downloading reverse dependencies ...
downloading abctools_1.1.7.tar.gz ... ok
downloading EasyABC_1.5.2.tar.gz ... ok
downloading ecolottery_1.0.0.tar.gz ... ok
downloading MaxWiK_1.0.5.tar.gz ... ok
downloading poems_1.3.1.tar.gz ... ok
downloading coala_0.7.2.tar.gz ... ok

installing dependencies ‘abc’, ‘abc.data’, ‘fossil’, ‘metRology’,
  ‘phyclust’, ‘PopGenome’, ‘rehh’, ‘scrm’, ‘trend’, ‘untb’

Warning: package ‘PopGenome’ 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 dependency ‘rehh.data’

begin installing package ‘rehh.data’
begin installing package ‘abc.data’
begin installing package ‘fossil’
begin installing package ‘untb’
begin installing package ‘metRology’
begin installing package ‘trend’
begin installing package ‘scrm’
begin installing package ‘phyclust’
* installing *source* package ‘rehh.data’ ...
** package ‘rehh.data’ successfully unpacked and MD5 sums checked
** using staged installation
** data
** inst
** 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 (rehh.data)
begin installing package ‘rehh’
* installing *source* package ‘abc.data’ ...
** package ‘abc.data’ successfully unpacked and MD5 sums checked
** using staged installation
** data
** 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 (abc.data)
begin installing package ‘abc’
* installing *source* package ‘trend’ ...
** package ‘trend’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmptg4fnz/R.INSTALL13e482fee3b15/trend/src'
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CToF90.c -o CToF90.o
gfortran-14   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c getpval.f -o getpval.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gfortran-14   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c mcbr.f -o mcbr.o
gfortran-14   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c mcbu.f -o mcbu.o
gfortran-14   -fpic  -g -O2 -Wall -pedantic -mtune=native  -c mcsnht.f -o mcsnht.o
gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o trend.so CToF90.o getpval.o init.o mcbr.o mcbu.o mcsnht.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmptg4fnz/R.INSTALL13e482fee3b15/trend/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-trend/00new/trend/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (trend)
* installing *source* package ‘fossil’ ...
** package ‘fossil’ 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
** 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 (fossil)
* installing *source* package ‘metRology’ ...
** package ‘metRology’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** 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 (metRology)
* installing *source* package ‘abc’ ...
** 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 (abc)
* installing *source* package ‘untb’ ...
** package ‘untb’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** demo
** 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 (untb)
* installing *source* package ‘rehh’ ...
** package ‘rehh’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkw1I6O/R.INSTALL13f024665fefd/rehh/src'
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_ASNEWICK.c -o CALL_ASNEWICK.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_EHH.c -o CALL_EHH.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_EHHS.c -o CALL_EHHS.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_FURCATION.c -o CALL_FURCATION.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_INTEGRAL.c -o CALL_INTEGRAL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_PAIRWISE_HAPLEN.c -o CALL_PAIRWISE_HAPLEN.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_SCAN_HH.c -o CALL_SCAN_HH.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_SCAN_HH_FULL.c -o CALL_SCAN_HH_FULL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c CALL_SFS_TESTS.c -o CALL_SFS_TESTS.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c asnewick.c -o asnewick.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c calc_ehh.c -o calc_ehh.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c calc_ehhs.c -o calc_ehhs.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c calc_furcation.c -o calc_furcation.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c calc_pairwise_haplen.c -o calc_pairwise_haplen.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c calc_sfs_tests.c -o calc_sfs_tests.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c haplotypes.c -o haplotypes.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c haplotypes_with_lengths.c -o haplotypes_with_lengths.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c haplotypes_with_nodes.c -o haplotypes_with_nodes.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c homozygosity.c -o homozygosity.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c integrate.c -o integrate.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sfs_moments.c -o sfs_moments.o
gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o rehh.so CALL_ASNEWICK.o CALL_EHH.o CALL_EHHS.o CALL_FURCATION.o CALL_INTEGRAL.o CALL_PAIRWISE_HAPLEN.o CALL_SCAN_HH.o CALL_SCAN_HH_FULL.o CALL_SFS_TESTS.o asnewick.o calc_ehh.o calc_ehhs.o calc_furcation.o calc_pairwise_haplen.o calc_sfs_tests.o haplotypes.o haplotypes_with_lengths.o haplotypes_with_nodes.o homozygosity.o init.o integrate.o sfs_moments.o -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkw1I6O/R.INSTALL13f024665fefd/rehh/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rehh/00new/rehh/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rehh)
* installing *source* package ‘phyclust’ ...
