* installing *source* package ‘phyclust’ ...
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/phyclust/src'
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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;
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
seq-gen/eigen.c:63:11: warning: variable 'det' set but not used [-Wunused-but-set-variable]
63 | double det=1.0;
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
1 warning generated.
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
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)
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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;
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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
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
| ^
2 warnings generated.
paml_baseml/treesub.c:3566:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
3566 | int tmp; //WCC:add
| ^
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/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/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/tools.c:98:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
98 | int i;
| ^
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/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/treesub.c:7989:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
7989 | int tmp;
| ^
paml_baseml/tools.c:1413:8: warning: variable 'rounds' set but not used [-Wunused-but-set-variable]
1413 | int rounds=0;
| ^
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/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/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];
| ^
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.
24 warnings generated.
/usr/local/clang19/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/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)