* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘castor’ ...
** this is package ‘castor’ version ‘1.8.4’
** package ‘castor’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-3) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-3) 15.2.0’
make[1]: Entering directory '/tmp/Rtmp76xc7l/R.INSTALL8f0754d3fcec2/castor/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c STMathExpression.cpp -o STMathExpression.o
STMathExpression.cpp:10: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10 | #pragma mark -
STMathExpression.cpp:11: warning: ignoring ‘#pragma mark String’ [-Wunknown-pragmas]
11 | #pragma mark String manipulations
STMathExpression.cpp:12: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12 | #pragma mark
STMathExpression.cpp:65: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
65 | #pragma mark -
STMathExpression.cpp:66: warning: ignoring ‘#pragma mark MathExpression’ [-Wunknown-pragmas]
66 | #pragma mark MathExpression
STMathExpression.cpp:67: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
67 | #pragma mark
STMathExpression.cpp: In static member function ‘static long int MathExpression::splitBinaryOperatorInverseOrder(const std::string&, long int, long int, const std::vector<long int>&)’:
STMathExpression.cpp:256:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
256 | else if(j==string::npos){ if(!STMath_isReal(expression.substr(0,i-1))) return getLeftMostOfPlusMinusOperatorChain(expression,start,i); }
| ~^~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘std::string MathExpression::parseBlock(const std::string&, long int, long int, const std::vector<long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, const std::map<std::__cxx11::basic_string<char>, long int>&, long int, bool)’:
STMathExpression.cpp:313:105: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
313 | if(isWhiteSpace(expression,start,end)) return "Missing "+(start==0 ? "leading expression" : (end==expression.size()-1 ? "trailing expression" : "expression between '"+expression.substr(0,start)+"' and '"+expression.substr(end+1)+"'"));
| ~~~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:359:37: warning: comparison of integer expressions of different signedness: ‘const long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
359 | if((rightMostBracket==string::npos) || (rightMostBracket<start)){
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:463:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
463 | for(long i=0; i<expression.length(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::findRoundBracketPairs(const std::string&, std::vector<long int>&)’:
STMathExpression.cpp:500:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
500 | for(long i=0; i<expression.length(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘void MathExpression::printDebug(std::ostream&) const’:
STMathExpression.cpp:953:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
953 | for(long i=0; i<variableValues.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:957:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
957 | for(long i=0; i<stackValues.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&) const’:
STMathExpression.cpp:981:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
981 | if(variableIDs[i]>=x.size()){ variableValues[i]=0; }
STMathExpression.cpp: In member function ‘double MathExpression::operator()(const std::vector<double>&, long int, ...) const’:
STMathExpression.cpp:1044:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘long unsigned int’ [-Wsign-compare]
1044 | if(variableIDs[i]>=x.size()+numberOfAdditionalVariables){ variableValues[i]=0; }
STMathExpression.cpp:1045:39: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘const long int’} and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1045 | else if(variableIDs[i]<x.size()){ variableValues[i]=x[variableIDs[i]]; }
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariable(const std::string&) const’:
STMathExpression.cpp:1195:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1195 | for(long i=0; i<variableNames.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In member function ‘bool MathExpression::dependsOnVariableWithPrefix(const std::string&) const’:
STMathExpression.cpp:1202:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1202 | for(long i=0; i<variableNames.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp: In static member function ‘static bool MathExpression::isValidName(const std::string&, std::string&)’:
STMathExpression.cpp:1258:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1258 | for(long i=0; i<s.size(); ++i){
| ~^~~~~~~~~
STMathExpression.cpp: In static member function ‘static std::string MathExpression::lowercase(std::string)’:
STMathExpression.cpp:1269:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1269 | for(long n=0; n<s.length(); ++n){ s[n] = tolower(s[n]); }
| ~^~~~~~~~~~~
STMathExpression.cpp: In function ‘Rcpp::List evaluate_univariate_expression_CPP(const std::string&, const std::string&, const std::vector<double>&)’:
STMathExpression.cpp:1378:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1378 | for(long i=0; i<X.size(); ++i){
| ~^~~~~~~~~
STMathExpression.cpp: In instantiation of ‘void MathExpression::printTuple(std::ostream&, const std::vector<T>&) const [with TYPE = long int; std::ostream = std::basic_ostream<char>]’:
STMathExpression.cpp:961:14: required from here
961 | printTuple(stream, stackArguments[i]);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
STMathExpression.cpp:1227:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1227 | for(long i=0; i<components.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phylogenetics_cpp_routines.cpp -o phylogenetics_cpp_routines.o
phylogenetics_cpp_routines.cpp:153: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
153 | #pragma mark -
phylogenetics_cpp_routines.cpp:154: warning: ignoring ‘#pragma mark Declarations’ [-Wunknown-pragmas]
154 | #pragma mark Declarations
phylogenetics_cpp_routines.cpp:155: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
155 | #pragma mark
phylogenetics_cpp_routines.cpp:167: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
167 | #pragma mark -
phylogenetics_cpp_routines.cpp:168: warning: ignoring ‘#pragma mark Functions’ [-Wunknown-pragmas]
168 | #pragma mark Functions for debugging
phylogenetics_cpp_routines.cpp:169: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
169 | #pragma mark
phylogenetics_cpp_routines.cpp:242: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
242 | #pragma mark -
phylogenetics_cpp_routines.cpp:243: warning: ignoring ‘#pragma mark Auxiliary’ [-Wunknown-pragmas]
243 | #pragma mark Auxiliary functions
phylogenetics_cpp_routines.cpp:244: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
244 | #pragma mark
phylogenetics_cpp_routines.cpp:1425: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
1425 | #pragma mark -
phylogenetics_cpp_routines.cpp:1426: warning: ignoring ‘#pragma mark Graphs’ [-Wunknown-pragmas]
1426 | #pragma mark Graphs
phylogenetics_cpp_routines.cpp:1427: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
1427 | #pragma mark
phylogenetics_cpp_routines.cpp:1572: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
1572 | #pragma mark -
phylogenetics_cpp_routines.cpp:1573: warning: ignoring ‘#pragma mark Polynomials’ [-Wunknown-pragmas]
1573 | #pragma mark Polynomials
phylogenetics_cpp_routines.cpp:1574: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
1574 | #pragma mark
phylogenetics_cpp_routines.cpp:2911: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
2911 | #pragma mark -
phylogenetics_cpp_routines.cpp:2912: warning: ignoring ‘#pragma mark Integration’ [-Wunknown-pragmas]
2912 | #pragma mark Integration, antiderivatives, derivatives
phylogenetics_cpp_routines.cpp:2913: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
2913 | #pragma mark
phylogenetics_cpp_routines.cpp:3416: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3416 | #pragma mark -
phylogenetics_cpp_routines.cpp:3417: warning: ignoring ‘#pragma mark Vectorized’ [-Wunknown-pragmas]
3417 | #pragma mark Vectorized basic arithmetics
phylogenetics_cpp_routines.cpp:3418: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3418 | #pragma mark
phylogenetics_cpp_routines.cpp:3567: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3567 | #pragma mark -
phylogenetics_cpp_routines.cpp:3568: warning: ignoring ‘#pragma mark Random’ [-Wunknown-pragmas]
3568 | #pragma mark Random numbers
phylogenetics_cpp_routines.cpp:3569: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3569 | #pragma mark
phylogenetics_cpp_routines.cpp:3963: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3963 | #pragma mark -
phylogenetics_cpp_routines.cpp:3964: warning: ignoring ‘#pragma mark Matrix’ [-Wunknown-pragmas]
3964 | #pragma mark Matrix algebra
phylogenetics_cpp_routines.cpp:3965: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
