downloading reverse dependencies ... downloading avotrex_1.3.0.tar.gz ... ok downloading orthGS_0.1.6.tar.gz ... ok downloading Quartet_1.2.7.tar.gz ... ok downloading Rogue_2.1.6.tar.gz ... ok downloading TBRDist_1.0.2.tar.gz ... ok downloading TotalCopheneticIndex_2.0.1.tar.gz ... ok downloading TreeDist_2.9.2.tar.gz ... ok downloading TreeSearch_1.5.1.tar.gz ... ok downloading phylosem_1.1.4.tar.gz ... ok installing dependencies ‘castor’, ‘fishtree’, ‘hypervolume’, ‘kdensity’, ‘phylopath’, ‘phylosignal’, ‘phyr’, ‘protoclust’, ‘Quartet’, ‘Rogue’, ‘Rphylopars’, ‘Ternary’, ‘TreeDist’, ‘TreeDistData’, ‘TreeSearch’, ‘TreeTools’, ‘Umatrix’ Warning: package ‘TreeDistData’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘nakagami’, ‘sads’, ‘ttutils’, ‘RcppHungarian’, ‘univariateML’, ‘EQL’, ‘AdaptGauss’ begin installing package ‘nakagami’ begin installing package ‘sads’ begin installing package ‘ttutils’ begin installing package ‘RcppHungarian’ begin installing package ‘AdaptGauss’ begin installing package ‘TreeTools’ begin installing package ‘castor’ begin installing package ‘hypervolume’ begin installing package ‘protoclust’ begin installing package ‘phylopath’ begin installing package ‘Rphylopars’ begin installing package ‘fishtree’ begin installing package ‘phyr’ begin installing package ‘phylosignal’ * installing *source* package ‘nakagami’ ... ** this is package ‘nakagami’ version ‘1.1.0’ ** package ‘nakagami’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nakagami) * installing *source* package ‘ttutils’ ... ** this is package ‘ttutils’ version ‘1.0-1.1’ ** package ‘ttutils’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ttutils) begin installing package ‘EQL’ * installing *source* package ‘protoclust’ ... ** this is package ‘protoclust’ version ‘1.6.4’ ** package ‘protoclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT1rP1K/R.INSTALL3c8bf31fba867f/protoclust/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hier.c -o hier.o hier.c: In function ‘hier’: hier.c:194:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 194 | for(j = 0; j < imerge; j++) | ^~~ hier.c:204:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 204 | ii = lt(imerge+1,imerge,n); | ^~ hier.c: In function ‘minimaxpoint’: hier.c:442:10: warning: ‘mm’ may be used uninitialized [-Wmaybe-uninitialized] 442 | return mm; | ^~ hier.c:428:7: note: ‘mm’ was declared here 428 | int mm; | ^~ hier.c: In function ‘findNN’: hier.c:346:29: warning: ‘nn’ may be used uninitialized [-Wmaybe-uninitialized] 346 | mincomplete = completelink(dmax, n, clusters[nn], nn, clusters[i], i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hier.c:328:7: note: ‘nn’ was declared here 328 | int nn; | ^~ hier.c: In function ‘hier’: hier.c:274:26: warning: ‘imerge’ may be used uninitialized [-Wmaybe-uninitialized] 274 | Cluster *cur = clusters[imerge]; | ^ hier.c:28:20: note: ‘imerge’ was declared here 28 | int i, j, k, ii, imerge, jmerge, reverse; | ^~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c protoclust_init.c -o protoclust_init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o protoclust.so hier.o protoclust_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT1rP1K/R.INSTALL3c8bf31fba867f/protoclust/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-protoclust/00new/protoclust/libs ** R ** 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 (protoclust) * installing *source* package ‘fishtree’ ... ** this is package ‘fishtree’ version ‘0.3.4’ ** package ‘fishtree’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fishtree) * installing *source* package ‘EQL’ ... ** this is package ‘EQL’ version ‘1.0-1’ ** package ‘EQL’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EQL) * installing *source* package ‘phylopath’ ... ** this is package ‘phylopath’ version ‘1.3.0’ ** package ‘phylopath’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phylopath) * installing *source* package ‘RcppHungarian’ ... ** this is package ‘RcppHungarian’ version ‘0.3’ ** package ‘RcppHungarian’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpa5zd3m/R.INSTALL3c8be96071cf95/RcppHungarian/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: ../inst/include/RcppHungarian.h: In member function ‘void HungarianAlgorithm::assignmentoptimal(int*, double*, double*, int, int)’: ../inst/include/RcppHungarian.h:169:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 169 | if (fabs(distMatrix[row + nOfRows*col]) < DBL_EPSILON) | ^~ ../inst/include/RcppHungarian.h:177:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 177 | for (row = 0; row std::numeric_limits::max()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c splits_to_tree.cpp -o splits_to_tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tips_in_splits.cpp -o tips_in_splits.o tips_in_splits.cpp: In function ‘Rcpp::IntegerVector tips_in_splits(Rcpp::RawMatrix)’: tips_in_splits.cpp:47:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 47 | ret[i] += decltype(ret[0])(bitcounts[splits(i, bin)]); | ~~~~~~~~~~~~~~~~~~~~~~~~^ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_shape.cpp -o tree_shape.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TreeTools.so ClusterTable.o RcppExports-manual.o RcppExports.o ape_reorder.o as_newick.o consensus.o descendant_edges.o int_to_tree.o kept_vertices.o minimum_spanning_tree.o path_lengths.o splits.o splits_to_tree.o tips_in_splits.o tree_shape.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6gBlik/R.INSTALL3c8be83a7ed7f0/TreeTools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TreeTools/00new/TreeTools/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘match’ from package ‘base’ in package ‘TreeTools’ Creating a generic function for ‘%in%’ from package ‘base’ in package ‘TreeTools’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** 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 (TreeTools) begin installing package ‘TreeDist’ begin installing package ‘Quartet’ * installing *source* package ‘phyr’ ... ** this is package ‘phyr’ version ‘1.1.0’ ** package ‘phyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4dptx2/R.INSTALL3c8bfcbd6067d/phyr/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binaryPGLMM.cpp -o binaryPGLMM.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cor_phylo.cpp -o cor_phylo.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pcd.cpp -o pcd.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pglmm_binary.cpp -o pglmm_binary.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pglmm_gaussian.cpp -o pglmm_gaussian.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c psv.cpp -o psv.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o phyr.so RcppExports.o binaryPGLMM.o cor_phylo.o pcd.o pglmm_binary.o pglmm_gaussian.o psv.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4dptx2/R.INSTALL3c8bfcbd6067d/phyr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-phyr/00new/phyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (phyr) * installing *source* package ‘TreeDist’ ... ** this is package ‘TreeDist’ version ‘2.9.2’ ** package ‘TreeDist’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdbqXfI/R.INSTALL3c90cd7cfb2432/TreeDist/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c day_1985.cpp -o day_1985.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lap.cpp -o lap.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mast.cpp -o mast.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nni_distance.cpp -o nni_distance.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c path_vector.cpp -o path_vector.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c reduce_tree.cpp -o reduce_tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c spr.cpp -o spr.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_distance_functions.cpp -o tree_distance_functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_distances.cpp -o tree_distances.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TreeDist.so RcppExports.o day_1985.o lap.o mast.o nni_distance.o path_vector.o reduce_tree.o spr.o tree_distance_functions.o tree_distances.