* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘phyclust’ ...
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpfTkQFp/R.INSTALL2c5d002606595b/phyclust/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RRand.c -o RRand.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zzz.c -o zzz.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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; i<tree.nbranch; i++)
| ^~~
In file included from paml_baseml/baseml.c:11:
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:3418:92: note: in expansion of macro ‘FPN’
3418 | fprintf(R_paml_baseml_file_pointer, "%3.0f",nodes[tree.branches[i][1]].label); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c: In function ‘readx’:
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: In function ‘NSameBranch’:
paml_baseml/treesub.c:3688:27: warning: variable ‘nsamespecies’ set but not used [-Wunused-but-set-variable]
3688 | int i,j,k, nsamebranch,nsamespecies;
| ^~~~~~~~~~~~
paml_baseml/treesub.c: In function ‘Perturbation’:
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: In function ‘StepwiseAdditionMP’:
paml_baseml/treesub.c:3873:10: warning: variable ‘z0’ set but not used [-Wunused-but-set-variable]
3873 | char *z0[NS];
| ^~
paml_baseml/treesub.c: In function ‘StepwiseAddition’:
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: In function ‘StarDecomposition’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/treesub.c:4141:7: note: in expansion of macro ‘FOR’
4141 | FOR (i, com.np) fprintf (fout,"%9.5f", x[i]); FPN (fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:4141:54: note: in expansion of macro ‘FPN’
4141 | FOR (i, com.np) fprintf (fout,"%9.5f", x[i]); FPN (fout);
| ^~~
paml_baseml/treesub.c:4111:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
4111 | int tmp;
| ^~~
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: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: In function ‘MultipleGenes’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/treesub.c:4362:7: note: in expansion of macro ‘FOR’
4362 | FOR (j,com.ns) com.z[j]+=posG0[ig]*nb; com.fpatt+=posG0[ig];
| ^~~
paml_baseml/treesub.c:4362:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
4362 | FOR (j,com.ns) com.z[j]+=posG0[ig]*nb; com.fpatt+=posG0[ig];
| ^~~
paml_baseml/treesub.c: In function ‘printSeqsMgenes2’:
paml_baseml/treesub.c:4486:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
4486 | if((h+1)%20==0) FPN(R_paml_baseml_file_pointer); if((h+1)%500==0) getchar();
| ^~
paml_baseml/treesub.c:4486:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
4486 | if((h+1)%20==0) FPN(R_paml_baseml_file_pointer); if((h+1)%500==0) getchar();
| ^~
paml_baseml/treesub.c: In function ‘rell’:
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:5007:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
5007 | int tmp;
| ^~~
paml_baseml/treesub.c: In function ‘getCodonNode1Site’:
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: In function ‘UpPassPPSG2000’:
paml_baseml/treesub.c:5918:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
5918 | for(i=0; i<nson; i++) fprintf(R_paml_baseml_file_pointer, " %2d", nBestScore[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:5918:90: note: in expansion of macro ‘FPN’
5918 | for(i=0; i<nson; i++) fprintf(R_paml_baseml_file_pointer, " %2d", nBestScore[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c: In function ‘print_lnf_site’:
paml_baseml/treesub.c:6751:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
6751 | if((h+1)%40 == 0)
| ^~
paml_baseml/treesub.c:6754:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
6754 | fprintf(flnf, "\n%6d %6.0f %16.10f %16.12f %12.4f ",
| ^~~~~~~
paml_baseml/treesub.c: In function ‘fx_r’:
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: In function ‘ReadTreeSeqs’:
paml_baseml/treesub.c:7989:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
7989 | int tmp;
| ^~~
paml_baseml/treesub.c: In function ‘GenerateGtree’:
paml_baseml/treesub.c:8152:32: warning: variable ‘ipop’ set but not used [-Wunused-but-set-variable]
8152 | int ns=data.ns[locus], i,j, ipop[NS], keep[NS], newnodeNO[2*NS-1];
| ^~~~
