* installing *source* package ‘phyclust’ ... ** using staged installation ** libs using C compiler: ‘Debian clang version 16.0.6 (11)’ clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust.c -o R_phyclust.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_edist.c -o R_phyclust_edist.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_em_step.c -o R_phyclust_em_step.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_label.c -o R_phyclust_label.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_logL.c -o R_phyclust_logL.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_logPt.c -o R_phyclust_logPt.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_se.c -o R_phyclust_se.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_se_update.c -o R_phyclust_se_update.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_struct.c -o R_phyclust_struct.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_phyclust_update.c -o R_phyclust_update.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c RRand.c -o RRand.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c R_RRand.c -o R_RRand.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c zzz.c -o zzz.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -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] double ttt = 0.; ^ 1 warning generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c msdir/ms.c -o msdir/ms.o msdir/ms.c:1149:15: warning: variable 'gset' set but not used [-Wunused-but-set-variable] static float gset; ^ 1 warning generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c msdir/ms_main.c -o msdir/ms_main.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c msdir/R_ms_main.c -o msdir/R_ms_main.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c msdir/R_rand.c -o msdir/R_rand.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c msdir/streec.c -o msdir/streec.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/aamodels.c -o seq-gen/aamodels.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -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] double det=1.0; ^ 1 warning generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/evolve.c -o seq-gen/evolve.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/gamma.c -o seq-gen/gamma.o seq-gen/gamma.c:45:5: warning: use of unary operator that may be intended as compound assignment (-=) r =- log(seq_gen_rndu()); ^~ 1 warning generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/global.c -o seq-gen/global.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/model.c -o seq-gen/model.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -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] char *i; //WCC:add ^ seq-gen/seq-gen.c:966:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] ReadFileParams(); ^ seq-gen/seq-gen.c:962:2: note: previous statement is here if (!quiet) ^ 2 warnings generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/treefile.c -o seq-gen/treefile.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c seq-gen/twister.c -o seq-gen/twister.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -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] int tmp; ^ paml_baseml/treesub.c:164:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; ^ paml_baseml/treesub.c:1706:16: warning: variable 'missing' set but not used [-Wunused-but-set-variable] int h, n=4, missing=0; ^ paml_baseml/treesub.c:2389:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/treesub.c:2390:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; //WCC:add ^ paml_baseml/treesub.c:2597:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/treesub.c:2598:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; //WCC:add ^ paml_baseml/treesub.c:3563:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/treesub.c:3752:8: warning: variable 'step' set but not used [-Wunused-but-set-variable] int step=0, ntree=0, nmove=0, improve=0, ineighb, i,j; ^ paml_baseml/treesub.c:3756:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/treesub.c:3997:29: warning: variable 'bestbranch' set but not used [-Wunused-but-set-variable] int ns0=com.ns, is, i,j, bestbranch=0, randadd=0, order[NS]; ^ paml_baseml/treesub.c:4103:36: warning: variable 'son1' set but not used [-Wunused-but-set-variable] int inode, nson=0, ison1,ison2, son1, son2; ^ paml_baseml/treesub.c:4103:42: warning: variable 'son2' set but not used [-Wunused-but-set-variable] int inode, nson=0, ison1,ison2, son1, son2; ^ paml_baseml/treesub.c:4108:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; ^ paml_baseml/treesub.c:5002:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; ^ paml_baseml/treesub.c:5003:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; ^ paml_baseml/treesub.c:5450:31: warning: variable 'nchange' set but not used [-Wunused-but-set-variable] int nid=tree.nnode-com.ns, nchange; ^ paml_baseml/treesub.c:5736:11: warning: variable 'hp' set but not used [-Wunused-but-set-variable] int i, hp; ^ paml_baseml/treesub.c:6860:25: warning: variable 'FPE' set but not used [-Wunused-but-set-variable] int h, ir, i,k, ig, FPE=0; ^ paml_baseml/treesub.c:7984:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; ^ paml_baseml/treesub.c:8921:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; ^ paml_baseml/treesub.c:9264:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; ^ paml_baseml/baseml.c:401:56: warning: variable 'np0' set but not used [-Wunused-but-set-variable] 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] double Qfactor,*p=com.pi, t=0, k1,k2, S,V, Y=p[0]+p[1],R=p[2]+p[3]; ^ 24 warnings generated. clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.o clang-16 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O3 -Wall -pedantic -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] int i; ^ paml_baseml/tools.c:967:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/tools.c:1126:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/tools.c:1409:8: warning: variable 'rounds' set but not used [-Wunused-but-set-variable] int rounds=0; ^ paml_baseml/tools.c:2712:10: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] for(i=1 ; i<=n ; i++) { ^ paml_baseml/tools.c:2710:7: note: previous statement is here if (q == (double)n) ^ paml_baseml/tools.c:4938:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; //WCC:add ^ paml_baseml/tools.c:5223:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/tools.c:5224:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; //WCC:add ^ paml_baseml/tools.c:5452:8: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int tmp; //WCC:add ^ paml_baseml/tools.c:5453:10: warning: variable 'tmp_c' set but not used [-Wunused-but-set-variable] char *tmp_c; //WCC:add ^ paml_baseml/tools.c:5777:28: warning: variable 'percentUse' set but not used [-Wunused-but-set-variable] double factor=2, step1, percentUse=0; ^ 11 warnings generated. clang-16 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -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 -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/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)