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdbqXfI/R.INSTALL3c90cd7cfb2432/TreeDist/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TreeDist/00new/TreeDist/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** 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 (TreeDist) begin installing package ‘Rogue’ * installing *source* package ‘castor’ ... ** this is package ‘castor’ version ‘1.8.3’ ** package ‘castor’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWwHs6I/R.INSTALL3c8bf2b45b9a9/castor/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c STMathExpression.cpp -o STMathExpression.o STMathExpression.cpp:10: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas] 10 | #pragma mark - STMathExpression.cpp:11: warning: ignoring ‘#pragma mark String’ [-Wunknown-pragmas] 11 | #pragma mark String manipulations STMathExpression.cpp:12: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas] 12 | #pragma mark STMathExpression.cpp:65: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas] 65 | #pragma mark - STMathExpression.cpp:66: warning: ignoring ‘#pragma mark MathExpression’ [-Wunknown-pragmas] 66 | #pragma mark MathExpression STMathExpression.cpp:67: warning: ignoring ‘#pragma mark ’ [-Wunknown-pragmas] 67 | #pragma mark STMathExpression.cpp: In static member function ‘static long int MathExpression::splitBinaryOperatorInverseOrder(const std::string&, long int, long int, const std::vector&)’: STMathExpression.cpp:256:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const std::__cxx11::basic_string::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&, const std::map, long int>&, const std::map, long int>&, long int, bool)’: STMathExpression.cpp:313:105: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string::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::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 359 | if((rightMostBracket==string::npos) || (rightMostBracket&)’: STMathExpression.cpp:463:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 463 | for(long i=0; i&)’: STMathExpression.cpp:500:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 500 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 953 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 957 | for(long i=0; i&) const’: STMathExpression.cpp:981:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits, long int>::value_type’ {aka ‘const long int’} and ‘std::vector::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&, long int, ...) const’: STMathExpression.cpp:1044:34: warning: comparison of integer expressions of different signedness: ‘const __gnu_cxx::__alloc_traits, 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, long int>::value_type’ {aka ‘const long int’} and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1045 | else if(variableIDs[i] >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1195 | for(long i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1202 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1258 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1269 | for(long n=0; n&)’: STMathExpression.cpp:1378:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1378 | for(long i=0; i&) const [with TYPE = long int; std::ostream = std::basic_ostream]’: 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::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1227 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 334 | for(long i=0; i >&)’: phylogenetics_cpp_routines.cpp:357:46: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 357 | while((max_Nparts<0) || (parts.size()::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 359 | if(pos==string::npos) break; | ~~~^~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:363:43: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 363 | if((max_Nparts<0) || (parts.size()&, long int)’: phylogenetics_cpp_routines.cpp:460:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 460 | for(long n=start; n&)’: phylogenetics_cpp_routines.cpp:707:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:722:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 722 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:740:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 740 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:747:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 747 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:776:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 776 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:807:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 807 | for(long i=0; i&, double)’: phylogenetics_cpp_routines.cpp:812:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 812 | for(long i=0; i&, double)’: phylogenetics_cpp_routines.cpp:819:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 819 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:829:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 829 | for(long i=0; i&)’: phylogenetics_cpp_routines.cpp:882:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 882 | for(long i=0; i >&, const std::vector >&)’: phylogenetics_cpp_routines.cpp:902:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare] 902 | for(long level=0; level, long int>::value_type’ {aka ‘long int’} and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 948 | if(pool2list[pool_index]==list2pool.size()-1){ phylogenetics_cpp_routines.cpp: In function ‘long int get_nearest_index(const std::vector&, long int)’: phylogenetics_cpp_routines.cpp:976:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 976 | 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:997:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 997 | for(long i=0; i >&, const lvector&, const dvector&, double, long int)’: phylogenetics_cpp_routines.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1599 | for(long i=0; i&, const std::vector&, long int, const std::vector&, const std::string&, long int)’: phylogenetics_cpp_routines.cpp:2820:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2820 | for(long t=0, g=-1; t&, double, const std::vector&, long int, const std::vector&)’: phylogenetics_cpp_routines.cpp:3260:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3260 | for(long t=0, g=0; t&, const std::vector&, long int, const std::vector&)’: phylogenetics_cpp_routines.cpp:3287:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3287 | for(long t=0, g=0, p; t >&, const std::vector >&, const std::vector >&, double)’: phylogenetics_cpp_routines.cpp:5835:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5835 | for(long r=0; r&, const double&, const std::vector&, const long int&, std::vector&, std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:5915:19: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5915 | for(k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5947 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8860 | for(long ng=0, og=0; ng::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 8897 | for(long ng=0, og=0; ng&, std::vector, bool, bool)’: phylogenetics_cpp_routines.cpp:9941:56: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9941 | for(long k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 9967 | for(long k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 10929 | for(long t=0; t&, const std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:12662:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12662 | for(long q=0; q&, const std::vector&, const tree_traversal&, dvector&)’: phylogenetics_cpp_routines.cpp:12791:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12791 | for(long q=0, clade; q&, const std::vector&, const std::vector&, bool, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:12897:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12897 | for(long t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12928 | for(long q=0; q&, const std::vector&, const std::vector&, bool, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:13016:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13016 | for(long t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13047 | for(long q=1; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13075 | for(long q=0; q&, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:13144:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13144 | for(long t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13174 | for(long q=0; q&, const std::vector&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:13266:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13266 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13286 | for(long q=0; q&, const std::vector&, const std::vector&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:13397:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13397 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13417 | for(long q=0; q&, const std::vector&, long int, double, double, bool, long int, bool)’: phylogenetics_cpp_routines.cpp:13624:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13624 | for(long q=0, clade; q&, const std::vector&, const std::vector&, long int)’: phylogenetics_cpp_routines.cpp:13732:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13732 | for(long q=0, clade; q&, const