3965 | #pragma mark
phylogenetics_cpp_routines.cpp:7173: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
7173 | #pragma mark -
phylogenetics_cpp_routines.cpp:7174: warning: ignoring ‘#pragma mark Numerical’ [-Wunknown-pragmas]
7174 | #pragma mark Numerical solvers
phylogenetics_cpp_routines.cpp:7175: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
7175 | #pragma mark
phylogenetics_cpp_routines.cpp:8586: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
8586 | #pragma mark -
phylogenetics_cpp_routines.cpp:8587: warning: ignoring ‘#pragma mark Time’ [-Wunknown-pragmas]
8587 | #pragma mark Time series analysis
phylogenetics_cpp_routines.cpp:8588: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
8588 | #pragma mark
phylogenetics_cpp_routines.cpp:9993: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
9993 | #pragma mark -
phylogenetics_cpp_routines.cpp:9994: warning: ignoring ‘#pragma mark Class’ [-Wunknown-pragmas]
9994 | #pragma mark Class: LinearInterpolationFunctor
phylogenetics_cpp_routines.cpp:9995: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
9995 | #pragma mark -
phylogenetics_cpp_routines.cpp:10473: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10473 | #pragma mark -
phylogenetics_cpp_routines.cpp:10474: warning: ignoring ‘#pragma mark Stochastic’ [-Wunknown-pragmas]
10474 | #pragma mark Stochastic processes
phylogenetics_cpp_routines.cpp:10475: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10475 | #pragma mark
phylogenetics_cpp_routines.cpp:10668: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10668 | #pragma mark -
phylogenetics_cpp_routines.cpp:10669: warning: ignoring ‘#pragma mark Deterministic’ [-Wunknown-pragmas]
10669 | #pragma mark Deterministic diversity dynamics
phylogenetics_cpp_routines.cpp:10670: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
10670 | #pragma mark
phylogenetics_cpp_routines.cpp:11769: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11769 | #pragma mark -
phylogenetics_cpp_routines.cpp:11770: warning: ignoring ‘#pragma mark Building’ [-Wunknown-pragmas]
11770 | #pragma mark Building auxiliary data structures
phylogenetics_cpp_routines.cpp:11771: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
11771 | #pragma mark
phylogenetics_cpp_routines.cpp:12457: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12457 | #pragma mark -
phylogenetics_cpp_routines.cpp:12458: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
12458 | #pragma mark Tree statistics
phylogenetics_cpp_routines.cpp:12459: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
12459 | #pragma mark
phylogenetics_cpp_routines.cpp:14574: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14574 | #pragma mark -
phylogenetics_cpp_routines.cpp:14575: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
14575 | #pragma mark Generating & manipulating trees
phylogenetics_cpp_routines.cpp:14576: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
14576 | #pragma mark
phylogenetics_cpp_routines.cpp:17948: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
17948 | #pragma mark -
phylogenetics_cpp_routines.cpp:17949: warning: ignoring ‘#pragma mark Comparing’ [-Wunknown-pragmas]
17949 | #pragma mark Comparing trees
phylogenetics_cpp_routines.cpp:17950: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
17950 | #pragma mark
phylogenetics_cpp_routines.cpp:18368: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18368 | #pragma mark -
phylogenetics_cpp_routines.cpp:18369: warning: ignoring ‘#pragma mark Tree’ [-Wunknown-pragmas]
18369 | #pragma mark Tree dating
phylogenetics_cpp_routines.cpp:18370: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18370 | #pragma mark
phylogenetics_cpp_routines.cpp:18469: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18469 | #pragma mark -
phylogenetics_cpp_routines.cpp:18470: warning: ignoring ‘#pragma mark Plotting’ [-Wunknown-pragmas]
18470 | #pragma mark Plotting trees
phylogenetics_cpp_routines.cpp:18471: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18471 | #pragma mark
phylogenetics_cpp_routines.cpp:18692: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18692 | #pragma mark -
phylogenetics_cpp_routines.cpp:18693: warning: ignoring ‘#pragma mark Writing’ [-Wunknown-pragmas]
18693 | #pragma mark Writing/reading trees
phylogenetics_cpp_routines.cpp:18694: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
18694 | #pragma mark
phylogenetics_cpp_routines.cpp:19183: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19183 | #pragma mark -
phylogenetics_cpp_routines.cpp:19184: warning: ignoring ‘#pragma mark Statistics’ [-Wunknown-pragmas]
19184 | #pragma mark Statistics of trait distribution
phylogenetics_cpp_routines.cpp:19185: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
19185 | #pragma mark
phylogenetics_cpp_routines.cpp:20561: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20561 | #pragma mark -
phylogenetics_cpp_routines.cpp:20562: warning: ignoring ‘#pragma mark Most’ [-Wunknown-pragmas]
20562 | #pragma mark Most recent common ancestors
phylogenetics_cpp_routines.cpp:20563: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
20563 | #pragma mark
phylogenetics_cpp_routines.cpp:21000: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
21000 | #pragma mark -
phylogenetics_cpp_routines.cpp:21001: warning: ignoring ‘#pragma mark Ancestral’ [-Wunknown-pragmas]
21001 | #pragma mark Ancestral state reconstruction
phylogenetics_cpp_routines.cpp:21002: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
21002 | #pragma mark
phylogenetics_cpp_routines.cpp:22707: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22707 | #pragma mark -
phylogenetics_cpp_routines.cpp:22708: warning: ignoring ‘#pragma mark MuSSE’ [-Wunknown-pragmas]
22708 | #pragma mark MuSSE model fitting
phylogenetics_cpp_routines.cpp:22709: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
22709 | #pragma mark
phylogenetics_cpp_routines.cpp:23973: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
23973 | #pragma mark -
phylogenetics_cpp_routines.cpp:23974: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
23974 | #pragma mark Homogenous Birth-Death models
phylogenetics_cpp_routines.cpp:23975: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
23975 | #pragma mark
phylogenetics_cpp_routines.cpp:25431: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25431 | #pragma mark -
phylogenetics_cpp_routines.cpp:25432: warning: ignoring ‘#pragma mark Homogenous’ [-Wunknown-pragmas]
25432 | #pragma mark Homogenous Birth-Death-Sampling model
phylogenetics_cpp_routines.cpp:25433: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
25433 | #pragma mark
phylogenetics_cpp_routines.cpp:26542: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26542 | #pragma mark -
phylogenetics_cpp_routines.cpp:26543: warning: ignoring ‘#pragma mark Simulate’ [-Wunknown-pragmas]
26543 | #pragma mark Simulate models of trait evolution
phylogenetics_cpp_routines.cpp:26544: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
26544 | #pragma mark
phylogenetics_cpp_routines.cpp:27056: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27056 | #pragma mark -
phylogenetics_cpp_routines.cpp:27057: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
27057 | #pragma mark Generating random trees via cladogenic models
phylogenetics_cpp_routines.cpp:27058: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
27058 | #pragma mark
phylogenetics_cpp_routines.cpp:29717: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29717 | #pragma mark -
phylogenetics_cpp_routines.cpp:29718: warning: ignoring ‘#pragma mark Generating’ [-Wunknown-pragmas]
29718 | #pragma mark Generating gene trees
phylogenetics_cpp_routines.cpp:29719: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
29719 | #pragma mark
phylogenetics_cpp_routines.cpp:30963: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
30963 | #pragma mark -
phylogenetics_cpp_routines.cpp:30964: warning: ignoring ‘#pragma mark Spherical’ [-Wunknown-pragmas]
30964 | #pragma mark Spherical Brownian motion
phylogenetics_cpp_routines.cpp:30965: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
30965 | #pragma mark
phylogenetics_cpp_routines.cpp:32497: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32497 | #pragma mark -
phylogenetics_cpp_routines.cpp:32498: warning: ignoring ‘#pragma mark Loading’ [-Wunknown-pragmas]
32498 | #pragma mark Loading files
phylogenetics_cpp_routines.cpp:32499: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32499 | #pragma mark
phylogenetics_cpp_routines.cpp:32683: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32683 | #pragma mark -
phylogenetics_cpp_routines.cpp:32684: warning: ignoring ‘#pragma mark Working’ [-Wunknown-pragmas]
32684 | #pragma mark Working with raw sequences
phylogenetics_cpp_routines.cpp:32685: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas]
32685 | #pragma mark
