downloading reverse dependencies ... downloading dispRity_1.8.tar.gz ... ok installing dependencies ‘castor’, ‘Claddis’, ‘geoscale’, ‘GET’, ‘phyclust’, ‘strap’ also installing the dependency ‘naturalsort’ begin installing package ‘naturalsort’ begin installing package ‘geoscale’ begin installing package ‘phyclust’ begin installing package ‘GET’ * installing *source* package ‘naturalsort’ ... ** package ‘naturalsort’ 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 (naturalsort) begin installing package ‘castor’ * installing *source* package ‘geoscale’ ... ** package ‘geoscale’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (geoscale) begin installing package ‘strap’ * installing *source* package ‘strap’ ... ** package ‘strap’ 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 ** 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 (strap) begin installing package ‘Claddis’ * installing *source* package ‘GET’ ... ** package ‘GET’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (GET) * installing *source* package ‘Claddis’ ... ** 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 ** 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 (Claddis) * installing *source* package ‘phyclust’ ... ** package ‘phyclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp16pAx8/R.INSTALL13b9fe46726a9a/phyclust/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust.c -o R_phyclust.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_edist.c -o R_phyclust_edist.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_em_step.c -o R_phyclust_em_step.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_label.c -o R_phyclust_label.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_logL.c -o R_phyclust_logL.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_logPt.c -o R_phyclust_logPt.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_se.c -o R_phyclust_se.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_se_update.c -o R_phyclust_se_update.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_struct.c -o R_phyclust_struct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_phyclust_update.c -o R_phyclust_update.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RRand.c -o RRand.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_RRand.c -o R_RRand.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zzz.c -o zzz.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_pam.c -o phyclust/phyclust_pam.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msdir/ms.c -o msdir/ms.o msdir/ms.c: In function ‘gensam’: msdir/ms.c:291:4: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 291 | else if( segsitesin > 0 ) { | ^~~~ msdir/ms.c:337:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 337 | free(seglst); | ^~~~ msdir/ms.c: In function ‘gasdev’: msdir/ms.c:1149:22: warning: variable ‘gset’ set but not used [-Wunused-but-set-variable] 1149 | static float gset; | ^~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msdir/ms_main.c -o msdir/ms_main.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msdir/R_ms_main.c -o msdir/R_ms_main.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msdir/R_rand.c -o msdir/R_rand.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msdir/streec.c -o msdir/streec.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/aamodels.c -o seq-gen/aamodels.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/eigen.c -o seq-gen/eigen.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/evolve.c -o seq-gen/evolve.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/gamma.c -o seq-gen/gamma.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/global.c -o seq-gen/global.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/model.c -o seq-gen/model.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/seq-gen.c -o seq-gen/seq-gen.o seq-gen/seq-gen.c: In function ‘ReadFileParams’: seq-gen/seq-gen.c:715:15: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 715 | char *i; //WCC:add | ^ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/treefile.c -o seq-gen/treefile.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seq-gen/twister.c -o seq-gen/twister.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c paml_baseml/baseml.c -o paml_baseml/baseml.o In file included from paml_baseml/baseml.c:130: paml_baseml/treesub.c: In function ‘ReadSeq’: paml_baseml/treesub.c:164:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable] 164 | char *tmp_c; | ^~~~~ paml_baseml/treesub.c:163:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 163 | int tmp; | ^~~ paml_baseml/treesub.c:160:9: warning: variable ‘str’ set but not used [-Wunused-but-set-variable] 160 | char str[4]=" "; | ^~~ paml_baseml/treesub.c:158:10: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 158 | int h,b[3]={0}; | ^ paml_baseml/treesub.c: In function ‘IdenticalSeqs’: paml_baseml/treesub.c:806:17: warning: variable ‘same’ set but not used [-Wunused-but-set-variable] 806 | int is,js,h, same,nkept=com.ns; | ^~~~ paml_baseml/treesub.c: In function ‘DistanceIJ’: paml_baseml/treesub.c:1709:16: warning: variable ‘missing’ set but not used [-Wunused-but-set-variable] 1709 | int h, n=4, missing=0; | ^~~~~~~ paml_baseml/treesub.c: In function ‘ReadTreeB’: paml_baseml/treesub.c:2393:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable] 2393 | char *tmp_c; //WCC:add | ^~~~~ paml_baseml/treesub.c:2392:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 2392 | int tmp; //WCC:add | ^~~ paml_baseml/treesub.c: In function ‘ReadTreeN’: paml_baseml/treesub.c:2601:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable] 2601 | char *tmp_c; //WCC:add | ^~~~~ paml_baseml/treesub.c:2600:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 2600 | int tmp; //WCC:add | ^~~ paml_baseml/treesub.c: In function ‘GetInitialsTimes’: paml_baseml/treesub.c:3417:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 3417 | for(i=0; iUNREST) GetStepMatrix(line); break; | ^~ paml_baseml/baseml.c:879:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 879 | if(com.model>UNREST) GetStepMatrix(line); break; | ^~~~~ paml_baseml/baseml.c: In function ‘SetxBound’: paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 20 | #define FOR(i,n) for(i=0; i&)’: 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/4.5/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:189, from /home/hornik/lib/R/Library/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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/4.5/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 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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/Rtmpg4thz0/R.INSTALL13ba6353bdb2d/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) checking Claddis_0.7.0.tar.gz ... checking dispRity_1.8.tar.gz ... Depends: Package: Claddis Depends: ape, phytools, strap, R (>= 3.5.0) Imports: clipr, geoscale, graphics, grDevices, methods, multicool, partitions, stats, utils Timings: user system elapsed Claddis 90.986 6.249 98.652 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 0 1 Check results summary: Claddis ... NOTE * checking CRAN incoming feasibility ... [6s/6s] NOTE rdepends_dispRity ... OK Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> normalizePath Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> R_check_outdirs -> normalizePath