installing dependencies ‘decoupleR’, ‘infercnv’, ‘Nebulosa’, ‘UCell’,
  ‘waffle’

Warning: package ‘waffle’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
also installing the dependencies ‘findpython’, ‘phyclust’, ‘HiddenMarkov’, ‘argparse’

begin installing package ‘findpython’
begin installing package ‘phyclust’
begin installing package ‘HiddenMarkov’
begin installing package ‘decoupleR’
begin installing package ‘Nebulosa’
begin installing package ‘UCell’
* installing *source* package ‘findpython’ ...
** this is package ‘findpython’ version ‘1.0.9’
** package ‘findpython’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (findpython)
begin installing package ‘argparse’
* installing *source* package ‘HiddenMarkov’ ...
** this is package ‘HiddenMarkov’ version ‘1.8-14’
** package ‘HiddenMarkov’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFgLNIw/R.INSTALL1c51c863a5208e/HiddenMarkov/src'
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c HiddenMarkov_init.c -o HiddenMarkov_init.o
gfortran-15  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c dthmm.f -o dthmm.o
gfortran-15  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c extract.f -o extract.o
gfortran-15  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c mmpp.f -o mmpp.o
gfortran-15  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c multiply.f -o multiply.o
gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o HiddenMarkov.so HiddenMarkov_init.o dthmm.o extract.o mmpp.o multiply.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFgLNIw/R.INSTALL1c51c863a5208e/HiddenMarkov/src'
installing to /home/hornik/tmp/CRAN_special_donttest/Library/00LOCK-HiddenMarkov/00new/HiddenMarkov/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HiddenMarkov)
* installing *source* package ‘argparse’ ...
** this is package ‘argparse’ version ‘2.3.1’
** package ‘argparse’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (argparse)
* installing *source* package ‘decoupleR’ ...
** this is package ‘decoupleR’ version ‘2.16.0’
** package ‘decoupleR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (decoupleR)
* installing *source* package ‘UCell’ ...
** this is package ‘UCell’ version ‘2.14.0’
** package ‘UCell’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (UCell)
* installing *source* package ‘Nebulosa’ ...
** this is package ‘Nebulosa’ version ‘1.20.0’
** package ‘Nebulosa’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Nebulosa)
* installing *source* package ‘phyclust’ ...
** this is package ‘phyclust’ version ‘0.1-34’
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6ipkNG/R.INSTALL1c51cc67a98da0/phyclust/src'
gcc-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -I"/home/hornik/tmp/R/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-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o phyclust.so R_phyclust.o R_phyclust_edist.o R_phyclust_em_step.o R_phyclust_find_consensus.o R_phyclust_label.o R_phyclust_logL.o R_phyclust_logPt.o R_phyclust_qmatrix.o R_phyclust_se.o R_phyclust_se_update.o R_phyclust_struct.o R_phyclust_update.o RRand.o R_RRand.o zzz.o phyclust/phyclust_ape_nj.o phyclust/phyclust_edist.o phyclust/phyclust_em_control.o phyclust/phyclust_em_fp.o phyclust/phyclust_em_phyclust_struct.o phyclust/phyclust_em_step.o phyclust/phyclust_em_tool.o phyclust/phyclust_file_input.o phyclust/phyclust_init_method.o phyclust/phyclust_init_method_ex.o phyclust/phyclust_init_method_kmed.o phyclust/phyclust_init_method_nj.o phyclust/phyclust_init_method_pam.o phyclust/phyclust_init_procedure.o phyclust/phyclust_label.o phyclust/phyclust_logpL.o phyclust/phyclust_optim_nmmin.o phyclust/phyclust_pam.o phyclust/phyclust_qmatrix_array.o phyclust/phyclust_qmatrix.o phyclust/phyclust_se_convolution_em_step.o phyclust/phyclust_se_convolution_em_tool.o phyclust/phyclust_se_convolution_logpL.o phyclust/phyclust_se_em_fp.o phyclust/phyclust_se_em_phyclust_struct.o phyclust/phyclust_se_em_tool.o phyclust/phyclust_se_pmatrix.o phyclust/phyclust_se_struct.o phyclust/phyclust_struct.o phyclust/phyclust_tool.o msdir/ms.o msdir/ms_main.o msdir/R_ms_main.o msdir/R_rand.o msdir/streec.o seq-gen/aamodels.o seq-gen/eigen.o seq-gen/evolve.o seq-gen/gamma.o seq-gen/global.o seq-gen/model.o seq-gen/nucmodels.o seq-gen/R_seq-gen_main.o seq-gen/seq-gen.o seq-gen/treefile.o seq-gen/twister.o paml_baseml/baseml.o paml_baseml/R_paml_baseml_main.o paml_baseml/tools.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6ipkNG/R.INSTALL1c51cc67a98da0/phyclust/src'
installing to /home/hornik/tmp/CRAN_special_donttest/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 ‘infercnv’
* installing *source* package ‘infercnv’ ...
** this is package ‘infercnv’ version ‘1.26.0’
** package ‘infercnv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (infercnv)

checking SCpubr_3.0.1.tar.gz ...

Depends:
Package: SCpubr
  Depends: R (>= 4.0.0)

Timings:
          user system elapsed
SCpubr 307.516 11.931 324.805

Results:
Check status summary:
                  NOTE
  Source packages    1

Check results summary:
SCpubr ... NOTE
* checking CRAN incoming feasibility ... [9s/10s] NOTE
* checking Rd cross-references ... NOTE