phylogenetics_cpp_routines.cpp: In function ‘void string_to_ascii(const std::string&, lvector&)’:
phylogenetics_cpp_routines.cpp:251:20: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
251 | 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:343:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
343 | 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:366:46: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
366 | while((max_Nparts<0) || (parts.size()<max_Nparts)){
| ~~~~~~~~~~~~^~~~~~~~~~~
phylogenetics_cpp_routines.cpp:368:23: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
368 | if(pos==string::npos) break;
| ~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:372:43: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
372 | 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:469:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
469 | 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:716:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
716 | 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:731:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
731 | 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:749:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
749 | 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:756:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
756 | 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:785:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
785 | 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:816:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
816 | 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:821:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
821 | 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:828:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
828 | 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:838:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
838 | 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:891:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
891 | 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:911:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
911 | 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:957:33: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long int>, long int>::value_type’ {aka ‘long int’} and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
957 | 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:985:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
985 | 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:1006:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1006 | for(long i=0; i<dense_row.size(); ++i){
| ~^~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘double sum_piecewise_polynomials(const std::vector<std::vector<double> >&, const lvector&, const dvector&, double, long int)’:
phylogenetics_cpp_routines.cpp:1608:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1608 | 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:2829:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2829 | 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:3269:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3269 | 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:3296:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3296 | 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:4493:17: warning: variable ‘info’ set but not used [-Wunused-but-set-variable]
4493 | 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:5844:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::complex<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
5844 | 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:5924:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
5924 | 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:5956:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
5956 | 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:8869:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
8869 | 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:8906:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
8906 | 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:9950:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
9950 | for(long k=0; k<invalids.size(); ++k){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9976:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
9976 | for(long k=0; k<invalids.size(); ++k){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In member function ‘void TreeSpeciationExtinctionModel::calculate_coalescent_diversities()’:
phylogenetics_cpp_routines.cpp:10938:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
10938 | 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:12666:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12666 | 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:12788:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12788 | 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:12894:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12894 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12925:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12925 | 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:13013:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13013 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13044:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13044 | for(long q=1; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13072:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13072 | 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:13134:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13134 | for(long t=0; t<onlyToTips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13164:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13164 | 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:13256:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13256 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13276:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13276 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: 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:13387:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13387 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13407:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13407 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: 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:13600:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13600 | 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:13701:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13701 | 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:13858:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13858 | for(long q=0; q<queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13882:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13882 | for(long c=0; c<only_clades.size(); ++c) include_clade[only_clades[c]] = true;
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:13883:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
13883 | 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:14028:45: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14028 | 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:14284:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14284 | 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:14439:16: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14439 | 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:14496:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14496 | while(queue_pointer<clades.size()){
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14513:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14513 | 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:14558:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14558 | 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:15117:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15117 | for(long c=0; c<clades_to_keep.size(); ++c){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15134:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15134 | 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:15958:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15958 | for(long t=0; t<target_tips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15981:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15981 | 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:16088:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16088 | for(long t=0, tip; t<target_tips.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16102:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16102 | for(long q=1; q<traversal_queue_root2tips.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16137:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16137 | 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:16404:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16404 | 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:16514:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16514 | 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:16854:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16854 | for(long n=0, node; n<nodes_to_merge.size(); ++n){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16864:49: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16864 | for(long n=0, e, pnode, child; n<nodes_to_merge.size(); ++n){