paml_baseml/treesub.c: In function ‘GetInitialsClock6Step1’:
paml_baseml/treesub.c:8809:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
8809 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", x[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:8809:90: note: in expansion of macro ‘FPN’
8809 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", x[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c:8810:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
8810 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:8810:90: note: in expansion of macro ‘FPN’
8810 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c:8811:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
8811 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:8811:90: note: in expansion of macro ‘FPN’
8811 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c: In function ‘AdHocRateSmoothing’:
paml_baseml/treesub.c:9000:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9000 | for(i=0; i<com.np; i++) fprintf(fout," %8.5f",x[i]); FPN(fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9000:60: note: in expansion of macro ‘FPN’
9000 | for(i=0; i<com.np; i++) fprintf(fout," %8.5f",x[i]); FPN(fout);
| ^~~
paml_baseml/treesub.c:9001:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9001 | for(i=0; i<tree.nbranch; i++) fprintf(fout," %8.5f", sqrt(varb[tree.branches[i][1]])); FPN(fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9001:94: note: in expansion of macro ‘FPN’
9001 | for(i=0; i<tree.nbranch; i++) fprintf(fout," %8.5f", sqrt(varb[tree.branches[i][1]])); FPN(fout);
| ^~~
paml_baseml/treesub.c:9007:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9007 | for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f",x[i]); FPN(fBV);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9007:66: note: in expansion of macro ‘FPN’
9007 | for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f",x[i]); FPN(fBV);
| ^~~
paml_baseml/treesub.c:9008:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9008 | for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f", sqrt(varb[tree.branches[i][1]])); FPN(fBV);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9008:94: note: in expansion of macro ‘FPN’
9008 | for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f", sqrt(varb[tree.branches[i][1]])); FPN(fBV);
| ^~~
paml_baseml/treesub.c:9053:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9053 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9053:94: note: in expansion of macro ‘FPN’
9053 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c:9054:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9054 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9054:94: note: in expansion of macro ‘FPN’
9054 | for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treesub.c:8926:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
8926 | int tmp;
| ^~~
paml_baseml/treesub.c: In function ‘DatingHeteroData’:
paml_baseml/treesub.c:9367:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
9367 | for(i=0;i<np;i++) fprintf(fout," %9.5f",x[i]); FPN(fout); fflush(fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/treesub.c:9367:52: note: in expansion of macro ‘FPN’
9367 | for(i=0;i<np;i++) fprintf(fout," %9.5f",x[i]); FPN(fout); fflush(fout);
| ^~~
paml_baseml/treesub.c:9269:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
9269 | int tmp;
| ^~~
paml_baseml/baseml.c: In function ‘Forestry’:
paml_baseml/baseml.c:544:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
544 | for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", x[i]); fprintf(frst2, "\n\n");
| ^~~
paml_baseml/baseml.c:544:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
544 | for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", x[i]); fprintf(frst2, "\n\n");
| ^~~~~~~
paml_baseml/baseml.c:545:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
545 | for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", g[i]); fprintf(frst2, "\n\n");
| ^~~
paml_baseml/baseml.c:545:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
545 | for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", g[i]); fprintf(frst2, "\n\n");
| ^~~~~~~