** package ‘phyclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNRnMiH/R.INSTALL13e5446635db6/phyclust/src'
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust.c -o R_phyclust.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_edist.c -o R_phyclust_edist.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_em_step.c -o R_phyclust_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_find_consensus.c -o R_phyclust_find_consensus.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_label.c -o R_phyclust_label.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_logL.c -o R_phyclust_logL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_logPt.c -o R_phyclust_logPt.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_qmatrix.c -o R_phyclust_qmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_se.c -o R_phyclust_se.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_se_update.c -o R_phyclust_se_update.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_struct.c -o R_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_phyclust_update.c -o R_phyclust_update.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c RRand.c -o RRand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_RRand.c -o R_RRand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c zzz.c -o zzz.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_ape_nj.c -o phyclust/phyclust_ape_nj.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_edist.c -o phyclust/phyclust_edist.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_control.c -o phyclust/phyclust_em_control.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_fp.c -o phyclust/phyclust_em_fp.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_phyclust_struct.c -o phyclust/phyclust_em_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_step.c -o phyclust/phyclust_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_em_tool.c -o phyclust/phyclust_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_file_input.c -o phyclust/phyclust_file_input.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method.c -o phyclust/phyclust_init_method.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_ex.c -o phyclust/phyclust_init_method_ex.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_kmed.c -o phyclust/phyclust_init_method_kmed.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_nj.c -o phyclust/phyclust_init_method_nj.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_method_pam.c -o phyclust/phyclust_init_method_pam.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_init_procedure.c -o phyclust/phyclust_init_procedure.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_label.c -o phyclust/phyclust_label.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_logpL.c -o phyclust/phyclust_logpL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_optim_nmmin.c -o phyclust/phyclust_optim_nmmin.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_pam.c -o phyclust/phyclust_pam.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_qmatrix_array.c -o phyclust/phyclust_qmatrix_array.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_qmatrix.c -o phyclust/phyclust_qmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_em_step.c -o phyclust/phyclust_se_convolution_em_step.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_em_tool.c -o phyclust/phyclust_se_convolution_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_convolution_logpL.c -o phyclust/phyclust_se_convolution_logpL.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_fp.c -o phyclust/phyclust_se_em_fp.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_phyclust_struct.c -o phyclust/phyclust_se_em_phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_em_tool.c -o phyclust/phyclust_se_em_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_pmatrix.c -o phyclust/phyclust_se_pmatrix.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_se_struct.c -o phyclust/phyclust_se_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_struct.c -o phyclust/phyclust_struct.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phyclust/phyclust_tool.c -o phyclust/phyclust_tool.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/ms.c -o msdir/ms.o
msdir/ms.c: In function ‘gensam’:
msdir/ms.c:291:4: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  291 |    else if( segsitesin > 0 ) {
      |    ^~~~
msdir/ms.c:337:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  337 |         free(seglst);
      |         ^~~~
msdir/ms.c: In function ‘gasdev’:
msdir/ms.c:1149:22: warning: variable ‘gset’ set but not used [-Wunused-but-set-variable]