| ~^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16928:89: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
16928 | 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:17025:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17025 | for(long s=0, clade, inedge, node, e; s<clades_to_shift.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17048:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17048 | for(long q=1, clade, node, inedge, e; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17082:47: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17082 | 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:17418:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17418 | 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:17877:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17877 | for(long f=0; f<fits.size(); ++f){
| ~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:17878:66: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
17878 | 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:17914:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
17914 | 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:18112:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18112 | 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:18342:60: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18342 | 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:18398:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18398 | 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:18422:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18422 | 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:18451:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18451 | for(long a=0; a<anchor_nodes.size(); ++a){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18456:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18456 | 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:18518:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18518 | for(long q=1, clade, parent; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18535:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18535 | 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:18601:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18601 | for(long q=0, clade, node, edge, child; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:18643:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
18643 | 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:19258:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19258 | 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:19571:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
19571 | 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:20620:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20620 | 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:20691:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20691 | for(long fc=0; fc<focal_clades.size(); ++fc){
| ~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20697:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20697 | 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:20825:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20825 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20844:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20844 | 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:20980:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
20980 | 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:21210:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21210 | 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:21572:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21572 | for(long n=0; n<posteriors.size(); ++n) posteriors[n] = exp(logposteriors[n]);
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21613:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
21613 | for(long q=0, new_root; q<depth_first_search_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericVector apply_fixed_rate_Markov_model_to_missing_clades_CPP(long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<double>&, double, long int, Rcpp::LogicalVector, std::vector<double>, bool)’:
phylogenetics_cpp_routines.cpp:22014:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22014 | 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:22070:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22070 | 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:22244:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22244 | 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:22505:30: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22505 | if(node_states.size()>Nnodes) node_states.resize(Nnodes);
| ~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22506:39: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22506 | if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:22507:29: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
22507 | 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:22548:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22548 | 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:22583:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22583 | 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:22602:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22602 | 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:22622:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22622 | 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:22824:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22824 | 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:22838:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22838 | 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:22930:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22930 | 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:22943:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22943 | for(long i=0; i<candidateY.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22948:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22948 | 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:22968:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22968 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:22990:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
22990 | 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:23013:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23013 | for(long s=0; s<candidateY.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23037:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23037 | 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:23220:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23220 | 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:23233:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23233 | 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:23250:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23250 | for(long s=0; s<candidate_state.size(); ++s){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23272:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23272 | 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:23521:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
23521 | 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:24346:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
24346 | 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:26602:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26602 | 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:26682:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26682 | 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:26764:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26764 | 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:26835:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26835 | 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:26915:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
26915 | 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:27007:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27007 | 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:27119:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27119 | for(long i=0; i<sampled_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27122:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27122 | for(long i=0; i<sampled_node_clades.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27128:53: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