paml_baseml/baseml.c:622:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
622 | if(finbasemlg) fclose(finbasemlg); if (frate) fclose(frate);
| ^~
paml_baseml/baseml.c:622:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
622 | if(finbasemlg) fclose(finbasemlg); if (frate) fclose(frate);
| ^~
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: In function ‘DetailOutput’:
paml_baseml/baseml.c:690:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
690 | for(i=0; i<com.nrate; i++) fprintf (fout, " %8.5f", x[k++]); FPN(fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/baseml.c:690:69: note: in expansion of macro ‘FPN’
690 | for(i=0; i<com.nrate; i++) fprintf (fout, " %8.5f", x[k++]); FPN(fout);
| ^~~
paml_baseml/baseml.c:697:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
697 | for(i=0; i<com.nrate; i++) fprintf(fout," %8.5f", x[k++]); FPN(fout);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/baseml.c:697:67: note: in expansion of macro ‘FPN’
697 | for(i=0; i<com.nrate; i++) fprintf(fout," %8.5f", x[k++]); FPN(fout);
| ^~~
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/baseml.c: In function ‘GetOptions’:
paml_baseml/baseml.c:879:19: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
879 | if(com.model>UNREST) 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<n; i++)
| ^~~
paml_baseml/baseml.c:1327:7: note: in expansion of macro ‘FOR’
1327 | FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/baseml.c:1327:76: note: in expansion of macro ‘FPN’
1327 | FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/baseml.c:1328:7: note: in expansion of macro ‘FOR’
1328 | FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/baseml.c:1328:76: note: in expansion of macro ‘FPN’
1328 | FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/treespace.c: In function ‘GetIofLHistory’:
paml_baseml/paml.h:25:31: warning: ‘s[1]’ may be used uninitialized [-Wmaybe-uninitialized]
25 | #define min2(a,b) ((a)<(b)?(a):(b))
| ~~~~~~~~~~~~^~~~~
paml_baseml/treespace.c:383:38: note: in expansion of macro ‘min2’
383 | k[nnode]=max2(s[0],s[1]); s[0]=min2(s[0],s[1]); s[1]=k[nnode];
| ^~~~
In file included from paml_baseml/baseml.c:131:
paml_baseml/treespace.c:375:52: note: ‘s[1]’ was declared here
375 | int index, i,j,k[NS+1], inode,nnode, nodea[NS], s[2];
| ^
paml_baseml/paml.h:25:31: warning: ‘s[0]’ may be used uninitialized [-Wmaybe-uninitialized]
25 | #define min2(a,b) ((a)<(b)?(a):(b))
| ~~~~~~~~~~~~^~~~~
paml_baseml/treespace.c:383:38: note: in expansion of macro ‘min2’
383 | k[nnode]=max2(s[0],s[1]); s[0]=min2(s[0],s[1]); s[1]=k[nnode];
| ^~~~
paml_baseml/treespace.c:375:52: note: ‘s[0]’ was declared here
375 | int index, i,j,k[NS+1], inode,nnode, nodea[NS], s[2];
| ^
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__HAVE_R_ -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c paml_baseml/tools.c -o paml_baseml/tools.o
paml_baseml/tools.c: In function ‘ScanFastaFile’:
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: In function ‘printsma’:
paml_baseml/tools.c:1019:9: warning: variable ‘codon’ set but not used [-Wunused-but-set-variable]
1019 | char codon[4]=" ";
| ^~~~~
In file included from paml_baseml/tools.c:3:
paml_baseml/tools.c: In function ‘strc’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:1106:4: note: in expansion of macro ‘FOR’
1106 | FOR (i,n) s[i]=(char)c; s[n]=0;
| ^~~
paml_baseml/tools.c:1106:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
1106 | FOR (i,n) s[i]=(char)c; s[n]=0;
| ^
paml_baseml/tools.c: In function ‘gfopen’:
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: In function ‘CDFBeta’:
paml_baseml/tools.c:2714:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2714 | if (q == (double)n)
| ^~
paml_baseml/tools.c:2716:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2716 | for(i=1 ; i<=n ; i++) {
| ^~~
paml_baseml/tools.c: In function ‘EigenTridagQLImplicit’:
paml_baseml/tools.c:4774:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
4774 | for (i=1;i<n;i++) e[i-1]=e[i]; e[n-1]=0;
| ^~~
paml_baseml/tools.c:4774:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
4774 | for (i=1;i<n;i++) e[i-1]=e[i]; e[n-1]=0;
| ^
paml_baseml/tools.c: In function ‘scanfile’:
