* installing *source* package ‘phyclust’ ... ** package ‘phyclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/phyclust/src' /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust.c -o R_phyclust.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_edist.c -o R_phyclust_edist.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_em_step.c -o R_phyclust_em_step.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_label.c -o R_phyclust_label.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_logL.c -o R_phyclust_logL.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_logPt.c -o R_phyclust_logPt.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_se.c -o R_phyclust_se.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_se_update.c -o R_phyclust_se_update.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_struct.c -o R_phyclust_struct.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_phyclust_update.c -o R_phyclust_update.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c RRand.c -o RRand.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_RRand.c -o R_RRand.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c zzz.c -o zzz.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_pam.c -o phyclust/phyclust_pam.o phyclust/phyclust_pam.c:255:13: warning: variable 'ttt' set but not used [-Wunused-but-set-variable] 255 | double ttt = 0.; | ^ 1 warning generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msdir/ms.c -o msdir/ms.o msdir/ms.c:1149:15: warning: variable 'gset' set but not used [-Wunused-but-set-variable] 1149 | static float gset; | ^ 1 warning generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msdir/ms_main.c -o msdir/ms_main.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msdir/R_ms_main.c -o msdir/R_ms_main.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msdir/R_rand.c -o msdir/R_rand.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c msdir/streec.c -o msdir/streec.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/aamodels.c -o seq-gen/aamodels.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/eigen.c -o seq-gen/eigen.o seq-gen/eigen.c:63:11: warning: variable 'det' set but not used [-Wunused-but-set-variable] 63 | double det=1.0; | ^ 1 warning generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/evolve.c -o seq-gen/evolve.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/gamma.c -o seq-gen/gamma.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/global.c -o seq-gen/global.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/model.c -o seq-gen/model.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/seq-gen.c -o seq-gen/seq-gen.o seq-gen/seq-gen.c:715:8: warning: variable 'i' set but not used [-Wunused-but-set-variable] 715 | char *i; //WCC:add | ^ seq-gen/seq-gen.c:966:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 966 | ReadFileParams(); | ^ seq-gen/seq-gen.c:962:2: note: previous statement is here 962 | if (!quiet) | ^ 2 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/treefile.c -o seq-gen/treefile.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c seq-gen/twister.c -o seq-gen/twister.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c paml_baseml/baseml.c -o paml_baseml/baseml.o In file included from paml_baseml/baseml.c:130: paml_baseml/treesub.c:163:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 163 | int tmp; | ^ 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:1709:16: warning: variable 'missing' set but not used [-Wunused-but-set-variable] 1709 | int h, n=4, missing=0; | ^ 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:2393:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 2393 | 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:2601:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 2601 | char *tmp_c; //WCC:add | ^ paml_baseml/treesub.c:3566:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 3566 | int tmp; //WCC:add | ^ paml_baseml/treesub.c:3755:8: warning: variable 'step' set but not used [-Wunused-but-set-variable] 3755 | int step=0, ntree=0, nmove=0, improve=0, ineighb, i,j; | ^ paml_baseml/treesub.c:3759:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 3759 | int tmp; //WCC:add | ^ paml_baseml/treesub.c:4000:29: warning: variable 'bestbranch' set but not used [-Wunused-but-set-variable] 4000 | int ns0=com.ns, is, i,j, bestbranch=0, randadd=0, order[NS]; | ^ paml_baseml/treesub.c:4106:36: warning: variable 'son1' set but not used [-Wunused-but-set-variable] 4106 | int inode, nson=0, ison1,ison2, son1, son2; | ^ paml_baseml/treesub.c:4106:42: warning: variable 'son2' set but not used [-Wunused-but-set-variable] 4106 | int inode, nson=0, ison1,ison2, son1, son2; | ^ paml_baseml/treesub.c:4111:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 4111 | int tmp; | ^ paml_baseml/treesub.c:5007:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 5007 | int tmp; | ^ paml_baseml/treesub.c:5008:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 5008 | char *tmp_c; | ^ paml_baseml/treesub.c:5455:31: warning: variable 'nchange' set but not used [-Wunused-but-set-variable] 5455 | int nid=tree.nnode-com.ns, nchange; | ^ paml_baseml/treesub.c:5741:11: warning: variable 'hp' set but not used [-Wunused-but-set-variable] 5741 | int i, hp; | ^ paml_baseml/treesub.c:6865:25: warning: variable 'FPE' set but not used [-Wunused-but-set-variable] 6865 | int h, ir, i,k, ig, FPE=0; | ^ paml_baseml/treesub.c:7989:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 7989 | int tmp; | ^ paml_baseml/treesub.c:8926:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 8926 | int tmp; | ^ paml_baseml/treesub.c:9269:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 9269 | int tmp; | ^ paml_baseml/baseml.c:401:56: warning: variable 'np0' set but not used [-Wunused-but-set-variable] 401 | int status=0, inbasemlg=0, i,j=0, itree=0,ntree, np,np0,iteration=1; | ^ paml_baseml/baseml.c:674:11: warning: variable 'Qfactor' set but not used [-Wunused-but-set-variable] 674 | double Qfactor,*p=com.pi, t=0, k1,k2, S,V, Y=p[0]+p[1],R=p[2]+p[3]; | ^ 24 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.o /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -D__HAVE_R_ -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c paml_baseml/tools.c -o paml_baseml/tools.o paml_baseml/tools.c:98:8: warning: variable 'i' set but not used [-Wunused-but-set-variable] 98 | int i; | ^ paml_baseml/tools.c:967:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 967 | int tmp; //WCC:add | ^ paml_baseml/tools.c:1130:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 1130 | int tmp; //WCC:add | ^ paml_baseml/tools.c:1413:8: warning: variable 'rounds' set but not used [-Wunused-but-set-variable] 1413 | int rounds=0; | ^ paml_baseml/tools.c:2716:10: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 2716 | for(i=1 ; i<=n ; i++) { | ^ paml_baseml/tools.c:2714:7: note: previous statement is here 2714 | if (q == (double)n) | ^ paml_baseml/tools.c:4942:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 4942 | char *tmp_c; //WCC:add | ^ paml_baseml/tools.c:5227:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 5227 | int tmp; //WCC:add | ^ paml_baseml/tools.c:5228:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 5228 | char *tmp_c; //WCC:add | ^ paml_baseml/tools.c:5456:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] 5456 | int tmp; //WCC:add | ^ paml_baseml/tools.c:5457:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] 5457 | char *tmp_c; //WCC:add | ^ paml_baseml/tools.c:5781:28: warning: variable 'percentUse' set but not used [-Wunused-but-set-variable] 5781 | double factor=2, step1, percentUse=0; | ^ 11 warnings generated. /usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o phyclust.so R_phyclust.o R_phyclust_edist.o R_phyclust_em_step.o R_phyclust_find_consensus.o R_phyclust_label.o R_phyclust_logL.o R_phyclust_logPt.o R_phyclust_qmatrix.o R_phyclust_se.o R_phyclust_se_update.o R_phyclust_struct.o R_phyclust_update.o RRand.o R_RRand.o zzz.o phyclust/phyclust_ape_nj.o phyclust/phyclust_edist.o phyclust/phyclust_em_control.o phyclust/phyclust_em_fp.o phyclust/phyclust_em_phyclust_struct.o phyclust/phyclust_em_step.o phyclust/phyclust_em_tool.o phyclust/phyclust_file_input.o phyclust/phyclust_init_method.o phyclust/phyclust_init_method_ex.o phyclust/phyclust_init_method_kmed.o phyclust/phyclust_init_method_nj.o phyclust/phyclust_init_method_pam.o phyclust/phyclust_init_procedure.o phyclust/phyclust_label.o phyclust/phyclust_logpL.o phyclust/phyclust_optim_nmmin.o phyclust/phyclust_pam.o phyclust/phyclust_qmatrix_array.o phyclust/phyclust_qmatrix.o phyclust/phyclust_se_convolution_em_step.o phyclust/phyclust_se_convolution_em_tool.o phyclust/phyclust_se_convolution_logpL.o phyclust/phyclust_se_em_fp.o phyclust/phyclust_se_em_phyclust_struct.o phyclust/phyclust_se_em_tool.o phyclust/phyclust_se_pmatrix.o phyclust/phyclust_se_struct.o phyclust/phyclust_struct.o phyclust/phyclust_tool.o msdir/ms.o msdir/ms_main.o msdir/R_ms_main.o msdir/R_rand.o msdir/streec.o seq-gen/aamodels.o seq-gen/eigen.o seq-gen/evolve.o seq-gen/gamma.o seq-gen/global.o seq-gen/model.o seq-gen/nucmodels.o seq-gen/R_seq-gen_main.o seq-gen/seq-gen.o seq-gen/treefile.o seq-gen/twister.o paml_baseml/baseml.o paml_baseml/R_paml_baseml_main.o paml_baseml/tools.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/phyclust/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/phyclust/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/phyclust/src' installing to /data/gannet/ripley/R/packages/tests-clang/phyclust.Rcheck/00LOCK-phyclust/00new/phyclust/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phyclust)