27128 | if(only_sampled_tips && (sampled_tips.size()<Ntips)){
| ~~~~~~~~~~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:27165:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27165 | for(long new_clade=0; new_clade<pruning_new2old_clade.size(); ++new_clade){
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27171:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27171 | for(long i=0; i<sampled_tips.size(); ++i){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27174:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27174 | 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:27259:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
27259 | 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:27259:133: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27259 | 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:27472:100: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27472 | 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:27472:167: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27472 | 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:27472:235: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
27472 | 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:27656:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27656 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27663:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27663 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:27670:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
27670 | 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:28324:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28324 | 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:28518:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare]
28518 | 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:28979:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28979 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28985:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28985 | for(long nc=0; nc<new2old_clade.size(); ++nc){
| ~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:28990:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
28990 | 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:29658:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29658 | 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:29902:44: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29902 | if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29904:42: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29904 | if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:29913:41: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29913 | 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:29966:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
29966 | 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:30016:64: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30016 | const bool got_allele_counts = (allele_counts.size()==NStips);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30017:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30017 | const bool got_population_sizes = (population_sizes.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30018:67: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30018 | const bool got_generation_times = (generation_times.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30019:65: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30019 | const bool got_mutation_rates = (mutation_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30042:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30042 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30059:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30059 | for(allele=0; allele<gene_orphans[stip].size(); ++allele){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30144:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30144 | 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:30298:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30298 | const bool got_population_sizes = (population_sizes.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30299:83: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30299 | const bool got_generation_times = (generation_times.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30300:81: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30300 | const bool got_mutation_rates = (mutation_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30301:80: warning: comparison of integer expressions of different signedness: ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30301 | const bool got_allele_counts = (allele_counts.size()==NStips);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp:30302:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30302 | const bool got_HGT_rates = (HGT_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30303:84: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30303 | const bool got_duplication_rates = (duplication_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30304:85: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
30304 | const bool got_loss_rates = (loss_rates.size()==NSclades);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:30325:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30325 | for(long q=0; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30332:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30332 | for(long q=0, clade; q<context.queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30435:66: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30435 | for(long l=0, locus, new_locus; l<clade_current_loci[mclade].size(); ++l){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:30461:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
30461 | 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:31273:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31273 | 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:31386:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31386 | 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:31859:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31859 | 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:31901:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31901 | 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:31939:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31939 | 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:32101:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32101 | for(long p=0; p<time_steps.size(); ++p){
| ~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List read_distances_list_CPP(const std::string&, const std::string&, const std::string&, long int, double, double, long int, long int, const std::string&)’:
phylogenetics_cpp_routines.cpp:32645:32: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32645 | if(parts.size()<=distances_column){
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32673:56: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
32673 | 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:32723:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32723 | for(long i=0; i<haystack.size(); ++i){
| ~^~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:32728:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32728 | 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:32808:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
32808 | 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:5335:29: required from here
5335 | multiply_array_with_scalar(A,factor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:589:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
589 | 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:5530:34: required from here
5530 | epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4936:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
4936 | 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:5530:77: required from here
5530 | epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
phylogenetics_cpp_routines.cpp:4944:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
4944 | 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:8743:48: required from here
8743 | const long NR = (end_c-start_c+1) + vector_sum(dN);
| ~~~~~~~~~~^~~~
phylogenetics_cpp_routines.cpp:701:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
701 | 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:8965:25: required from here
8965 | if(!LUsolveLinearSystem( &matrix[0],
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
8966 | &scratchSpace[0],
| ~~~~~~~~~~~~~~~~~
8967 | 3,
| ~~
8968 | &b[0],
| ~~~~~~
8969 | epsilon*3,
| ~~~~~~~~~~
8970 | 5,
| ~~
8971 | &sol[0])){
| ~~~~~~~~
phylogenetics_cpp_routines.cpp:4786:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4786 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4787:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4787 | for(j=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4802:87: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