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: In function ‘DescriptiveStatistics’:
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:5227:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
5227 | int tmp; //WCC:add
| ^~~
paml_baseml/tools.c: In function ‘DescriptiveStatisticsSimple’:
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:5456:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
5456 | int tmp; //WCC:add
| ^~~
paml_baseml/tools.c: In function ‘Newton’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:6118:4: note: in expansion of macro ‘FOR’
6118 | FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]); FPN (R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/tools.c:6118:73: note: in expansion of macro ‘FPN’
6118 | FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]); FPN (R_paml_baseml_file_pointer);
| ^~~
paml_baseml/tools.c: In function ‘ming2’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:6254:7: note: in expansion of macro ‘FOR’
6254 | FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/tools.c:6254:74: note: in expansion of macro ‘FPN’
6254 | FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][0]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:6255:7: note: in expansion of macro ‘FOR’
6255 | FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/tools.c:6255:74: note: in expansion of macro ‘FPN’
6255 | FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][1]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:6268:7: note: in expansion of macro ‘FOR’
6268 | FOR(i,n) fprintf(R_paml_baseml_file_pointer, " %8.5f", x[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/tools.c:6268:71: note: in expansion of macro ‘FPN’
6268 | FOR(i,n) fprintf(R_paml_baseml_file_pointer, " %8.5f", x[i]); FPN(R_paml_baseml_file_pointer);
| ^~~
paml_baseml/tools.c: In function ‘ming1’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
20 | #define FOR(i,n) for(i=0; i<n; i++)
| ^~~
paml_baseml/tools.c:6440:7: note: in expansion of macro ‘FOR’
6440 | FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]); FPN (R_paml_baseml_file_pointer);
| ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
22 | #define FPN(file) fputc('\n', file)
| ^~~~~
paml_baseml/tools.c:6440:76: note: in expansion of macro ‘FPN’
6440 | FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]); FPN (R_paml_baseml_file_pointer);
| ^~~
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/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.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpfTkQFp/R.INSTALL2c5d002606595b/phyclust/src'
make[1]: Entering directory '/tmp/RtmpfTkQFp/R.INSTALL2c5d002606595b/phyclust/src'
make[1]: Leaving directory '/tmp/RtmpfTkQFp/R.INSTALL2c5d002606595b/phyclust/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
converting help for package ‘phyclust’
finding HTML links ... done
00_phyclust-package html
11_d.Color html
11_d.EMC html
11_d.EMControl html
11_d.boundary.method html
11_d.code.type html
11_d.edist.model html
11_d.em.method html
11_d.identifier html
11_d.init.method html
11_d.init.procedure html
11_d.label.method html
11_d.se.model html
11_d.show.option html
11_d.standard.code html
11_d.substitution html
RRand html
as.star.tree html
bootstrap.seq html
bootstrap.seq.data html
bootstrap.star.trees html
bootstrap.star.trees.seq html
code2nid html
code2snp html
data.fasta.pony html
data.phylip.crohn html
data.phylip.pony html
file.read html
file.write html
find.best html
find.consensus html
gen.equal.star.anc.dec html
gen.seq html
gen.star.tree html
gen.unit.K html
get.rooted.tree.height html
getcut.fun html
haplo.post.prob html
ms html
nid.aid.cid html
paml.baseml html
phyclust.Pt html
phyclust html
phyclust.e.step html
phyclust.edist html
phyclust.em.step html
phyclust.logL html
phyclust.m.step html
phyclust.se html
phyclust.se.update html
phyclust.update html
plotdots html
plotgaps html
plothist html
plotnj html
plotstruct html
print.summary html
prune.Mu html
read.seqgen html
rescale.rooted.tree html
seq.data html
seqgen html
snp2sid html
zz_all.internal html
zz_all.internal.tzeng html
** 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)