()<max_sampled_tips)) && ((max_extant_tips<=0) || (extant_tips.size()<max_extant_tips)) && ((max_extinct_tips<=0) || (extinct_tips.size()<max_extinct_tips))){
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27759:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27759 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27766:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27766 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27773:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
27773 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_BM_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:28427:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
28427 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_OU_rates_CPP(long int, double, double, double, double, double, double, double, double, double, double, double, double, double, double, bool, long int, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:28621:75: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const long int' [-Wsign-compare]
28621 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)<max_tips)) && ((max_time<=0) || (time+1/total_rate<max_time)) && ((max_time_since_equilibrium<0) || (time-equilibrium_time+1/total_rate<max_time_since_equilibrium))){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_Mk_rates_CPP(long int, long int, long int, double, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, bool, bool, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:29082:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29082 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29088:34: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29088 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29093:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29093 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_random_tree_tdSSE_CPP(long int, double, long int, long int, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, bool, long int, bool, bool, bool, bool)':
phylogenetics_cpp_routines.cpp:29761:38: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29761 | for(long stip=0; stip<extant_tips[state].size(); ++stip){
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void aux_coalesce_genes(const std::vector<double>&, double, EdgeLengthUnit, double, double, long int, std::vector<long int>&, long int&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:30005:44: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
30005 | if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30007:42: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
30007 | if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30016:41: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30016 | for(long orphan=0, clade; orphan<orphan_clades.size(); ++orphan){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void add_edges_from_branching_heights(const std::vector<double>&, std::vector<long int>&, long int&, std::vector<double>&, std::vector<long int>&, std::vector<double>&)':
phylogenetics_cpp_routines.cpp:30069:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
30069 | if(clade_heights.size()<=next_clade) clade_heights.resize(next_clade+1);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool generate_gene_tree_in_species_tree_MSC(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, long int&, long int&, long int&, long int&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, std::vector<long int>&, std::vector<double>&, std::string&)':
phylogenetics_cpp_routines.cpp:30119:64: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30119 | const bool got_allele_counts = (allele_counts.size()==NStips);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30120:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30120 | const bool got_population_sizes = (population_sizes.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30121:67: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30121 | const bool got_generation_times = (generation_times.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30122:65: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30122 | const bool got_mutation_rates = (mutation_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30145:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30145 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30162:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30162 | for(allele=0; allele<gene_orphans[stip].size(); ++allele){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30247:50: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30247 | for(long orphan=0; orphan<gene_orphans[context.root].size()-1; ++orphan){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List generate_gene_tree_in_species_tree_MSC_HGT_DL_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<long int>&, const std::string&, long int, bool, bool, long int, bool, bool, double, double, bool)':
phylogenetics_cpp_routines.cpp:30401:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30401 | const bool got_population_sizes = (population_sizes.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30402:83: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30402 | const bool got_generation_times = (generation_times.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30403:81: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30403 | const bool got_mutation_rates = (mutation_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30404:80: warning: comparison of integer expressions of different signedness: 'std::vector<long int>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30404 | const bool got_allele_counts = (allele_counts.size()==NStips);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30405:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30405 | const bool got_HGT_rates = (HGT_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30406:84: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30406 | const bool got_duplication_rates = (duplication_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30407:85: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