4802 | 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:9335:40: required from here
9335 | if(fitLeastSquares_affine_real_scalar(X, logY, start, end, Xshift[n], false, false, A[n], rate[n], RSS, count[n])){
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:9197:21: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
9197 | if((x.size()<=end) || (y.size()<=end)) return false;
| ~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:9197:40: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare]
9197 | 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:9769:24: required from here
9769 | Acoeff *= (Ngrid-1.0)/Aend;
| ^~~~
phylogenetics_cpp_routines.cpp:3459:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3459 | 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:12152:33: required from here
12152 | get_tree_traversal_root_to_tips(Ntips,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
12153 | Nnodes,
| ~~~~~~~
12154 | Nedges,
| ~~~~~~~
12155 | -1,
| ~~~
12156 | tree_edge,
| ~~~~~~~~~~
12157 | include_tips,
| ~~~~~~~~~~~~~
12158 | false,
| ~~~~~~
12159 | queue,
| ~~~~~~
12160 | node2first_edge,
| ~~~~~~~~~~~~~~~~
12161 | node2last_edge,
| ~~~~~~~~~~~~~~~
12162 | edges,
| ~~~~~~
12163 | false,
| ~~~~~~
12164 | "");
| ~~~
phylogenetics_cpp_routines.cpp:12125:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12125 | 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:12798:36: required from here
12798 | const double root_age = vector_max(ages);
| ~~~~~~~~~~^~~~~~
phylogenetics_cpp_routines.cpp:779:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
779 | 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:13867:14: required from here
13867 | qsortIndices(distances_from_root, chronological_clade_order);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:1080:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1080 | 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:14166:33: required from here
14166 | const long Nsplits = vector_max(node2child_count);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:779:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
779 | 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:14809:30: required from here
14809 | sort_tree_edges_root_to_tips( Ntips,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
14810 | Nnodes,
| ~~~~~~~
14811 | Nedges,
| ~~~~~~~
14812 | depth_first_search,
| ~~~~~~~~~~~~~~~~~~~
14813 | root_to_tips,
| ~~~~~~~~~~~~~
14814 | tree_edge,
| ~~~~~~~~~~
14815 | new2old_edge);
| ~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14781:36: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14781 | 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:15045:40: required from here
15045 | get_tree_with_collapsed_monofurcations( Ntips,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
15046 | Nnodes,
| ~~~~~~~
15047 | Nedges,
| ~~~~~~~
15048 | root,
| ~~~~~
15049 | force_keep_root,
| ~~~~~~~~~~~~~~~~
15050 | force_keep_nodes,
| ~~~~~~~~~~~~~~~~~
15051 | tree_edge,
| ~~~~~~~~~~
15052 | edge_length,
| ~~~~~~~~~~~~
15053 | new_tree_edge,
| ~~~~~~~~~~~~~~
15054 | new_edge_length,
| ~~~~~~~~~~~~~~~~
15055 | new2old_node,
| ~~~~~~~~~~~~~
15056 | new_root,
| ~~~~~~~~~
15057 | root_shift);
| ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14941:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14941 | for(long fn=0, node; fn<force_keep_nodes.size(); ++fn){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14955:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14955 | for(long q=0; q<traversal_queue.size(); ++q){
| ~^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:14978:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
14978 | 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:15657:32: required from here
15657 | get_subtree_with_specific_tips( Ntips,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
15658 | Nnodes,
| ~~~~~~~
15659 | Nedges,
| ~~~~~~~
15660 | tree_edge,
| ~~~~~~~~~~
15661 | edge_length,
| ~~~~~~~~~~~~
15662 | tips_to_keep,
| ~~~~~~~~~~~~~
15663 | collapse_monofurcations,
| ~~~~~~~~~~~~~~~~~~~~~~~~
15664 | force_keep_root,
| ~~~~~~~~~~~~~~~~
15665 | lvector(),
| ~~~~~~~~~~
15666 | new_tree_edge,
| ~~~~~~~~~~~~~~
15667 | new_edge_length,
| ~~~~~~~~~~~~~~~~
15668 | new2old_clade,
| ~~~~~~~~~~~~~~
15669 | new_root,
| ~~~~~~~~~
15670 | old_stem_edge,
| ~~~~~~~~~~~~~~
15671 | Ntips_kept,
| ~~~~~~~~~~~
15672 | Nnodes_kept,
| ~~~~~~~~~~~~
15673 | Nedges_kept,
| ~~~~~~~~~~~~
15674 | root_shift);
| ~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15515:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15515 | for(long t=0; t<tips_to_keep.size(); ++t){
| ~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15518:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15518 | for(long fn=0; fn<force_keep_nodes.size(); ++fn){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:15591:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15591 | 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:16884:26: required from here
16884 | get_distances_from_root(Ntips, Nnodes, Nedges, tree_edge, edge_length, context, clade_times);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:12746:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
12746 | 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:18344:33: required from here
18344 | fa = find_in_ascending_list(membershipsA[nodeA],f,fa+1);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:495:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
495 | 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:22813:19: required from here
22813 | shape = initial/initial_mean;
| ^~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3541:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3541 | 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:22876:27: required from here
22876 | rateY = YA - currentY*rateS;
| ^~~~~
phylogenetics_cpp_routines.cpp:3441:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3441 | 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:22876:27: required from here
22876 | rateY = YA - currentY*rateS;
| ^~~~~
phylogenetics_cpp_routines.cpp:3495:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3495 | 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:22985:66: required from here
22985 | candidate_state = previous_state*(1-lambda) + candidate_state*lambda;
| ^~~~~~
phylogenetics_cpp_routines.cpp:3468:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3468 | 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:23049:22: required from here
23049 | return contains_nan(state);
| ~~~~~~~~~~~~^~~~~~~
phylogenetics_cpp_routines.cpp:874:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
874 | 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:23409:32: required from here
23409 | posteriors[node] *= modelD.initial;
| ^~~~~~~
phylogenetics_cpp_routines.cpp:3432:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3432 | 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:23430:30: required from here
23430 | const double S = vector_sum(posteriors[node]);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:701:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
701 | 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:23431:23: required from here
23431 | posteriors[node] /= S;
| ^
phylogenetics_cpp_routines.cpp:3550:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3550 | 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:23439:56: required from here
23439 | loglikelihood += log(vector_sum(posteriors[root_node]*root_prior));
| ^~~~~~~~~~
phylogenetics_cpp_routines.cpp:3423:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3423 | 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:23949:38: required from here
23949 | loglikelihood += log(scalar_product(substem_D,substem_prior));
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:724:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare]
724 | 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:24348:83: required from here
24348 | dvector coarse_diversification_rates = lambdas; coarse_diversification_rates -= mus;
| ^~~
phylogenetics_cpp_routines.cpp:3513:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3513 | 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:24968:48: required from here
24968 | dvector coarse_abs_diversification_rates = abs(coarse_diversification_rates);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:3559:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3559 | 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:25460:26: required from here
25460 | return lambda.getMaxAbs() + mu.getMaxAbs() + psi.getMaxAbs();
| ~~~~~~~~~~~~~~~~^~
phylogenetics_cpp_routines.cpp:2655:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2655 | 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:25465:26: required from here