std::vector&, double, double, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:13889:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13889 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13913 | for(long c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 13914 | for(long c=0; c&, const std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:14066:45: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14066 | for(long q=1, clade, pnode, cnode; q&, const std::vector&)’: phylogenetics_cpp_routines.cpp:14324:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14324 | for(long q=0, clade; q&, long int, long int, long int)’: phylogenetics_cpp_routines.cpp:14493:16: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14493 | while(k&, long int)’: phylogenetics_cpp_routines.cpp:14550:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14550 | while(queue_pointer::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14567 | for(long c=0, clade; c&, const std::vector&, long int)’: phylogenetics_cpp_routines.cpp:14615:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14615 | for(long q=0; q&, const std::vector&, const std::vector&, bool, bool, bool, bool)’: phylogenetics_cpp_routines.cpp:15174:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15174 | for(long c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15191 | for(long q=0; q, bool, const std::vector&, bool)’: phylogenetics_cpp_routines.cpp:16015:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16015 | for(long t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16038 | for(long q=1, cnode, pnode; q, bool, const std::vector&, bool)’: phylogenetics_cpp_routines.cpp:16145:29: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16145 | for(long t=0, tip; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16159 | for(long q=1; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16194 | for(long q=1; q&, const std::vector&, double)’: phylogenetics_cpp_routines.cpp:16461:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16461 | for(long q=0; q&, const std::vector&, double, double)’: phylogenetics_cpp_routines.cpp:16571:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16571 | for(long q=0; q&, const std::vector&, const std::vector&, bool, bool)’: phylogenetics_cpp_routines.cpp:16911:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16911 | for(long n=0, node; n::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16921 | for(long n=0, e, pnode, child; n::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 16985 | for(long q=0, clade, node, absorbing_ancestor, parent, child, e, edge, inedge; q&, const std::vector&, const std::vector&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:17082:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17082 | for(long s=0, clade, inedge, node, e; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17105 | for(long q=1, clade, node, inedge, e; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17139 | for(long q=1, clade, inedge; q&, const std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:17475:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17475 | for(long q=0, clade; q&, const std::vector >&, const std::vector >&, const std::string&, const std::string&, bool)’: phylogenetics_cpp_routines.cpp:17954:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17954 | for(long f=0; f >::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 17955 | 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, std::vector, const std::vector&, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:17991:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 17991 | for(long i=0; i&, long int, long int, long int, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:18189:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18189 | for(long m=0, Tnode, Rnode; m&, long int, long int, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:18419:60: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18419 | for(long fb=0, fa=-1, f; fb relative_to_absolute_node_ages_CPP(long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:18475:44: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18475 | for(long q=1, clade, node, pnode; q propagate_min_ages_upstream_CPP(long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:18499:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18499 | for(long a=0; a propagate_max_ages_downstream_CPP(long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&)’: phylogenetics_cpp_routines.cpp:18528:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18528 | for(long a=0; a::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18533 | for(long q=0, clade, node, pnode; q, const std::vector&)’: phylogenetics_cpp_routines.cpp:18595:39: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18595 | for(long q=1, clade, parent; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18612 | for(long q=0, clade, node; q&, const std::vector&, const std::vector&, double, bool, bool, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, bool, std::vector&, std::vector&, std::vector&, double&, double&, double&, double&, long int&, std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:19209:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 19209 | for(long q=0; q&, const std::vector&, const std::vector&, double, bool, bool, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, std::vector&, double&, double&, double&, double&, long int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:19522:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 19522 | for(long q=0, dominant_state; q&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:20571:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20571 | for(long q=0, parent; q&, const std::vector&)’: phylogenetics_cpp_routines.cpp:20642:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20642 | for(long fc=0; fc::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20648 | for(long fc=0; fc&, const std::vector&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:20776:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20776 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20795 | for(long q=0; q&, const std::vector&)’: phylogenetics_cpp_routines.cpp:20931:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20931 | for(long t=0; t&, const std::vector&, const std::vector&, const std::vector&, double, bool, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:21161:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 21161 | for(long q=0; q&, const std::vector&, const std::vector&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const Rcpp::ComplexVector&, const std::vector&, const std::string&, const std::vector&, bool, bool, double, double, long int, bool)’: phylogenetics_cpp_routines.cpp:21523:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 21523 | for(long n=0; n::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 21564 | for(long q=0, new_root; q&, const std::vector&, const std::vector&, double, long int, Rcpp::LogicalVector, std::vector, bool)’: phylogenetics_cpp_routines.cpp:21968:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 21968 | for(long q=0, node, clade; q&, std::vector, std::vector)’: phylogenetics_cpp_routines.cpp:22024:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22024 | for(long q=0, node, clade; q&, const std::vector&, const std::vector&, bool)’: phylogenetics_cpp_routines.cpp:22198:42: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22198 | for(long q=0, new_root; q&, const std::vector&, const std::vector&, bool)’: phylogenetics_cpp_routines.cpp:22459:30: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 22459 | if(node_states.size()>Nnodes) node_states.resize(Nnodes); | ~~~~~~~~~~~~~~~~~~^~~~~~~ phylogenetics_cpp_routines.cpp:22460:39: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 22460 | if(node_standard_errors.size()>Nnodes) node_standard_errors.resize(Nnodes); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ phylogenetics_cpp_routines.cpp:22461:29: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 22461 | 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&, Rcpp::LogicalVector, std::vector)’: phylogenetics_cpp_routines.cpp:22502:37: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22502 | for(long q=0, node, clade; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22537 | for(long i=0, tip; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22556 | for(long i=0, tip; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22576 | for(long i=0, tip; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22781 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22795 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22887 