30407 | const bool got_loss_rates = (loss_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30428:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30428 | for(long q=0; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30435:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30435 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30538:66: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30538 | for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30564:39: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
30564 | for(long l=0, locus; l<clade_current_loci[mclade].size(); ++l){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, double, double, double, dvector&, dvector&)':
phylogenetics_cpp_routines.cpp:31376:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31376 | for(long q=0, parent, child, e, edge; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List simulate_SBM_trajectory_CPP(const std::vector<double>&, double, double, double, double)':
phylogenetics_cpp_routines.cpp:31489:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31489 | for(long t=1; t<times.size(); ++t){
| ~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function 'double Spherical_Brownian_Motion_LL::operator()(double) const':
phylogenetics_cpp_routines.cpp:31962:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31962 | for(long p=0; p<time_steps.size(); ++p){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List SBM_LLs_of_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, long int)':
phylogenetics_cpp_routines.cpp:32004:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32004 | for(long d=0; d<diffusivities.size(); ++d){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List SBM_LLs_of_sampled_transitions_CPP(double, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, long int, long int, const std::vector<double>&, double, long int)':
phylogenetics_cpp_routines.cpp:32042:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32042 | for(long d=0; d<diffusivities.size(); ++d){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double SBM_planar_diffusivity_estimate(const dvector&, const dvector&, const std::vector<char>&)':
phylogenetics_cpp_routines.cpp:32204:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32204 | for(long p=0; p<time_steps.size(); ++p){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List read_distances_list_CPP(const std::string&, const std::string&, const std::string&, bool, long int, double, double, long int, long int, const std::string&)':
phylogenetics_cpp_routines.cpp:32752:32: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
32752 | if(parts.size()<=distances_column){
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32780:56: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
32780 | if((max_Nedges>=0) && (distances.size()>=max_Nedges)) break;
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool char_in_string(char, const std::string&, bool)':
phylogenetics_cpp_routines.cpp:32830:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32830 | for(long i=0; i<haystack.size(); ++i){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32835:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32835 | for(long i=0; i<haystack.size(); ++i){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List place_paired_end_reads_CPP(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, long int, long int)':
phylogenetics_cpp_routines.cpp:32915:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
32915 | for(long s=0; s<forward_reads.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void multiply_array_with_scalar(ARRAY_TYPE&, double) [with ARRAY_TYPE = std::vector<double>]':
phylogenetics_cpp_routines.cpp:5355:29: required from here
phylogenetics_cpp_routines.cpp:590:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
590 | for(long i=0; i<X.size(); ++i) X[i] *= scalar;
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'double get_norm_L2_of_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]':
phylogenetics_cpp_routines.cpp:5550:34: required from here
phylogenetics_cpp_routines.cpp:4956:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
4956 | for(long i=0; i<X.size(); ++i) S += SQR(X[i]);
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'double get_norm_L2_of_inverted_vector(const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]':
phylogenetics_cpp_routines.cpp:5550:77: required from here
phylogenetics_cpp_routines.cpp:4964:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
4964 | for(long i=0; i<X.size(); ++i) S += SQR(1.0/X[i]);
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'TYPE vector_sum(const std::vector<T>&) [with TYPE = long int]':
phylogenetics_cpp_routines.cpp:8763:48: required from here
phylogenetics_cpp_routines.cpp:702:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
702 | for(long i=0; i<values.size(); ++i) S += values[i];
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:8985:25: required from here
phylogenetics_cpp_routines.cpp:4806:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4806 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4807:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4807 | for(j=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4822:87: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
4822 | while((errorInLinearSolution(matrix, N, b, x) > maxError) && (impCount<maxImprovements)){