25465 | return lambda.getMaxAbs(start_time,end_time) + mu.getMaxAbs(start_time,end_time) + psi.getMaxAbs(start_time,end_time);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:2666:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
2666 | 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:25888:20: required from here
25888 | NCSAcrossings += 1l;
| ^~
phylogenetics_cpp_routines.cpp:3486:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3486 | 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:27131:52: required from here
27131 | lvector force_keep_nodes = sampled_node_clades - Ntips;
| ^~~~~
phylogenetics_cpp_routines.cpp:3504:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3504 | 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:27592:27: required from here
27592 | remove_item_from_vector(extant_tips, tip);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:927:17: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
927 | 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:31419:22: required from here
31419 | simulate_SBM_on_tree( Ntips,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
31420 | Nnodes,
| ~~~~~~~
31421 | Nedges,
| ~~~~~~~
31422 | tree_edge,
| ~~~~~~~~~~
31423 | edge_length,
| ~~~~~~~~~~~~
31424 | radius,
| ~~~~~~~
31425 | diffusivity_integral,
| ~~~~~~~~~~~~~~~~~~~~~
31426 | root_theta,
| ~~~~~~~~~~~
31427 | root_phi,
| ~~~~~~~~~
31428 | clade_theta,
| ~~~~~~~~~~~~
31429 | clade_phi);
| ~~~~~~~~~~
phylogenetics_cpp_routines.cpp:31321:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
31321 | 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:4793:21: required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
4793 | if(!LUDecomposition(scratchSpace, N, pivoting_indices, Psign)){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8965:25: required from here
8965 | if(!LUsolveLinearSystem( &matrix[0],
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
8966 | &scratchSpace[0],
| ~~~~~~~~~~~~~~~~~
8967 | 3,
| ~~
8968 | &b[0],
| ~~~~~~
8969 | epsilon*3,
| ~~~~~~~~~~
8970 | 5,
| ~~
8971 | &sol[0])){
| ~~~~~~~~
phylogenetics_cpp_routines.cpp:4641:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4641 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4642:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4642 | for(j=0, big=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4651:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4651 | for(j=0; j<N; ++j){
| ~^~
phylogenetics_cpp_routines.cpp:4658:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4658 | for(i=j; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4668:35: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4668 | for(k=0; k<N; ++k){
| ~^~
phylogenetics_cpp_routines.cpp:4680:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4680 | if(j < N-1){
| ~~^~~~~
phylogenetics_cpp_routines.cpp:4682:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4682 | 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:4798:21: required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
4798 | LUSolveLinearSystem(scratchSpace, N, pivoting_indices, x);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8965:25: required from here
8965 | if(!LUsolveLinearSystem( &matrix[0],
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
8966 | &scratchSpace[0],
| ~~~~~~~~~~~~~~~~~
8967 | 3,
| ~~
8968 | &b[0],
| ~~~~~~
8969 | epsilon*3,
| ~~~~~~~~~~
8970 | 5,
| ~~
8971 | &sol[0])){
| ~~~~~~~~
phylogenetics_cpp_routines.cpp:4703:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4703 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4716:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4716 | 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:4803:35: required from ‘bool LUsolveLinearSystem(const TYPE*, TYPE*, long unsigned int, const TYPE*, double, unsigned int, TYPE*) [with TYPE = double]’
4803 | LUImproveSolutionToLinearSystem(matrix, scratchSpace, N, pivoting_indices, b, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:8965:25: required from here
8965 | if(!LUsolveLinearSystem( &matrix[0],
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
8966 | &scratchSpace[0],
| ~~~~~~~~~~~~~~~~~
8967 | 3,
| ~~
8968 | &b[0],
| ~~~~~~
8969 | epsilon*3,
| ~~~~~~~~~~
8970 | 5,
| ~~
8971 | &sol[0])){
| ~~~~~~~~
phylogenetics_cpp_routines.cpp:4754:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4754 | for(i=0; i<N; ++i){
| ~^~
phylogenetics_cpp_routines.cpp:4756:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4756 | for(j=0; j<N; ++j){ s += matrix[i*N+j] * x[j]; }
| ~^~
phylogenetics_cpp_routines.cpp:4760:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare]
4760 | 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:5409:27: required from ‘long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector<double>]’
5409 | if(find_first_occurrence(sum_of_powers, 0.0)<0) return (p+1);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:21514:94: required from here
21514 | const long min_polynomials = min_polynomials_for_positive_exponential_of_irreducible_matrix(Nstates, transition_matrix);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:477:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
477 | 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:10203:64: 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>]’
10203 | referenceValues[0] = referenceValues[referenceCount-1] = 0.5*(referenceValues[0] + referenceValues[referenceCount-1]);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23382:141: required from here
23382 | modelD.E = LinearInterpolationFunctor<MuSSEstateE>(modelE.ages,modelE.trajectory,false,modelE.trajectory[0],modelE.trajectory.back(),true,0);
| ^
phylogenetics_cpp_routines.cpp:3450:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
3450 | 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:7467:21: 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>]’
7467 | linear_combination(1.0,currentPoint,current_dt1,k1,point2); // point2 = currentPoint + k1*current_dt1;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:23484:9: required from here
23483 | bool success = RungeKutta2<MuSSEstateE,MuSSEmodelE,ProgressReporter>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23484 | (0, // start_time
| ^~~~~~~~~~~~~~~~~
23485 | oldest_age, // end_time
| ~~~~~~~~~~~~~~~~~~~~~~~
23486 | max(0.000001*oldest_age,min(0.2*oldest_age,relative_ODE_step/maxErate)), // default integration time step
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23487 | modelE,
| ~~~~~~~
23488 | minRecordingTimeStep,
| ~~~~~~~~~~~~~~~~~~~~~
23489 | maxRecordingTimeStep,
| ~~~~~~~~~~~~~~~~~~~~~
23490 | guessNrecordings,
| ~~~~~~~~~~~~~~~~~
23491 | E_value_step, // recordingRelValueStep
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23492 | 5, // maxTimeStepRefinements
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23493 | 4, // refinement_factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23494 | ProgressReporter(true),
| ~~~~~~~~~~~~~~~~~~~~~~~
23495 | (runtime_out_seconds>0 ? max(runtime_out_seconds*0.01, runtime_out_seconds+start_runtime-get_thread_monotonic_walltime_seconds()) : 0.0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
23496 | warningMessage);
| ~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:440:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
440 | 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:1331:25: warning: ‘t1’ may be used uninitialized [-Wmaybe-uninitialized]
1331 | W += (t2-t1) * abs(CDFY-CDFX);
| ~~~^~~~
phylogenetics_cpp_routines.cpp:1315:32: note: ‘t1’ was declared here
1315 | double CDFX=0, CDFY=0, t1, t2;
| ^~
phylogenetics_cpp_routines.cpp: In function ‘double solve_polynomial_via_bisection(const double*, long int, double, double, double, double, double, double, long int)’:
phylogenetics_cpp_routines.cpp:2269:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
2269 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2215:36: note: ‘c’ was declared here
2215 | double a = Xmin, b = Xmax, c;
| ^
phylogenetics_cpp_routines.cpp: In function ‘double legendre_polynomial(long int, double)’:
phylogenetics_cpp_routines.cpp:30983:16: warning: ‘Pn’ may be used uninitialized [-Wmaybe-uninitialized]
30983 | return Pn;
| ^~
phylogenetics_cpp_routines.cpp:30977:16: note: ‘Pn’ was declared here
30977 | double Pn;
| ^~
phylogenetics_cpp_routines.cpp: In function ‘double solve_piecewise_polynomial_bisection(const dvector&, const dvector&, long int, bool, double, double, double, bool, double, double, long int, long int&, long int&)’:
phylogenetics_cpp_routines.cpp:2352:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
2352 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2290:36: note: ‘c’ was declared here
2290 | 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:2449:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized]