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22900 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22905 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22925 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22947 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22970 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 22994 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23177 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23190 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23207 | for(long s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23229 | for(long s=0; s&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, double, double, double, double, bool, std::vector >&, std::string&, double&, long int&, MuSSEmodelE&, MuSSEmodelD&, std::vector > >&, std::vector >&)’: phylogenetics_cpp_routines.cpp:23478:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 23478 | for(long a=0; a&, const std::vector&, const std::vector&, std::vector, const std::vector&, double, double, double, double, long int, double, bool)’: phylogenetics_cpp_routines.cpp:24303:40: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 24303 | for(long i=0; i&, const std::vector&, const std::vector&, const std::vector&, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26559:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26559 | for(long q=0; q&, const std::vector&, double, double, double, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26639:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26639 | for(long q=0; q&, const std::vector&, double, double, double, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26721:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26721 | for(long q=0; q&, const std::vector&, const std::vector&, double, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26792:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26792 | for(long q=0; q&, const std::vector&, const std::vector&, const std::vector&, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26872:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26872 | for(long q=0; q&, const std::vector&, const std::vector&, double, bool, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26964:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 26964 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27076 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27079 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 27085 | if(only_sampled_tips && (sampled_tips.size()::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27122 | for(long new_clade=0; new_clade::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27128 | for(long i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27131 | for(long i=0; i&, const std::vector&, const std::vector&, bool, bool, long int, bool, bool, bool, bool)’: phylogenetics_cpp_routines.cpp:27217:75: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const long int’ [-Wsign-compare] 27217 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 27217 | while(((max_tips<=0) || ((coalescent ? extant_tips.size() : Ntips)&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, const std::vector&, const std::vector&, const std::vector&, bool, bool, double, bool, bool, bool, bool)’: phylogenetics_cpp_routines.cpp:27432:100: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 27432 | while(((max_tips<=0) || (Ntips::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 27432 | while(((max_tips<=0) || (Ntips::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 27432 | while(((max_tips<=0) || (Ntips::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27618 | for(long nc=0; nc::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27625 | for(long nc=0; nc::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27632 | for(long nc=0; nc&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, bool, bool, bool, bool, bool, bool)’: phylogenetics_cpp_routines.cpp:28941:34: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 28941 | for(long nc=0; nc::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 28947 | for(long nc=0; nc::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 28952 | for(long nc=0; nc&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, bool, long int, bool, bool, bool, bool)’: phylogenetics_cpp_routines.cpp:29620:38: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 29620 | for(long stip=0; stip&, double, EdgeLengthUnit, double, double, long int, std::vector&, long int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:29864:44: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 29864 | if(clade2tail_length.size()<=next_clade) clade2tail_length.resize(next_clade+1); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:29866:42: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 29866 | if(clade2tail_time.size()<=next_clade) clade2tail_time.resize(next_clade+1); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:29875:41: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 29875 | for(long orphan=0, clade; orphan&, std::vector&, long int&, std::vector&, std::vector&, std::vector&)’: phylogenetics_cpp_routines.cpp:29928:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 29928 | 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&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::string&, long int, bool, bool, long int, long int&, long int&, long int&, long int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::string&)’: phylogenetics_cpp_routines.cpp:29978:64: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 29978 | const bool got_allele_counts = (allele_counts.size()==NStips); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ phylogenetics_cpp_routines.cpp:29979:67: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 29979 | const bool got_population_sizes = (population_sizes.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:29980:67: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 29980 | const bool got_generation_times = (generation_times.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:29981:65: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 29981 | const bool got_mutation_rates = (mutation_rates.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30007:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30007 | for(long q=0, clade; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30024 | for(allele=0; allele::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30109 | for(long orphan=0; orphan&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::string&, long int, bool, bool, long int, bool, bool, double, double, bool)’: phylogenetics_cpp_routines.cpp:30263:83: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30263 | const bool got_population_sizes = (population_sizes.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30264:83: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30264 | const bool got_generation_times = (generation_times.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30265:81: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30265 | const bool got_mutation_rates = (mutation_rates.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30266:80: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30266 | const bool got_allele_counts = (allele_counts.size()==NStips); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ phylogenetics_cpp_routines.cpp:30267:84: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30267 | const bool got_HGT_rates = (HGT_rates.size()==NSclades); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30268:84: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30268 | const bool got_duplication_rates = (duplication_rates.size()==NSclades); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30269:85: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 30269 | const bool got_loss_rates = (loss_rates.size()==NSclades); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:30290:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30290 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30297 | for(long q=0, clade; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30400 | for(long l=0, locus, new_locus; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 30426 | for(long l=0, locus; l&, const std::vector&, double, double, double, double, dvector&, dvector&)’: phylogenetics_cpp_routines.cpp:31245:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31245 | for(long q=0, parent, child, e, edge; q&, double, double, double, double)’: phylogenetics_cpp_routines.cpp:31361:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31361 | for(long t=1; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31834 | for(long