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'bool fitLeastSquares_affine_real_scalar(const std::vector<T>&, const std::vector<T>&, long int, long int, double, bool, bool, REAL_TYPE&, REAL_TYPE&, REAL_TYPE&, long int&) [with REAL_TYPE = double]':
phylogenetics_cpp_routines.cpp:9355:40: required from here
phylogenetics_cpp_routines.cpp:9217:21: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
9217 | if((x.size()<=end) || (y.size()<=end)) return false;
| ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9217:40: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'const long int' [-Wsign-compare]
9217 | if((x.size()<=end) || (y.size()<=end)) return false;
| ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T>& operator*=(std::vector<T>&, double) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:9789:24: required from here
phylogenetics_cpp_routines.cpp:3479:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3479 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void get_tree_traversal_root_to_tips(long int, long int, long int, long int, const ARRAY_TYPE&, bool, bool, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, std::vector<long int>&, bool, const std::string&) [with ARRAY_TYPE = std::vector<long int>; std::string = std::__cxx11::basic_string<char>]':
phylogenetics_cpp_routines.cpp:12172:33: required from here
phylogenetics_cpp_routines.cpp:12145:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12145 | while(queue_pointer<queue.size()){
| ~~~~~~~~~~~~~^~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'TYPE vector_max(const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:12818:36: required from here
phylogenetics_cpp_routines.cpp:780:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
780 | for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void qsortIndices(const std::vector<T>&, std::vector<long int>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:13887:14: required from here
phylogenetics_cpp_routines.cpp:1081:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
1081 | for(long n=0; n<sortedIndices.size(); ++n) sortedIndices[n] = n;
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'TYPE vector_max(const std::vector<T>&) [with TYPE = long int]':
phylogenetics_cpp_routines.cpp:14186:33: required from here
phylogenetics_cpp_routines.cpp:780:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
780 | for(long i=0; i<values.size(); ++i) A = (A<values[i] ? values[i] : A);
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void sort_tree_edges_root_to_tips(long int, long int, long int, bool, bool, const ARRAY_TYPE&, std::vector<long int>&) [with ARRAY_TYPE = std::vector<long int>]':
phylogenetics_cpp_routines.cpp:14839:30: required from here
phylogenetics_cpp_routines.cpp:14811:36: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14811 | while(queue_pointer<scratch_queue.size()){
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void get_tree_with_collapsed_monofurcations(long int, long int, long int, long int, bool, const lvector&, const ARRAY_INT&, const ARRAY_DOUBLE&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]':
phylogenetics_cpp_routines.cpp:15075:40: required from here
phylogenetics_cpp_routines.cpp:14971:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14971 | for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14985:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
14985 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15008:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15008 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void get_subtree_with_specific_tips(long int, long int, long int, const ARRAY_INT&, const ARRAY_DOUBLE&, const ARRAY_INT&, bool, bool, const lvector&, std::vector<long int>&, std::vector<double>&, std::vector<long int>&, long int&, long int&, long int&, long int&, long int&, double&) [with ARRAY_INT = std::vector<long int>; ARRAY_DOUBLE = std::vector<double>; lvector = std::vector<long int>]':
phylogenetics_cpp_routines.cpp:15687:32: required from here
phylogenetics_cpp_routines.cpp:15545:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15545 | for(long t=0; t<tips_to_keep.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15548:26: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15548 | for(long fn=0; fn<force_keep_nodes.size(); ++fn){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15621:37: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
15621 | for(long fn=0, new_clade; fn<force_keep_nodes.size(); ++fn){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void get_distances_from_root(long int, long int, long int, const ARRAY_TYPE_INT&, const ARRAY_TYPE_D&, const tree_context&, dvector&) [with ARRAY_TYPE_INT = std::vector<long int>; ARRAY_TYPE_D = std::vector<double>; dvector = std::vector<double>]':
phylogenetics_cpp_routines.cpp:16914:26: required from here
phylogenetics_cpp_routines.cpp:12766:31: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
12766 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'long int find_in_ascending_list(const std::vector<T>&, TYPE2, long int) [with TYPE1 = long int; TYPE2 = long int]':
phylogenetics_cpp_routines.cpp:18374:33: required from here
phylogenetics_cpp_routines.cpp:496:28: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
496 | for(long n=start; n<haystack.size(); ++n){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator/(std::vector<T>, double) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:22916:19: required from here
phylogenetics_cpp_routines.cpp:3561:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3561 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator*(std::vector<T>, double) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:22979:27: required from here
