* installing *source* package ‘phyclust’ ...
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/phyclust/src'
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust.c -o R_phyclust.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_edist.c -o R_phyclust_edist.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_em_step.c -o R_phyclust_em_step.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_label.c -o R_phyclust_label.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_logL.c -o R_phyclust_logL.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_logPt.c -o R_phyclust_logPt.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_se.c -o R_phyclust_se.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_se_update.c -o R_phyclust_se_update.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_struct.c -o R_phyclust_struct.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_phyclust_update.c -o R_phyclust_update.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RRand.c -o RRand.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_RRand.c -o R_RRand.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c zzz.c -o zzz.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_pam.c -o phyclust/phyclust_pam.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c msdir/ms_main.c -o msdir/ms_main.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c msdir/R_ms_main.c -o msdir/R_ms_main.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c msdir/R_rand.c -o msdir/R_rand.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c msdir/streec.c -o msdir/streec.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/aamodels.c -o seq-gen/aamodels.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/eigen.c -o seq-gen/eigen.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/evolve.c -o seq-gen/evolve.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/gamma.c -o seq-gen/gamma.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/global.c -o seq-gen/global.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/model.c -o seq-gen/model.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/treefile.c -o seq-gen/treefile.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seq-gen/twister.c -o seq-gen/twister.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c paml_baseml/baseml.c -o paml_baseml/baseml.o
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.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
| ^~~
gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -D__HAVE_R_ -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c paml_baseml/tools.c -o paml_baseml/tools.o
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/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/treesub.c:3688:27: warning: variable 'nsamespecies' set but not used [-Wunused-but-set-variable]
3688 | int i,j,k, nsamebranch,nsamespecies;
| ^~~~~~~~~~~~
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/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/tools.c: In function 'CDFBeta':
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/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/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/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/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/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/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/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/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/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);
| ^~~
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 -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o phyclust.so R_phyclust.o R_phyclust_edist.o R_phyclust_em_step.o R_phyclust_find_consensus.o R_phyclust_label.o R_phyclust_logL.o R_phyclust_logPt.o R_phyclust_qmatrix.o R_phyclust_se.o R_phyclust_se_update.o R_phyclust_struct.o R_phyclust_update.o RRand.o R_RRand.o zzz.o phyclust/phyclust_ape_nj.o phyclust/phyclust_edist.o phyclust/phyclust_em_control.o phyclust/phyclust_em_fp.o phyclust/phyclust_em_phyclust_struct.o phyclust/phyclust_em_step.o phyclust/phyclust_em_tool.o phyclust/phyclust_file_input.o phyclust/phyclust_init_method.o phyclust/phyclust_init_method_ex.o phyclust/phyclust_init_method_kmed.o phyclust/phyclust_init_method_nj.o phyclust/phyclust_init_method_pam.o phyclust/phyclust_init_procedure.o phyclust/phyclust_label.o phyclust/phyclust_logpL.o phyclust/phyclust_optim_nmmin.o phyclust/phyclust_pam.o phyclust/phyclust_qmatrix_array.o phyclust/phyclust_qmatrix.o phyclust/phyclust_se_convolution_em_step.o phyclust/phyclust_se_convolution_em_tool.o phyclust/phyclust_se_convolution_logpL.o phyclust/phyclust_se_em_fp.o phyclust/phyclust_se_em_phyclust_struct.o phyclust/phyclust_se_em_tool.o phyclust/phyclust_se_pmatrix.o phyclust/phyclust_se_struct.o phyclust/phyclust_struct.o phyclust/phyclust_tool.o msdir/ms.o msdir/ms_main.o msdir/R_ms_main.o msdir/R_rand.o msdir/streec.o seq-gen/aamodels.o seq-gen/eigen.o seq-gen/evolve.o seq-gen/gamma.o seq-gen/global.o seq-gen/model.o seq-gen/nucmodels.o seq-gen/R_seq-gen_main.o seq-gen/seq-gen.o seq-gen/treefile.o seq-gen/twister.o paml_baseml/baseml.o paml_baseml/R_paml_baseml_main.o paml_baseml/tools.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/phyclust/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/phyclust/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/phyclust/src'
installing to /data/gannet/ripley/R/packages/tests-devel/phyclust.Rcheck/00LOCK-phyclust/00new/phyclust/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phyclust)