 1149 |         static float gset;
      |                      ^~~~
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/ms_main.c -o msdir/ms_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/R_ms_main.c -o msdir/R_ms_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/R_rand.c -o msdir/R_rand.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c msdir/streec.c -o msdir/streec.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/aamodels.c -o seq-gen/aamodels.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/eigen.c -o seq-gen/eigen.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/evolve.c -o seq-gen/evolve.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/gamma.c -o seq-gen/gamma.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/global.c -o seq-gen/global.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/model.c -o seq-gen/model.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/nucmodels.c -o seq-gen/nucmodels.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/R_seq-gen_main.c -o seq-gen/R_seq-gen_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/seq-gen.c -o seq-gen/seq-gen.o
seq-gen/seq-gen.c: In function ‘ReadFileParams’:
seq-gen/seq-gen.c:715:15: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
  715 |         char *i;        //WCC:add
      |               ^
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/treefile.c -o seq-gen/treefile.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c seq-gen/twister.c -o seq-gen/twister.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c paml_baseml/baseml.c -o paml_baseml/baseml.o
In file included from paml_baseml/baseml.c:130:
paml_baseml/treesub.c: In function ‘ReadSeq’:
paml_baseml/treesub.c:164:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
  164 |    char *tmp_c;
      |          ^~~~~
paml_baseml/treesub.c:163:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
  163 |    int tmp;
      |        ^~~
paml_baseml/treesub.c:160:9: warning: variable ‘str’ set but not used [-Wunused-but-set-variable]
  160 |    char str[4]="   ";
      |         ^~~
paml_baseml/treesub.c:158:10: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  158 |    int h,b[3]={0};
      |          ^
paml_baseml/treesub.c: In function ‘IdenticalSeqs’:
paml_baseml/treesub.c:806:17: warning: variable ‘same’ set but not used [-Wunused-but-set-variable]
  806 |    int is,js,h, same,nkept=com.ns;
      |                 ^~~~
paml_baseml/treesub.c: In function ‘DistanceIJ’:
paml_baseml/treesub.c:1709:16: warning: variable ‘missing’ set but not used [-Wunused-but-set-variable]
 1709 |    int h, n=4, missing=0;
      |                ^~~~~~~
paml_baseml/treesub.c: In function ‘ReadTreeB’:
paml_baseml/treesub.c:2393:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 2393 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/treesub.c:2392:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 2392 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘ReadTreeN’:
paml_baseml/treesub.c:2601:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 2601 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/treesub.c:2600:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 2600 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘GetInitialsTimes’:
paml_baseml/treesub.c:3417:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3417 |          for(i=0; i<tree.nbranch; i++)
      |          ^~~
In file included from paml_baseml/baseml.c:11:
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:3418:92: note: in expansion of macro ‘FPN’
 3418 |             fprintf(R_paml_baseml_file_pointer, "%3.0f",nodes[tree.branches[i][1]].label); FPN(R_paml_baseml_file_pointer);
      |                                                                                            ^~~
paml_baseml/treesub.c: In function ‘readx’:
paml_baseml/treesub.c:3566:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 3566 |    int tmp;             //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘NSameBranch’:
paml_baseml/treesub.c:3688:27: warning: variable ‘nsamespecies’ set but not used [-Wunused-but-set-variable]
 3688 |    int i,j,k, nsamebranch,nsamespecies;
      |                           ^~~~~~~~~~~~
paml_baseml/treesub.c: In function ‘Perturbation’:
paml_baseml/treesub.c:3759:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 3759 |    int tmp;             //WCC:add
      |        ^~~
paml_baseml/treesub.c: In function ‘StepwiseAdditionMP’:
paml_baseml/treesub.c:3873:10: warning: variable ‘z0’ set but not used [-Wunused-but-set-variable]
 3873 |    char *z0[NS];
      |          ^~