phylogenetics_cpp_routines.cpp:3461:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3461 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator-(std::vector<T>, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:22979:27: required from here
phylogenetics_cpp_routines.cpp:3515:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3515 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator+(std::vector<T>, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23088:66: required from here
phylogenetics_cpp_routines.cpp:3488:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3488 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'bool contains_nan(const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23152:22: required from here
phylogenetics_cpp_routines.cpp:875:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
875 | for(long i=0; i<values.size(); ++i){
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T>& operator*=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23512:32: required from here
phylogenetics_cpp_routines.cpp:3452:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3452 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'TYPE vector_sum(const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23533:30: required from here
phylogenetics_cpp_routines.cpp:702:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
702 | for(long i=0; i<values.size(); ++i) S += values[i];
| ~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T>& operator/=(std::vector<T>&, double) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23534:23: required from here
phylogenetics_cpp_routines.cpp:3570:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3570 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator*(std::vector<T>, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:23542:56: required from here
phylogenetics_cpp_routines.cpp:3443:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3443 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'TYPE scalar_product(const std::vector<T>&, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:24052:38: required from here
phylogenetics_cpp_routines.cpp:725:24: warning: comparison of integer expressions of different signedness: 'long int' and 'const long long unsigned int' [-Wsign-compare]
725 | for(long i=0; i<min(A.size(),B.size()); ++i) S += A[i] * B[i];
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T>& operator-=(std::vector<T>&, const std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:24451:83: required from here
phylogenetics_cpp_routines.cpp:3533:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3533 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> abs(std::vector<T>) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:25071:48: required from here
phylogenetics_cpp_routines.cpp:3579:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3579 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs() const [with VALUE_TYPE = double]':
phylogenetics_cpp_routines.cpp:25563:26: required from here
phylogenetics_cpp_routines.cpp:2675:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
2675 | for(long i=0; i<X.size()-1; ++i){
| ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'VALUE_TYPE PiecewisePolynomial<VALUE_TYPE>::getMaxAbs(double, double) const [with VALUE_TYPE = double]':
phylogenetics_cpp_routines.cpp:25568:26: required from here
phylogenetics_cpp_routines.cpp:2686:32: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
2686 | for(long i=0; i<X.size()-1; ++i){
| ~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T>& operator+=(std::vector<T>&, const TYPE&) [with TYPE = long int]':
phylogenetics_cpp_routines.cpp:25991:20: required from here
phylogenetics_cpp_routines.cpp:3506:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3506 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator-(std::vector<T>, const TYPE&) [with TYPE = long int]':
phylogenetics_cpp_routines.cpp:27234:52: required from here
phylogenetics_cpp_routines.cpp:3524:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3524 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void remove_item_from_vector(std::vector<T>&, long int) [with TYPE = long int]':
phylogenetics_cpp_routines.cpp:27695:27: required from here
phylogenetics_cpp_routines.cpp:928:17: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
928 | if(index==list.size()-1){
| ~~~~~^~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void simulate_SBM_on_tree(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, double, const DFUNCTOR&, double, double, dvector&, dvector&) [with DFUNCTOR = PiecewisePolynomial<double>; dvector = std::vector<double>]':
phylogenetics_cpp_routines.cpp:31522:22: required from here
phylogenetics_cpp_routines.cpp:31424:48: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<long int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
31424 | for(long q=0, parent, child, e, edge; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:4813:21: required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8985:25: required from here
phylogenetics_cpp_routines.cpp:4661:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4661 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4662:34: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4662 | for(j=0, big=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4671:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4671 | for(j=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4678:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4678 | for(i=j; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4688:35: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4688 | for(k=0; k<N; ++k){
| ~^~
phylogenetics_cpp_routines.cpp:4700:22: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4700 | if(j < N-1){
| ~~^~~~~
phylogenetics_cpp_routines.cpp:4702:37: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4702 | for(i=j+1; i<N; ++i){ matrix[i*N+j] *= dummyT; }