p=0; p&, const std::vector&, const std::vector&, double, long int)’: phylogenetics_cpp_routines.cpp:31876:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31876 | for(long d=0; d&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, long int, const std::vector&, double, long int)’: phylogenetics_cpp_routines.cpp:31914:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31914 | for(long d=0; d&)’: phylogenetics_cpp_routines.cpp:32076:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 32076 | for(long p=0; p >::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 32557 | if(parts.size()<=distances_column){ | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:32585:56: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 32585 | if((max_Nedges>=0) && (distances.size()>=max_Nedges)) break; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ phylogenetics_cpp_routines.cpp: In instantiation of ‘void multiply_array_with_scalar(ARRAY_TYPE&, double) [with ARRAY_TYPE = std::vector]’: phylogenetics_cpp_routines.cpp:5326:29: required from here 5326 | multiply_array_with_scalar(A,factor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:580:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 580 | for(long i=0; i]’: phylogenetics_cpp_routines.cpp:5521:34: required from here 5521 | epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:4927:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4927 | for(long i=0; i]’: phylogenetics_cpp_routines.cpp:5521:77: required from here 5521 | epsilon /= get_norm_L2_of_vector(balances) * get_norm_L2_of_inverted_vector(balances); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ phylogenetics_cpp_routines.cpp:4935:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4935 | for(long i=0; i&) [with TYPE = long int]’: phylogenetics_cpp_routines.cpp:8734:48: required from here 8734 | const long NR = (end_c-start_c+1) + vector_sum(dN); | ~~~~~~~~~~^~~~ phylogenetics_cpp_routines.cpp:692:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 692 | for(long i=0; i maxError) && (impCount&, const std::vector&, long int, long int, double, bool, bool, REAL_TYPE&, REAL_TYPE&, REAL_TYPE&, long int&) [with REAL_TYPE = double]’: phylogenetics_cpp_routines.cpp:9326:40: required from here 9326 | if(fitLeastSquares_affine_real_scalar(X, logY, start, end, Xshift[n], false, false, A[n], rate[n], RSS, count[n])){ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:9188:21: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 9188 | if((x.size()<=end) || (y.size()<=end)) return false; | ~~~~~~~~~^~~~~~ phylogenetics_cpp_routines.cpp:9188:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘const long int’ [-Wsign-compare] 9188 | if((x.size()<=end) || (y.size()<=end)) return false; | ~~~~~~~~~^~~~~~ phylogenetics_cpp_routines.cpp: In instantiation of ‘std::vector& operator*=(std::vector&, double) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:9760:24: required from here 9760 | Acoeff *= (Ngrid-1.0)/Aend; | ^~~~ phylogenetics_cpp_routines.cpp:3450:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3450 | for(long i=0; i&, std::vector&, std::vector&, std::vector&, bool, const std::string&) [with ARRAY_TYPE = std::vector; std::string = std::__cxx11::basic_string]’: phylogenetics_cpp_routines.cpp:12143:33: required from here 12143 | get_tree_traversal_root_to_tips(Ntips, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 12144 | Nnodes, | ~~~~~~~ 12145 | Nedges, | ~~~~~~~ 12146 | -1, | ~~~ 12147 | tree_edge, | ~~~~~~~~~~ 12148 | include_tips, | ~~~~~~~~~~~~~ 12149 | false, | ~~~~~~ 12150 | queue, | ~~~~~~ 12151 | node2first_edge, | ~~~~~~~~~~~~~~~~ 12152 | node2last_edge, | ~~~~~~~~~~~~~~~ 12153 | edges, | ~~~~~~ 12154 | false, | ~~~~~~ 12155 | ""); | ~~~ phylogenetics_cpp_routines.cpp:12116:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12116 | while(queue_pointer&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:12801:36: required from here 12801 | const double root_age = vector_max(ages); | ~~~~~~~~~~^~~~~~ phylogenetics_cpp_routines.cpp:770:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 770 | for(long i=0; i&, std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:13898:14: required from here 13898 | qsortIndices(distances_from_root, chronological_clade_order); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:1071:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1071 | for(long n=0; n&) [with TYPE = long int]’: phylogenetics_cpp_routines.cpp:14197:33: required from here 14197 | const long Nsplits = vector_max(node2child_count); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:770:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 770 | for(long i=0; i&) [with ARRAY_TYPE = std::vector]’: phylogenetics_cpp_routines.cpp:14866:30: required from here 14866 | sort_tree_edges_root_to_tips( Ntips, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 14867 | Nnodes, | ~~~~~~~ 14868 | Nedges, | ~~~~~~~ 14869 | depth_first_search, | ~~~~~~~~~~~~~~~~~~~ 14870 | root_to_tips, | ~~~~~~~~~~~~~ 14871 | tree_edge, | ~~~~~~~~~~ 14872 | new2old_edge); | ~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:14838:36: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14838 | while(queue_pointer&, std::vector&, std::vector&, long int&, double&) [with ARRAY_INT = std::vector; ARRAY_DOUBLE = std::vector; lvector = std::vector]’: phylogenetics_cpp_routines.cpp:15102:40: required from here 15102 | get_tree_with_collapsed_monofurcations( Ntips, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 15103 | Nnodes, | ~~~~~~~ 15104 | Nedges, | ~~~~~~~ 15105 | root, | ~~~~~ 15106 | force_keep_root, | ~~~~~~~~~~~~~~~~ 15107 | force_keep_nodes, | ~~~~~~~~~~~~~~~~~ 15108 | tree_edge, | ~~~~~~~~~~ 15109 | edge_length, | ~~~~~~~~~~~~ 15110 | new_tree_edge, | ~~~~~~~~~~~~~~ 15111 | new_edge_length, | ~~~~~~~~~~~~~~~~ 15112 | new2old_node, | ~~~~~~~~~~~~~ 15113 | new_root, | ~~~~~~~~~ 15114 | root_shift); | ~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:14998:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 14998 | for(long fn=0, node; fn::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15012 | for(long q=0; q::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15035 | for(long q=0; q&, std::vector&, std::vector&, long int&, long int&, long int&, long int&, long int&, double&) [with ARRAY_INT = std::vector; ARRAY_DOUBLE = std::vector; lvector = std::vector]’: phylogenetics_cpp_routines.cpp:15714:32: required from here 15714 | get_subtree_with_specific_tips( Ntips, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 15715 | Nnodes, | ~~~~~~~ 15716 | Nedges, | ~~~~~~~ 15717 | tree_edge, | ~~~~~~~~~~ 15718 | edge_length, | ~~~~~~~~~~~~ 15719 | tips_to_keep, | ~~~~~~~~~~~~~ 15720 | collapse_monofurcations, | ~~~~~~~~~~~~~~~~~~~~~~~~ 15721 | force_keep_root, | ~~~~~~~~~~~~~~~~ 15722 | lvector(), | ~~~~~~~~~~ 15723 | new_tree_edge, | ~~~~~~~~~~~~~~ 15724 | new_edge_length, | ~~~~~~~~~~~~~~~~ 15725 | new2old_clade, | ~~~~~~~~~~~~~~ 15726 | new_root, | ~~~~~~~~~ 15727 | old_stem_edge, | ~~~~~~~~~~~~~~ 15728 | Ntips_kept, | ~~~~~~~~~~~ 15729 | Nnodes_kept, | ~~~~~~~~~~~~ 15730 | Nedges_kept, | ~~~~~~~~~~~~ 15731 | root_shift); | ~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:15572:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15572 | for(long t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15575 | for(long fn=0; fn::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 15648 | for(long fn=0, new_clade; fn; ARRAY_TYPE_D = std::vector; dvector = std::vector]’: phylogenetics_cpp_routines.cpp:16941:26: required from here 16941 | get_distances_from_root(Ntips, Nnodes, Nedges, tree_edge, edge_length, traversal, clade_times); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:12742:31: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 12742 | for(long q=0, clade; q&, TYPE2, long int) [with TYPE1 = long int; TYPE2 = long int]’: phylogenetics_cpp_routines.cpp:18421:33: required from here 18421 | fa = find_in_ascending_list(membershipsA[nodeA],f,fa+1); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:486:28: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 486 | for(long n=start; n operator/(std::vector, double) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:22770:19: required from here 22770 | shape = initial/initial_mean; | ^~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:3532:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3532 | for(long i=0; i operator*(std::vector, double) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:22833:27: required from here 22833 | rateY = YA - currentY*rateS; | ^~~~~ phylogenetics_cpp_routines.cpp:3432:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3432 | for(long i=0; i operator-(std::vector, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:22833:27: required from here 22833 | rateY = YA - currentY*rateS; | ^~~~~ phylogenetics_cpp_routines.cpp:3486:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3486 | for(long i=0; i operator+(std::vector, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:22942:66: required from here 22942 | candidate_state = previous_state*(1-lambda) + candidate_state*lambda; | ^~~~~~ phylogenetics_cpp_routines.cpp:3459:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3459 | for(long i=0; i&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23006:22: required from here 23006 | return contains_nan(state); | ~~~~~~~~~~~~^~~~~~~ phylogenetics_cpp_routines.cpp:865:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 865 | for(long i=0; i& operator*=(std::vector&, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23366:32: required from here 23366 | posteriors[node] *= modelD.initial; | ^~~~~~~ phylogenetics_cpp_routines.cpp:3423:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3423 | for(long i=0; i&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23387:30: required from here 23387 | const double S = vector_sum(posteriors[node]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:692:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 692 | for(long i=0; i& operator/=(std::vector&, double) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23388:23: required from here 23388 | posteriors[node] /= S; | ^ phylogenetics_cpp_routines.cpp:3541:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3541 | for(long i=0; i operator*(std::vector, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23396:56: required from here 23396 | loglikelihood += log(vector_sum(posteriors[root_node]*root_prior)); | ^~~~~~~~~~ phylogenetics_cpp_routines.cpp:3414:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3414 | for(long i=0; i&, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:23906:38: required from here 23906 | loglikelihood += log(scalar_product(substem_D,substem_prior)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:715:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const long unsigned int’ [-Wsign-compare] 715 | for(long i=0; i& operator-=(std::vector&, const std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:24305:83: required from here 24305 | dvector coarse_diversification_rates = lambdas; coarse_diversification_rates -= mus; | ^~~ phylogenetics_cpp_routines.cpp:3504:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3504 | for(long i=0; i abs(std::vector) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:24925:48: required from here 24925 | dvector coarse_abs_diversification_rates = abs(coarse_diversification_rates); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:3550:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3550 | for(long i=0; i::getMaxAbs() const [with VALUE_TYPE = double]’: phylogenetics_cpp_routines.cpp:25417:26: required from here 25417 | return lambda.getMaxAbs() + mu.getMaxAbs() + psi.getMaxAbs(); | ~~~~~~~~~~~~~~~~^~ phylogenetics_cpp_routines.cpp:2646:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2646 | for(long i=0; i::getMaxAbs(double, double) const [with VALUE_TYPE = double]’: phylogenetics_cpp_routines.cpp:25422:26: required from here 25422 | return lambda.getMaxAbs(start_time,end_time) + mu.getMaxAbs(start_time,end_time) + psi.getMaxAbs(start_time,end_time); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:2657:32: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2657 | for(long i=0; i& operator+=(std::vector&, const TYPE&) [with TYPE = long int]’: phylogenetics_cpp_routines.cpp:25845:20: required from here 25845 | NCSAcrossings += 1l; | ^~ phylogenetics_cpp_routines.cpp:3477:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3477 | for(long i=0; i operator-(std::vector, const TYPE&) [with TYPE = long int]’: phylogenetics_cpp_routines.cpp:27088:52: required from here 27088 | lvector force_keep_nodes = sampled_node_clades - Ntips; | ^~~~~ phylogenetics_cpp_routines.cpp:3495:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3495 | for(long i=0; i&, long int) [with TYPE = long int]’: phylogenetics_cpp_routines.cpp:27554:27: required from here 27554 | remove_item_from_vector(extant_tips, tip); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:918:17: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 918 | 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&, const std::vector&, double, const DFUNCTOR&, double, double, dvector&, dvector&) [with DFUNCTOR = PiecewisePolynomial; dvector = std::vector]’: phylogenetics_cpp_routines.cpp:31394:22: required from here 31394 | simulate_SBM_on_tree( Ntips, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 31395 | Nnodes, | ~~~~~~~ 31396 | Nedges, | ~~~~~~~ 31397 | tree_edge, | ~~~~~~~~~~ 31398 | edge_length, | ~~~~~~~~~~~~ 31399 | radius, | ~~~~~~~ 31400 | diffusivity_integral, | ~~~~~~~~~~~~~~~~~~~~~ 31401 | root_theta, | ~~~~~~~~~~~ 31402 | root_phi, | ~~~~~~~~~ 31403 | clade_theta, | ~~~~~~~~~~~~ 31404 | clade_phi); | ~~~~~~~~~~ phylogenetics_cpp_routines.cpp:31296:48: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 31296 | for(long q=0, parent, child, e, edge; q&, TYPE2) [with TYPE1 = double; TYPE2 = double]’: phylogenetics_cpp_routines.cpp:5400:27: required from ‘long int min_polynomials_for_positive_exponential_of_irreducible_matrix(long int, const ARRAY_TYPE&) [with ARRAY_TYPE = std::vector]’ 5400 | if(find_first_occurrence(sum_of_powers, 0.0)<0) return (p+1); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:21465:94: required from here 21465 | const long min_polynomials = min_polynomials_for_positive_exponential_of_irreducible_matrix(Nstates, transition_matrix); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:468:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 468 | for(long n=0; n operator*(double, std::vector) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:10194:64: required from ‘LinearInterpolationFunctor::LinearInterpolationFunctor(const std::vector&, const std::vector&, bool, const VALUE_TYPE&, const VALUE_TYPE&, bool, double) [with VALUE_TYPE = std::vector]’ 10194 | referenceValues[0] = referenceValues[referenceCount-1] = 0.5*(referenceValues[0] + referenceValues[referenceCount-1]); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:23339:141: required from here 23339 | modelD.E = LinearInterpolationFunctor(modelE.ages,modelE.trajectory,false,modelE.trajectory[0],modelE.trajectory.back(),true,0); | ^ phylogenetics_cpp_routines.cpp:3441:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3441 | for(long i=0; i&, double, const std::vector&, std::vector&) [with TYPE = double]’: phylogenetics_cpp_routines.cpp:7458:21: 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; MODEL = MuSSEmodelE; PROGRESS_REPORTER = ProgressReporter; std::string = std::__cxx11::basic_string]’ 7458 | linear_combination(1.0,currentPoint,current_dt1,k1,point2); // point2 = currentPoint + k1*current_dt1; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:23441:9: required from here 23440 | bool success = RungeKutta2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23441 | (0, // start_time | ^~~~~~~~~~~~~~~~~ 23442 | oldest_age, // end_time | ~~~~~~~~~~~~~~~~~~~~~~~ 23443 | max(0.000001*oldest_age,min(0.2*oldest_age,relative_ODE_step/maxErate)), // default integration time step | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23444 | modelE, | ~~~~~~~ 23445 | minRecordingTimeStep, | ~~~~~~~~~~~~~~~~~~~~~ 23446 | maxRecordingTimeStep, | ~~~~~~~~~~~~~~~~~~~~~ 23447 | guessNrecordings, | ~~~~~~~~~~~~~~~~~ 23448 | E_value_step, // recordingRelValueStep | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23449 | 5, // maxTimeStepRefinements | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23450 | 4, // refinement_factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23451 | ProgressReporter(true), | ~~~~~~~~~~~~~~~~~~~~~~~ 23452 | (runtime_out_seconds>0 ? max(runtime_out_seconds*0.01, runtime_out_seconds+start_runtime-get_thread_monotonic_walltime_seconds()) : 0.0), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 23453 | warningMessage); | ~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:431:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | for(long i=0; i&, const std::vector&)’: phylogenetics_cpp_routines.cpp:1322:25: warning: ‘t1’ may be used uninitialized [-Wmaybe-uninitialized] 1322 | W += (t2-t1) * abs(CDFY-CDFX); | ~~~^~~~ phylogenetics_cpp_routines.cpp:1306:32: note: ‘t1’ was declared here 1306 | 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:2260:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized] 