paml_baseml/treesub.c: In function ‘StepwiseAddition’:
paml_baseml/treesub.c:4000:29: warning: variable ‘bestbranch’ set but not used [-Wunused-but-set-variable]
 4000 |    int ns0=com.ns, is, i,j, bestbranch=0, randadd=0, order[NS];
      |                             ^~~~~~~~~~
paml_baseml/treesub.c: In function ‘StarDecomposition’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/treesub.c:4141:7: note: in expansion of macro ‘FOR’
 4141 |       FOR (i, com.np) fprintf (fout,"%9.5f", x[i]);  FPN (fout);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:4141:54: note: in expansion of macro ‘FPN’
 4141 |       FOR (i, com.np) fprintf (fout,"%9.5f", x[i]);  FPN (fout);
      |                                                      ^~~
paml_baseml/treesub.c:4111:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 4111 |    int tmp;
      |        ^~~
paml_baseml/treesub.c:4106:42: warning: variable ‘son2’ set but not used [-Wunused-but-set-variable]
 4106 |    int inode, nson=0, ison1,ison2, son1, son2;
      |                                          ^~~~
paml_baseml/treesub.c:4106:36: warning: variable ‘son1’ set but not used [-Wunused-but-set-variable]
 4106 |    int inode, nson=0, ison1,ison2, son1, son2;
      |                                    ^~~~
paml_baseml/treesub.c: In function ‘MultipleGenes’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/treesub.c:4362:7: note: in expansion of macro ‘FOR’
 4362 |       FOR (j,com.ns) com.z[j]+=posG0[ig]*nb;   com.fpatt+=posG0[ig];
      |       ^~~
paml_baseml/treesub.c:4362:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 4362 |       FOR (j,com.ns) com.z[j]+=posG0[ig]*nb;   com.fpatt+=posG0[ig];
      |                                                ^~~
paml_baseml/treesub.c: In function ‘printSeqsMgenes2’:
paml_baseml/treesub.c:4486:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 4486 |       if((h+1)%20==0) FPN(R_paml_baseml_file_pointer); if((h+1)%500==0) getchar();
      |       ^~
paml_baseml/treesub.c:4486:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 4486 |       if((h+1)%20==0) FPN(R_paml_baseml_file_pointer); if((h+1)%500==0) getchar();
      |                                                        ^~
paml_baseml/treesub.c: In function ‘rell’:
paml_baseml/treesub.c:5008:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 5008 |    char *tmp_c;
      |          ^~~~~
paml_baseml/treesub.c:5007:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 5007 |    int tmp;
      |        ^~~
paml_baseml/treesub.c: In function ‘getCodonNode1Site’:
paml_baseml/treesub.c:5741:11: warning: variable ‘hp’ set but not used [-Wunused-but-set-variable]
 5741 |    int i, hp;
      |           ^~
paml_baseml/treesub.c: In function ‘UpPassPPSG2000’:
paml_baseml/treesub.c:5918:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 5918 |       for(i=0; i<nson; i++) fprintf(R_paml_baseml_file_pointer, " %2d", nBestScore[i]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:5918:90: note: in expansion of macro ‘FPN’
 5918 |       for(i=0; i<nson; i++) fprintf(R_paml_baseml_file_pointer, " %2d", nBestScore[i]);  FPN(R_paml_baseml_file_pointer);
      |                                                                                          ^~~
paml_baseml/treesub.c: In function ‘print_lnf_site’:
paml_baseml/treesub.c:6751:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 6751 | if((h+1)%40 == 0)
      | ^~
paml_baseml/treesub.c:6754:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 6754 |    fprintf(flnf, "\n%6d %6.0f %16.10f %16.12f %12.4f  ",
      |    ^~~~~~~
paml_baseml/treesub.c: In function ‘fx_r’:
paml_baseml/treesub.c:6865:25: warning: variable ‘FPE’ set but not used [-Wunused-but-set-variable]
 6865 |    int  h, ir, i,k, ig, FPE=0;
      |                         ^~~
paml_baseml/treesub.c: In function ‘ReadTreeSeqs’:
paml_baseml/treesub.c:7989:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 7989 |    int tmp;
      |        ^~~
paml_baseml/treesub.c: In function ‘GenerateGtree’:
paml_baseml/treesub.c:8152:32: warning: variable ‘ipop’ set but not used [-Wunused-but-set-variable]
 8152 |    int ns=data.ns[locus], i,j, ipop[NS], keep[NS], newnodeNO[2*NS-1];
      |                                ^~~~
paml_baseml/treesub.c: In function ‘GetInitialsClock6Step1’:
paml_baseml/treesub.c:8809:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 8809 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", x[i]);      FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:8809:90: note: in expansion of macro ‘FPN’