| ~^~
phylogenetics_cpp_routines.cpp: In instantiation of 'void LUSolveLinearSystem(const TYPE*, long unsigned int, const long unsigned int*, TYPE*) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:4818:21: required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8985:25: required from here
phylogenetics_cpp_routines.cpp:4723:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4723 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4736:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4736 | for(j=i+1; j<N; ++j){ sum -= LUmatrix[i*N+j]*b[j]; }
| ~^~
phylogenetics_cpp_routines.cpp: In instantiation of 'void LUImproveSolutionToLinearSystem(const TYPE*, const TYPE*, long unsigned int, const long unsigned int*, const TYPE*, TYPE*) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:4823:35: required from 'bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]'
phylogenetics_cpp_routines.cpp:8985:25: required from here
phylogenetics_cpp_routines.cpp:4774:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4774 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4776:27: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4776 | for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
| ~^~
phylogenetics_cpp_routines.cpp:4780:19: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare]
4780 | for(i=0; i<N; ++i){ x[i] -= r[i]; }
| ~^~
phylogenetics_cpp_routines.cpp: In instantiation of 'long int find_first_occurrence(const std::vector<T>&, TYPE2) [with TYPE1 = double; TYPE2 = double]':
phylogenetics_cpp_routines.cpp:5429:27: required from 'long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]'
phylogenetics_cpp_routines.cpp:21544:94: required from here
phylogenetics_cpp_routines.cpp:478:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
478 | for(long n=0; n<haystack.size(); ++n){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'std::vector<T> operator*(double, std::vector<T>) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:10223:64: required from 'LinearInterpolationFunctor<VALUE_TYPE>::LinearInterpolationFunctor(const std::vector<double>&, const std::vector<T>&, bool, const VALUE_TYPE&, const VALUE_TYPE&, bool, double) [with VALUE_TYPE = std::vector<double>]'
phylogenetics_cpp_routines.cpp:23485:141: required from here
phylogenetics_cpp_routines.cpp:3470:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
3470 | for(long i=0; i<x.size(); ++i){
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In instantiation of 'void linear_combination(double, const std::vector<T>&, double, const std::vector<T>&, std::vector<T>&) [with TYPE = double]':
phylogenetics_cpp_routines.cpp:7487:21: required from 'bool RungeKutta2(double, double, double, MODEL&, double, double, double, double, long int, double, const PROGRESS_REPORTER&, double, std::string&) [with COORDINATE = std::vector<double>; MODEL = MuSSEmodelE; PROGRESS_REPORTER = ProgressReporter; std::string = std::__cxx11::basic_string<char>]'
phylogenetics_cpp_routines.cpp:23587:9: required from here
phylogenetics_cpp_routines.cpp:441:24: warning: comparison of integer expressions of different signedness: 'long int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
441 | for(long i=0; i<X.size(); ++i) result[i] = a*X[i] + b*Y[i];
| ~^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'double first_Wasserstein_distance_CPP(const std::vector<double>&, const std::vector<double>&)':
phylogenetics_cpp_routines.cpp:1332:25: warning: 't1' may be used uninitialized [-Wmaybe-uninitialized]
1332 | W += (t2-t1) * abs(CDFY-CDFX);
| ~~~^~~~
phylogenetics_cpp_routines.cpp:1316:32: note: 't1' was declared here
1316 | double CDFX=0, CDFY=0, t1, t2;
| ^~
phylogenetics_cpp_routines.cpp: In function 'double legendre_polynomial(long int, double)':
phylogenetics_cpp_routines.cpp:31086:16: warning: 'Pn' may be used uninitialized [-Wmaybe-uninitialized]
31086 | return Pn;
| ^~
phylogenetics_cpp_routines.cpp:31080:16: note: 'Pn' was declared here
31080 | double Pn;
| ^~
phylogenetics_cpp_routines.cpp: In function 'double solve_polynomial_via_bisection(const double*, long int, double, double, double, double, double, double, long int)':
phylogenetics_cpp_routines.cpp:2289:16: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
2289 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2235:36: note: 'c' was declared here
2235 | double a = Xmin, b = Xmax, c;
| ^
phylogenetics_cpp_routines.cpp: In function 'double solve_piecewise_polynomial_bisection(const dvector&, const dvector&, long int, bool, double, double, double, bool, double, double, long int, long int&, long int&)':
phylogenetics_cpp_routines.cpp:2372:16: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
2372 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2310:36: note: 'c' was declared here
2310 | double a = Xmin, b = Xmax, c;
| ^
phylogenetics_cpp_routines.cpp: In function 'double solve_piecewise_polynomial_sum_bisection(const dvector&, const std::vector<std::vector<double> >&, const lvector&, bool, const dvector&, double, double, double, bool, double, double, long int, long int&, long int&)':
phylogenetics_cpp_routines.cpp:2469:16: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
2469 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2402:36: note: 'c' was declared here
2402 | double a = Xmin, b = Xmax, c;
| ^
phylogenetics_cpp_routines.cpp: In function 'bool get_dominant_eigenvalue(long int, const dvector&, long int, double, dvector&, double&)':
phylogenetics_cpp_routines.cpp:6060:37: warning: 'best_error' may be used uninitialized [-Wmaybe-uninitialized]
6060 | return (best_error<tolerance);
| ^
phylogenetics_cpp_routines.cpp:5990:43: note: 'best_error' was declared here
5990 | double XAX, error, best_lambda=0, best_error=INFTY_D;