2449 | return c; // did not converge, but the last c is the best estimate
| ^
phylogenetics_cpp_routines.cpp:2382:36: note: ‘c’ was declared here
2382 | 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:6040:37: warning: ‘error’ may be used uninitialized [-Wmaybe-uninitialized]
6040 | return (best_error<tolerance);
| ^
phylogenetics_cpp_routines.cpp:5970:21: note: ‘error’ was declared here
5970 | double XAX, error, best_lambda=0, best_error=INFTY_D;
| ^~~~~
In file included from /usr/include/c++/15/cmath:59,
from phylogenetics_cpp_routines.cpp:31:
In function ‘constexpr double std::abs(double)’,
inlined from ‘VALUE_TYPE polynomial_bound_abs(long int, const VALUE_TYPE*, double, double) [with VALUE_TYPE = double]’ at phylogenetics_cpp_routines.cpp:1747:17:
/usr/include/c++/15/bits/std_abs.h:78:30: warning: ‘Yvertex’ may be used uninitialized [-Wmaybe-uninitialized]
78 | { return __builtin_fabs(__x); }
| ^
phylogenetics_cpp_routines.cpp: In function ‘VALUE_TYPE polynomial_bound_abs(long int, const VALUE_TYPE*, double, double) [with VALUE_TYPE = double]’:
phylogenetics_cpp_routines.cpp:1745:28: note: ‘Yvertex’ was declared here
1745 | VALUE_TYPE Yvertex;
| ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List HBD_PSR_loglikelihood_CPP(const std::vector<double>&, double, const std::vector<double>&, const std::vector<double>&, long int, const std::string&, double, double)’:
phylogenetics_cpp_routines.cpp:25402:51: warning: ‘W_degree’ may be used uninitialized [-Wmaybe-uninitialized]
25402 | const double origin_W = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:25330:24: note: ‘W_degree’ was declared here
25330 | long I_degree, W_degree, NRG;
| ^~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List HBD_PDR_loglikelihood_CPP(const std::vector<double>&, double, double, const std::vector<double>&, const std::vector<double>&, long int, const std::string&, double, double, std::vector<double>, long int)’:
phylogenetics_cpp_routines.cpp:25229:102: warning: ‘Zdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25229 | branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset);
| ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25195:14: note: ‘Zdegree’ was declared here
25195 | long Zdegree, EZdegree, Wdegree;
| ^~~~~~~
phylogenetics_cpp_routines.cpp:25230:102: warning: ‘Wdegree’ may be used uninitialized [-Wmaybe-uninitialized]
25230 | branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset);
| ~~~~~~~~^~~
phylogenetics_cpp_routines.cpp:25195:33: note: ‘Wdegree’ was declared here
25195 | long Zdegree, EZdegree, Wdegree;
| ^~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘bool LUDecomposition(TYPE*, long unsigned int, long unsigned int*, int&) [with TYPE = double]’:
phylogenetics_cpp_routines.cpp:4676:39: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized]
4676 | pivoting_indices[j] = imax;
| ^~~~
phylogenetics_cpp_routines.cpp:4635:16: note: ‘imax’ was declared here
4635 | 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:10927:96: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
10927 | coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:10904:59: note: ‘coalescent_diversity_at_resolution_age’ was declared here
10904 | double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List simulate_deterministic_diversity_growth_CPP(double, double, double, double, double, double, double, double, long int, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, bool, const std::vector<double>&, double, double, double, double, bool, bool, bool, bool, bool, bool, double)’:
phylogenetics_cpp_routines.cpp:11148:86: warning: ‘Pmissing_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11148 | const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age);
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11123:24: note: ‘Pmissing_at_resolution_age’ was declared here
11123 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:11156:88: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized]
11156 | 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:11123:87: note: ‘coalescent_diversity_at_resolution_age’ was declared here
11123 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_trait_richness_collectors_curve_CPP(long int, long int, long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, const std::vector<long int>&, long int, const std::string&, bool)’:
phylogenetics_cpp_routines.cpp:20191:49: warning: ‘tip’ may be used uninitialized [-Wmaybe-uninitialized]
20191 | tip_included[tip] = true;
| ^
phylogenetics_cpp_routines.cpp:20054:14: note: ‘tip’ was declared here
20054 | long tip, clade, count_tips_remaining;
| ^~~
phylogenetics_cpp_routines.cpp:20151:76: warning: ‘count_tips_remaining’ may be used uninitialized [-Wmaybe-uninitialized]
20151 | long tip_counter = uniformIntWithin(0,count_tips_remaining-1);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:20054:26: note: ‘count_tips_remaining’ was declared here
20054 | long tip, clade, count_tips_remaining;
| ^~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:192,
from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
from phylogenetics_cpp_routines.cpp:39:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:471:46,
inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:495:40,
inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:744:34,
inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
inlined from ‘static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/converter.h:80:23,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:530:13,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:523:46,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:512:34,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<double>; TArgs = {Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1169:24,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<SEXPREC*>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<long int>; TArgs = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1146:29,
inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<SEXPREC*>, Rcpp::traits::named_object<long int>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/vector/Vector.h:1128:50,
inlined from ‘Rcpp::List read_Newick_string_CPP(std::string, bool, bool, bool, bool)’ at phylogenetics_cpp_routines.cpp:19175:39:
/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: ‘root_edge’ may be used uninitialized [-Wmaybe-uninitialized]
448 | r_vector_start<RTYPE>(x)[0] = object;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List read_Newick_string_CPP(std::string, bool, bool, bool, bool)’:
phylogenetics_cpp_routines.cpp:19091:29: note: ‘root_edge’ was declared here
19091 | double edge_length, root_edge;
| ^~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector<long int>, bool, const std::vector<long int>&, bool)’:
phylogenetics_cpp_routines.cpp:16149:111: warning: ‘best_Ntargets_upstream’ may be used uninitialized [-Wmaybe-uninitialized]
16149 | else if((!descends_from_best_edge[tip]) && (Nnontargets_downstream_per_clade[tip]==1) && targets_should_be_upstream) misplaced_nontargets.push_back(tip); // misplaced upstream non-target
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16110:30: note: ‘best_Ntargets_upstream’ was declared here
16110 | long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
| ^~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16131:42: warning: ‘best_Nmisplaced_targets’ may be used uninitialized [-Wmaybe-uninitialized]
16131 | misplaced_targets.reserve(best_Nmisplaced_targets);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16110:80: note: ‘best_Nmisplaced_targets’ was declared here
16110 | long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
| ^~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16132:45: warning: ‘best_Nmisplaced_nontargets’ may be used uninitialized [-Wmaybe-uninitialized]
16132 | misplaced_nontargets.reserve(best_Nmisplaced_nontargets);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp:16110:105: note: ‘best_Nmisplaced_nontargets’ was declared here
16110 | long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector<long int>&, const std::vector<double>&, const std::vector<long int>&, bool, const std::string&)’:
phylogenetics_cpp_routines.cpp:13316:155: warning: ‘mrca’ may be used uninitialized [-Wmaybe-uninitialized]
13316 | 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:13289:30: note: ‘mrca’ was declared here
13289 | long cladeA, cladeB, mrca;
| ^~~~
gcc-15 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o castor.so RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp76xc7l/R.INSTALL8f0754d3fcec2/castor/src'
make[1]: Entering directory '/tmp/Rtmp76xc7l/R.INSTALL8f0754d3fcec2/castor/src'
make[1]: Leaving directory '/tmp/Rtmp76xc7l/R.INSTALL8f0754d3fcec2/castor/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-castor/00new/castor/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (castor)