2260 | return c; // did not converge, but the last c is the best estimate | ^ phylogenetics_cpp_routines.cpp:2206:36: note: ‘c’ was declared here 2206 | double a = Xmin, b = Xmax, c; | ^ phylogenetics_cpp_routines.cpp: In function ‘double legendre_polynomial(long int, double)’: phylogenetics_cpp_routines.cpp:30948:16: warning: ‘Pn’ may be used uninitialized [-Wmaybe-uninitialized] 30948 | return Pn; | ^~ phylogenetics_cpp_routines.cpp:30942:16: note: ‘Pn’ was declared here 30942 | 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:2343:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized] 2343 | return c; // did not converge, but the last c is the best estimate | ^ phylogenetics_cpp_routines.cpp:2281:36: note: ‘c’ was declared here 2281 | double a = Xmin, b = Xmax, c; | ^ phylogenetics_cpp_routines.cpp: In function ‘double solve_piecewise_polynomial_sum_bisection(const dvector&, const std::vector >&, const lvector&, bool, const dvector&, double, double, double, bool, double, double, long int, long int&, long int&)’: phylogenetics_cpp_routines.cpp:2440:16: warning: ‘c’ may be used uninitialized [-Wmaybe-uninitialized] 2440 | return c; // did not converge, but the last c is the best estimate | ^ phylogenetics_cpp_routines.cpp:2373:36: note: ‘c’ was declared here 2373 | 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:6031:37: warning: ‘error’ may be used uninitialized [-Wmaybe-uninitialized] 6031 | return (best_error&, double, const std::vector&, const std::vector&, long int, const std::string&, double, double)’: phylogenetics_cpp_routines.cpp:25359:51: warning: ‘W_degree’ may be used uninitialized [-Wmaybe-uninitialized] 25359 | const double origin_W = polynomial_value(W_degree,&refined_W_coeff[origin_rg*(W_degree+1)],oldest_age-age_offset); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:25287:24: note: ‘W_degree’ was declared here 25287 | long I_degree, W_degree, NRG; | ^~~~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List HBD_PDR_loglikelihood_CPP(const std::vector&, double, double, const std::vector&, const std::vector&, long int, const std::string&, double, double, std::vector, long int)’: phylogenetics_cpp_routines.cpp:25186:102: warning: ‘Zdegree’ may be used uninitialized [-Wmaybe-uninitialized] 25186 | branching_Z = polynomial_value(Zdegree, &Zcoeff[d][current_g*(Zdegree+1)], branching_age-age_offset); | ~~~~~~~~^~~ phylogenetics_cpp_routines.cpp:25152:14: note: ‘Zdegree’ was declared here 25152 | long Zdegree, EZdegree, Wdegree; | ^~~~~~~ phylogenetics_cpp_routines.cpp:25187:102: warning: ‘Wdegree’ may be used uninitialized [-Wmaybe-uninitialized] 25187 | branching_W = polynomial_value(Wdegree, &Wcoeff[d][current_g*(Wdegree+1)], branching_age-age_offset); | ~~~~~~~~^~~ phylogenetics_cpp_routines.cpp:25152:33: note: ‘Wdegree’ was declared here 25152 | 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:4658:17: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized] 4658 | if(j != imax){ | ^~ phylogenetics_cpp_routines.cpp:4626:16: note: ‘imax’ was declared here 4626 | long i,imax,j,k; | ^~~~ phylogenetics_cpp_routines.cpp: In member function ‘void TreeSpeciationExtinctionModel::get_coalescent_trajectory(double, double, std::vector&) const’: phylogenetics_cpp_routines.cpp:10918:96: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized] 10918 | coalescent[t].Pmissing = coalescent_diversity_at_resolution_age/coalescent[t].diversity; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:10895:59: note: ‘coalescent_diversity_at_resolution_age’ was declared here 10895 | double total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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&, const std::vector&, const std::vector&, const std::vector&, bool, bool, long int)’: phylogenetics_cpp_routines.cpp:26558:27: warning: ‘parent’ may be used uninitialized [-Wmaybe-uninitialized] 26558 | long clade, edge, parent, parent_state, state=0; | ^~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_trait_richness_collectors_curve_CPP(long int, long int, long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, const std::string&, bool)’: phylogenetics_cpp_routines.cpp:20142:49: warning: ‘tip’ may be used uninitialized [-Wmaybe-uninitialized] 20142 | tip_included[tip] = true; | ^ phylogenetics_cpp_routines.cpp:20005:14: note: ‘tip’ was declared here 20005 | long tip, clade, count_tips_remaining; | ^~~ In function ‘long int uniformIntWithin(long int, long int)’, inlined from ‘Rcpp::List get_trait_richness_collectors_curve_CPP(long int, long int, long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, const std::string&, bool)’ at phylogenetics_cpp_routines.cpp:20102:41: phylogenetics_cpp_routines.cpp:3574:72: warning: ‘count_tips_remaining’ may be used uninitialized [-Wmaybe-uninitialized] 3574 | return min(maximum, (long) floor(minimum + (maximum-minimum+1) * R::runif(0.0,1.0))); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_trait_richness_collectors_curve_CPP(long int, long int, long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, const std::string&, bool)’: phylogenetics_cpp_routines.cpp:20005:26: note: ‘count_tips_remaining’ was declared here 20005 | long tip, clade, count_tips_remaining; | ^~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List get_HBDS_model_loglikelihood_CPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, long int, const std::string&, double, double, double)’: phylogenetics_cpp_routines.cpp:25908:110: warning: ‘logPhi_degree’ may be used uninitialized [-Wmaybe-uninitialized] 25908 | CSA_logPhi = polynomial_value(logPhi_degree, &logPhi_coeff[k][sg*(logPhi_degree+1)], age-(splines_slideX ? Phi_ages[k][sg] : 0.0)); | ~~~~~~~~~~~~~~^~~ phylogenetics_cpp_routines.cpp:25794:42: note: ‘logPhi_degree’ was declared here 25794 | long dummyL1, dummyL2, I_degree, logPhi_degree, E_degree; | ^~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::List find_edge_splitting_tree_CPP(long int, long int, long int, std::vector, bool, const std::vector&, bool)’: phylogenetics_cpp_routines.cpp:16205:108: warning: ‘best_Ntargets_upstream’ may be used uninitialized [-Wmaybe-uninitialized] 16205 | else if((!descends_from_best_edge[tip]) && (Ntargets_downstream_per_clade[tip]==1) && (!targets_should_be_upstream)) misplaced_targets.push_back(tip); // misplaced upstream target | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:16167:30: note: ‘best_Ntargets_upstream’ was declared here 16167 | long best_edge = -1, best_Ntargets_upstream, best_Ntargets_downstream, best_Nmisplaced_targets, best_Nmisplaced_nontargets; | ^~~~~~~~~~~~~~~~~~~~~~ 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&, const std::vector&, const std::vector&, bool, const std::vector&, double, double, double, double, bool, bool, bool, bool, bool, bool, double)’: phylogenetics_cpp_routines.cpp:11139:86: warning: ‘Pmissing_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized] 11139 | const double effective_rarefaction = rarefaction * (1-Pmissing_at_resolution_age); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:11114:24: note: ‘Pmissing_at_resolution_age’ was declared here 11114 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ phylogenetics_cpp_routines.cpp:11147:88: warning: ‘coalescent_diversity_at_resolution_age’ may be used uninitialized [-Wmaybe-uninitialized] 11147 | 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:11114:87: note: ‘coalescent_diversity_at_resolution_age’ was declared here 11114 | double Pmissing_at_resolution_age, total_diversity_at_resolution_age, coalescent_diversity_at_resolution_age; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:189, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from phylogenetics_cpp_routines.cpp:39: In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’, inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:465:46, inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:489:40, inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:744:34, inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap_end.h:30:38, inlined from ‘static SEXPREC* Rcpp::internal::generic_element_converter::get(const T&) [with T = double; int RTYPE = 19]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/converter.h:80:23, inlined from ‘static void Rcpp::Vector::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:532:13, inlined from ‘static void Rcpp::Vector::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:525:46, inlined from ‘static void Rcpp::Vector::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:514:34, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1168:32, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static