| ^~~~~~~~~~
In file included from d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\cmath:49,
from phylogenetics_cpp_routines.cpp:31:
In function 'constexpr double std::abs(double)',
inlined from 'VALUE_TYPE polynomial_bound_abs(long int, const VALUE_TYPE*, double, double) [with VALUE_TYPE = double]' at phylogenetics_cpp_routines.cpp:1767:17:
d:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\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:1765:28: note: 'Yvertex' was declared here
1765 | 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:4687:17: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
4687 | if(j != imax){
| ^~
phylogenetics_cpp_routines.cpp:4655:16: note: 'imax' was declared here
4655 | long i,imax,j,k;
| ^~~~
phylogenetics_cpp_routines.cpp: In member function 'void TreeSpeciationExtinctionModel::get_coalescent_trajectory(double, double, std::vector<TreeStateHistory>&) const':
phylogenetics_cpp_routines.cpp:10947:96: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
10947 | coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10924:59: note: 'coalescent_diversity_at_resolution_age' was declared here
10924 | double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'bool RungeKutta2(double, double, double, MODEL&, long int, long int, double, const PROGRESS_REPORTER&, double, std::string&) [with COORDINATE = TreeStateHistory; MODEL = TreeSpeciationExtinctionModel; PROGRESS_REPORTER = ProgressReporter]':
phylogenetics_cpp_routines.cpp:7216:20: warning: 'k1.TreeStateHistory::Pmissing' may be used uninitialized [-Wmaybe-uninitialized]
7216 | COORDINATE k1, k2, kConsensus;
| ^~
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:26704:27: warning: 'parent' may be used uninitialized [-Wmaybe-uninitialized]
26704 | long clade, edge, parent, parent_state, state=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:20221:49: warning: 'tip' may be used uninitialized [-Wmaybe-uninitialized]
20221 | tip_included[tip] = true;
| ^
phylogenetics_cpp_routines.cpp:20084:14: note: 'tip' was declared here
20084 | long tip, clade, count_tips_remaining;
| ^~~
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:20181:41:
phylogenetics_cpp_routines.cpp:3603:72: warning: 'count_tips_remaining' may be used uninitialized [-Wmaybe-uninitialized]
3603 | 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:20084:26: note: 'count_tips_remaining' was declared here
20084 | 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:11168:86: warning: 'Pmissing_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11168 | const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11143:24: note: 'Pmissing_at_resolution_age' was declared here
11143 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11176:88: warning: 'coalescent_diversity_at_resolution_age' may be used uninitialized [-Wmaybe-uninitialized]
11176 | Pmissing = 1.0 - coalescent_diversity_at_resolution_age/total_diversities[t]; // effective Pmissing, based on coalescent and total diversity after collapsing and rarefaction
phylogenetics_cpp_routines.cpp:11143:87: note: 'coalescent_diversity_at_resolution_age' was declared here
11143 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::List HBD_PDR_loglikelihood_CPP(const std::vector<double>&, double, double, const std::vector<double>&, const std::vector<double>&, long int, const std::string&, double, double, std::vector<double>, long int)':
phylogenetics_cpp_routines.cpp:25332:102: warning: 'Zdegree' may be used uninitialized [-Wmaybe-uninitialized]
25332 | branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
| ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25298:14: note: 'Zdegree' was declared here
25298 | long Zdegree, EZdegree, Wdegree;
| ^~~~~~~
phylogenetics_cpp_routines.cpp:25333:102: warning: 'Wdegree' may be used uninitialized [-Wmaybe-uninitialized]
25333 | branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
| ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25298:33: note: 'Wdegree' was declared here
25298 | long Zdegree, EZdegree, Wdegree;
| ^~~~~~~
phylogenetics_cpp_routines.cpp: In function '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:26054:110: warning: 'logPhi_degree' may be used uninitialized [-Wmaybe-uninitialized]
26054 | CSA_logPhi = polynomial_value(logPhi_degree, &logPhi_coeff[k][sg*(logPhi_degree+1)], age-(splines_slideX ? Phi_ages[k][sg] : 0.0));
| ~~~~~~~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25940:42: note: 'logPhi_degree' was declared here
25940 | 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:25505:51: warning: 'W_degree' may be used uninitialized [-Wmaybe-uninitialized]
25505 | const double origin_W = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25433:24: note: 'W_degree' was declared here
25433 | long I_degree, W_degree, NRG;
| ^~~~~~~~
phylogenetics_cpp_routines.cpp: In function 'Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)':
phylogenetics_cpp_routines.cpp:13336:155: warning: 'mrca' may be used uninitialized [-Wmaybe-uninitialized]
13336 | distances(i,j) = distance_from_root_per_clade[cladeA] + distance_from_root_per_clade[cladeB] - 2*distance_from_root_per_clade[mrca];
| ^
phylogenetics_cpp_routines.cpp:13309:30: note: 'mrca' was declared here
13309 | long cladeA, cladeB, mrca;
| ^~~~
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_02_04_01_50_01_15123/RtmpED2USy/R.INSTALL1a28c5e212057/castor/src'
make[1]: Entering directory '/d/temp/2026_02_04_01_50_01_15123/RtmpED2USy/R.INSTALL1a28c5e212057/castor/src'
make[1]: Leaving directory '/d/temp/2026_02_04_01_50_01_15123/RtmpED2USy/R.INSTALL1a28c5e212057/castor/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-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
* MD5 sums
packaged installation of 'castor' as castor_1.8.5.zip
* DONE (castor)