downloading reverse dependencies ...
downloading iNEXT.4steps_1.0.1.tar.gz ... ok
downloading iNEXT.beta3D_1.0.2.tar.gz ... ok

installing dependencies ‘iNEXT.3D’, ‘phyclust’

begin installing package ‘phyclust’
* installing *source* package ‘phyclust’ ...
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-1) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwZBEUX/R.INSTALL2d770b5f621d8/phyclust/src'
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust.c -o R_phyclust.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_edist.c -o R_phyclust_edist.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_em_step.c -o R_phyclust_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_label.c -o R_phyclust_label.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_logL.c -o R_phyclust_logL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_logPt.c -o R_phyclust_logPt.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_se.c -o R_phyclust_se.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_se_update.c -o R_phyclust_se_update.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_struct.c -o R_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_update.c -o R_phyclust_update.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c RRand.c -o RRand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_RRand.c -o R_RRand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c zzz.c -o zzz.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_pam.c -o phyclust/phyclust_pam.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/ms.c -o msdir/ms.o
msdir/ms.c: In function ‘gensam’:
msdir/ms.c:291:4: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  291 |    else if( segsitesin > 0 ) {
      |    ^~~~
msdir/ms.c:337:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  337 |         free(seglst);
      |         ^~~~
msdir/ms.c: In function ‘gasdev’:
msdir/ms.c:1149:22: warning: variable ‘gset’ set but not used [-Wunused-but-set-variable]
 1149 |         static float gset;
      |                      ^~~~
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/ms_main.c -o msdir/ms_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/R_ms_main.c -o msdir/R_ms_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/R_rand.c -o msdir/R_rand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/streec.c -o msdir/streec.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/aamodels.c -o seq-gen/aamodels.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/eigen.c -o seq-gen/eigen.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/evolve.c -o seq-gen/evolve.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/gamma.c -o seq-gen/gamma.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/global.c -o seq-gen/global.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/model.c -o seq-gen/model.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/seq-gen.c -o seq-gen/seq-gen.o
seq-gen/seq-gen.c: In function ‘ReadFileParams’:
seq-gen/seq-gen.c:715:15: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
  715 |         char *i;        //WCC:add
      |               ^
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/treefile.c -o seq-gen/treefile.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/twister.c -o seq-gen/twister.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c paml_baseml/baseml.c -o paml_baseml/baseml.o
In file included from paml_baseml/baseml.c:130:
paml_baseml/treesub.c: In function ‘ReadSeq’:
paml_baseml/treesub.c:164:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
  164 |    char *tmp_c;
      |          ^~~~~
paml_baseml/treesub.c:163:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
  163 |    int tmp;
      |        ^~~
paml_baseml/treesub.c:160:9: warning: variable ‘str’ set but not used [-Wunused-but-set-variable]
  160 |    char str[4]="   ";
      |         ^~~
paml_baseml/treesub.c:158:10: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  158 |    int h,b[3]={0};
      |          ^
paml_baseml/treesub.c: In function ‘IdenticalSeqs’:
paml_baseml/treesub.c:806:17: warning: variable ‘same’ set but not used [-Wunused-but-set-variable]
  806 |    int is,js,h, same,nkept=com.ns;
      |                 ^~~~
paml_baseml/treesub.c: In function ‘DistanceIJ’:
paml_baseml/treesub.c:1709:16: warning: variable ‘missing’ set but not used [-Wunused-but-set-variable]
 1709 |    int h, n=4, missing=0;
      |                ^~~~~~~
paml_baseml/treesub.c: In function ‘ReadTreeB’:
paml_baseml/treesub.c:2393:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 2393 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/treesub.c:2392:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 2392 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘ReadTreeN’:
paml_baseml/treesub.c:2601:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 2601 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/treesub.c:2600:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 2600 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘GetInitialsTimes’:
paml_baseml/treesub.c:3417:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3417 |          for(i=0; 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-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c 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-14 -shared -L/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwZBEUX/R.INSTALL2d770b5f621d8/phyclust/src'
installing to /home/hornik/tmp/CRAN/Library/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)
begin installing package ‘iNEXT.3D’
* installing *source* package ‘iNEXT.3D’ ...
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpW6avNb/R.INSTALL2d781677252276/iNEXT.3D/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c FDRcpp.cpp -o FDRcpp.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c PDRcpp.cpp -o PDRcpp.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c TDRcpp.cpp -o TDRcpp.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o iNEXT.3D.so FDRcpp.o PDRcpp.o RcppExports.o TDRcpp.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpW6avNb/R.INSTALL2d781677252276/iNEXT.3D/src'
installing to /home/hornik/tmp/CRAN/Library/00LOCK-iNEXT.3D/00new/iNEXT.3D/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (iNEXT.3D)

checking iNEXT.3D_1.0.6.tar.gz ...
checking iNEXT.4steps_1.0.1.tar.gz ...
checking iNEXT.beta3D_1.0.2.tar.gz ...

Depends:
Package: iNEXT.3D
  Depends: R (>= 4.0)
  Imports: stats, tibble, ggplot2, reshape2, tidytree, phyclust, dplyr,
    ape, Rcpp
  LinkingTo: Rcpp

Timings:
            user system elapsed
iNEXT.3D 197.423  6.545 204.862

Results:
Check status summary:
                  OK
  Source packages  1
  Reverse depends  2

Check results summary:
iNEXT.3D ... OK
rdepends_iNEXT.4steps ... OK
rdepends_iNEXT.beta3D ... OK