void Rcpp::Vector::replace_element_impl(iterator&, Rcpp::Shield&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object; TArgs = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1169:37, inlined from ‘static Rcpp::Vector Rcpp::Vector::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1148:37, inlined from ‘static Rcpp::Vector Rcpp::Vector::create(const T& ...) [with T = {Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object, Rcpp::traits::named_object}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1131:33, inlined from ‘Rcpp::List read_Newick_string_CPP(std::string, bool, bool, bool, bool)’ at phylogenetics_cpp_routines.cpp:19126:39: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: ‘root_edge’ may be used uninitialized [-Wmaybe-uninitialized] 442 | r_vector_start(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:19042:29: note: ‘root_edge’ was declared here 19042 | double edge_length, root_edge; | ^~~~~~~~~ phylogenetics_cpp_routines.cpp: In function ‘Rcpp::NumericMatrix get_distance_matrix_between_clades_CPP(long int, long int, long int, const std::vector&, const std::vector&, const std::vector&, bool, const std::string&)’: phylogenetics_cpp_routines.cpp:13326:155: warning: ‘mrca’ may be used uninitialized [-Wmaybe-uninitialized] 13326 | 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:13299:30: note: ‘mrca’ was declared here 13299 | long cladeA, cladeB, mrca; | ^~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o castor.so RcppExports.o STMathExpression.o phylogenetics_cpp_routines.o registerDynamicSymbol.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWwHs6I/R.INSTALL3c8bf2b45b9a9/castor/src' installing to /home/hornik/tmp/CRAN_recheck/Library/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) * installing *source* package ‘Rogue’ ... ** this is package ‘Rogue’ version ‘2.1.6’ ** package ‘Rogue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOUeOxJ/R.INSTALL3c92bd2f54d769/Rogue/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c graph_geodesic.c -o graph_geodesic.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Array.c -o rnr/Array.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/BitVector.c -o rnr/BitVector.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Dropset.c -o rnr/Dropset.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/HashTable.c -o rnr/HashTable.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/List.c -o rnr/List.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Node.c -o rnr/Node.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/ProfileElem.c -o rnr/ProfileElem.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/RogueNaRok.c -o rnr/RogueNaRok.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Tree.c -o rnr/Tree.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/common.c -o rnr/common.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/legacy.c -o rnr/legacy.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/newFunctions.c -o rnr/newFunctions.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rogue_init.c -o Rogue_init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o Rogue.so graph_geodesic.o rnr/Array.o rnr/BitVector.o rnr/Dropset.o rnr/HashTable.o rnr/List.o rnr/Node.o rnr/ProfileElem.o rnr/RogueNaRok.o rnr/Tree.o rnr/common.o rnr/legacy.o rnr/newFunctions.o Rogue_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOUeOxJ/R.INSTALL3c92bd2f54d769/Rogue/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rogue/00new/Rogue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** 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 (Rogue) begin installing package ‘TreeSearch’ * installing *source* package ‘Quartet’ ... ** this is package ‘Quartet’ version ‘1.2.7’ ** package ‘Quartet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMynuzL/R.INSTALL3c90d06d65e429/Quartet/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AbstractDistanceCalculator.cpp -o AbstractDistanceCalculator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AllQuartets.cpp -o AllQuartets.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c EdgeParser.cpp -o EdgeParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDT.cpp -o HDT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingCCToC.cpp -o HDTCountingCCToC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingCTransform.cpp -o HDTCountingCTransform.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingG.cpp -o HDTCountingG.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingIGToC.cpp -o HDTCountingIGToC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingLeaf.cpp -o HDTCountingLeaf.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTFactory.cpp -o HDTFactory.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTListUtils.cpp -o HDTListUtils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c NewickParser.cpp -o NewickParser.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c QuartetDistanceCalculator.cpp -o QuartetDistanceCalculator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RootedTree.cpp -o RootedTree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RootedTreeFactory.cpp -o RootedTreeFactory.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TripletDistanceCalculator.cpp -o TripletDistanceCalculator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c int_stuff.cpp -o int_stuff.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rQuartetDist.cpp -o rQuartetDist.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rTripletDist.cpp -o rTripletDist.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o Quartet.so AbstractDistanceCalculator.o AllQuartets.o EdgeParser.o HDT.o HDTCountingCCToC.o HDTCountingCTransform.o HDTCountingG.o HDTCountingIGToC.o HDTCountingLeaf.o HDTFactory.o HDTListUtils.o NewickParser.o QuartetDistanceCalculator.o RcppExports.o RootedTree.o RootedTreeFactory.o TripletDistanceCalculator.o int_stuff.o rQuartetDist.o rTripletDist.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMynuzL/R.INSTALL3c90d06d65e429/Quartet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Quartet/00new/Quartet/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (Quartet) * installing *source* package ‘TreeSearch’ ... ** this is package ‘TreeSearch’ version ‘1.5.1’ ** package ‘TreeSearch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMOrrYK/R.INSTALL3c939bb61c3d8/TreeSearch/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphy.c -o RMorphy.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphyUtils.c -o RMorphyUtils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TreeSearch-init.c -o TreeSearch-init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitch.c -o fitch.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c morphy.c -o morphy.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c morphy_score.cpp -o morphy_score.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mpl.c -o mpl.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rearrange.cpp -o rearrange.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c statedata.c -o statedata.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wagner.c -o wagner.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TreeSearch.so RMorphy.o RMorphyUtils.o RcppExports.o TreeSearch-init.o fitch.o morphy.o morphy_score.o mpl.o rearrange.o statedata.o wagner.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMOrrYK/R.INSTALL3c939bb61c3d8/TreeSearch/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TreeSearch/00new/TreeSearch/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** 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 (TreeSearch) checking TreeTools_1.13.1.tar.gz ... checking avotrex_1.3.0.tar.gz ... checking orthGS_0.1.6.tar.gz ... checking Quartet_1.2.7.tar.gz ... checking TBRDist_1.0.2.tar.gz ... checking Rogue_2.1.6.tar.gz ... checking TreeDist_2.9.2.tar.gz ... checking TotalCopheneticIndex_2.0.1.tar.gz ... checking TreeSearch_1.5.1.tar.gz ... checking phylosem_1.1.4.tar.gz ... Depends: Package: TreeTools Depends: R (>= 3.4.0), ape (>= 5.6), Imports: bit64, lifecycle, colorspace, fastmatch (>= 1.1.3), methods, PlotTools, RCurl, R.cache, Rdpack (>= 2.3), LinkingTo: Rcpp Timings: user system elapsed TreeTools 132.199 9.515 146.481 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 2 7 Check results summary: TreeTools ... NOTE * checking CRAN incoming feasibility ... [7s/11s] NOTE rdepends_avotrex ... OK rdepends_orthGS ... OK rdepends_phylosem ... OK rdepends_Quartet ... OK rdepends_Rogue ... OK rdepends_TBRDist ... NOTE * checking C++ specification ... NOTE rdepends_TotalCopheneticIndex ... OK rdepends_TreeDist ... OK rdepends_TreeSearch ... NOTE * checking Rd cross-references ... NOTE