 8809 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", x[i]);      FPN(R_paml_baseml_file_pointer);
      |                                                                                          ^~~
paml_baseml/treesub.c:8810:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 8810 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:8810:90: note: in expansion of macro ‘FPN’
 8810 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |                                                                                          ^~~
paml_baseml/treesub.c:8811:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 8811 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:8811:90: note: in expansion of macro ‘FPN’
 8811 |       for(i=0; i<com.np; i++) fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |                                                                                          ^~~
paml_baseml/treesub.c: In function ‘AdHocRateSmoothing’:
paml_baseml/treesub.c:9000:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9000 |       for(i=0; i<com.np; i++) fprintf(fout," %8.5f",x[i]); FPN(fout);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9000:60: note: in expansion of macro ‘FPN’
 9000 |       for(i=0; i<com.np; i++) fprintf(fout," %8.5f",x[i]); FPN(fout);
      |                                                            ^~~
paml_baseml/treesub.c:9001:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9001 |       for(i=0; i<tree.nbranch; i++) fprintf(fout," %8.5f", sqrt(varb[tree.branches[i][1]])); FPN(fout);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9001:94: note: in expansion of macro ‘FPN’
 9001 |       for(i=0; i<tree.nbranch; i++) fprintf(fout," %8.5f", sqrt(varb[tree.branches[i][1]])); FPN(fout);
      |                                                                                              ^~~
paml_baseml/treesub.c:9007:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9007 |       for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f",x[i]); FPN(fBV);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9007:66: note: in expansion of macro ‘FPN’
 9007 |       for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f",x[i]); FPN(fBV);
      |                                                                  ^~~
paml_baseml/treesub.c:9008:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9008 |       for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f", sqrt(varb[tree.branches[i][1]])); FPN(fBV);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9008:94: note: in expansion of macro ‘FPN’
 9008 |       for(i=0; i<tree.nbranch; i++) fprintf(fBV," %12.9f", sqrt(varb[tree.branches[i][1]])); FPN(fBV);
      |                                                                                              ^~~
paml_baseml/treesub.c:9053:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9053 |          for(i=0; i<com.np; i++)  fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |          ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9053:94: note: in expansion of macro ‘FPN’
 9053 |          for(i=0; i<com.np; i++)  fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |                                                                                              ^~~
paml_baseml/treesub.c:9054:10: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9054 |          for(i=0; i<com.np; i++)  fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |          ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9054:94: note: in expansion of macro ‘FPN’
 9054 |          for(i=0; i<com.np; i++)  fprintf(R_paml_baseml_file_pointer, " %10.5f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |                                                                                              ^~~
paml_baseml/treesub.c:8926:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 8926 |    int tmp;
      |        ^~~
paml_baseml/treesub.c: In function ‘DatingHeteroData’:
paml_baseml/treesub.c:9367:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 9367 |    for(i=0;i<np;i++) fprintf(fout," %9.5f",x[i]);  FPN(fout);  fflush(fout);
      |    ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/treesub.c:9367:52: note: in expansion of macro ‘FPN’
 9367 |    for(i=0;i<np;i++) fprintf(fout," %9.5f",x[i]);  FPN(fout);  fflush(fout);
      |                                                    ^~~
paml_baseml/treesub.c:9269:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 9269 |    int tmp;
      |        ^~~
paml_baseml/baseml.c: In function ‘Forestry’:
paml_baseml/baseml.c:544:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  544 |             for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", x[i]);  fprintf(frst2, "\n\n");
      |             ^~~
paml_baseml/baseml.c:544:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  544 |             for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", x[i]);  fprintf(frst2, "\n\n");
      |                                                                        ^~~~~~~
paml_baseml/baseml.c:545:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  545 |             for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", g[i]);  fprintf(frst2, "\n\n");
      |             ^~~
paml_baseml/baseml.c:545:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  545 |             for(i=0; i<com.ntime; i++) fprintf(frst2," %9.6f", g[i]);  fprintf(frst2, "\n\n");
      |                                                                        ^~~~~~~
paml_baseml/baseml.c:622:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  622 |    if(finbasemlg) fclose(finbasemlg);   if (frate) fclose(frate);
      |    ^~
paml_baseml/baseml.c:622:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  622 |    if(finbasemlg) fclose(finbasemlg);   if (frate) fclose(frate);
      |                                         ^~
paml_baseml/baseml.c:401:56: warning: variable ‘np0’ set but not used [-Wunused-but-set-variable]
  401 |    int status=0, inbasemlg=0, i,j=0, itree=0,ntree, np,np0,iteration=1;
      |                                                        ^~~
paml_baseml/baseml.c: In function ‘DetailOutput’:
paml_baseml/baseml.c:690:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  690 |       for(i=0; i<com.nrate; i++) fprintf (fout, " %8.5f", x[k++]);  FPN(fout);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/baseml.c:690:69: note: in expansion of macro ‘FPN’
  690 |       for(i=0; i<com.nrate; i++) fprintf (fout, " %8.5f", x[k++]);  FPN(fout);
      |                                                                     ^~~
paml_baseml/baseml.c:697:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  697 |       for(i=0; i<com.nrate; i++) fprintf(fout," %8.5f", x[k++]);  FPN(fout);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/baseml.c:697:67: note: in expansion of macro ‘FPN’
  697 |       for(i=0; i<com.nrate; i++) fprintf(fout," %8.5f", x[k++]);  FPN(fout);
      |                                                                   ^~~
paml_baseml/baseml.c:674:11: warning: variable ‘Qfactor’ set but not used [-Wunused-but-set-variable]
  674 |    double Qfactor,*p=com.pi, t=0, k1,k2, S,V, Y=p[0]+p[1],R=p[2]+p[3];
      |           ^~~~~~~
paml_baseml/baseml.c: In function ‘GetOptions’:
paml_baseml/baseml.c:879:19: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  879 |                   if(com.model>UNREST) GetStepMatrix(line);  break;
      |                   ^~
paml_baseml/baseml.c:879:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  879 |                   if(com.model>UNREST) GetStepMatrix(line);  break;
      |                                                              ^~~~~
paml_baseml/baseml.c: In function ‘SetxBound’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/baseml.c:1327:7: note: in expansion of macro ‘FOR’
 1327 |       FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/baseml.c:1327:76: note: in expansion of macro ‘FPN’
 1327 |       FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][0]);  FPN(R_paml_baseml_file_pointer);
      |                                                                            ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/baseml.c:1328:7: note: in expansion of macro ‘FOR’
 1328 |       FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/baseml.c:1328:76: note: in expansion of macro ‘FPN’
 1328 |       FOR(i,np) fprintf(R_paml_baseml_file_pointer, " %10.6f", xb[i][1]);  FPN(R_paml_baseml_file_pointer);
      |                                                                            ^~~
paml_baseml/treespace.c: In function ‘GetIofLHistory’:
paml_baseml/paml.h:25:31: warning: ‘s[1]’ may be used uninitialized [-Wmaybe-uninitialized]
   25 | #define min2(a,b) ((a)<(b)?(a):(b))
      |                   ~~~~~~~~~~~~^~~~~
paml_baseml/treespace.c:383:38: note: in expansion of macro ‘min2’
  383 |       k[nnode]=max2(s[0],s[1]); s[0]=min2(s[0],s[1]); s[1]=k[nnode];
      |                                      ^~~~
In file included from paml_baseml/baseml.c:131:
paml_baseml/treespace.c:375:52: note: ‘s[1]’ was declared here
  375 |    int index, i,j,k[NS+1], inode,nnode, nodea[NS], s[2];
      |                                                    ^
paml_baseml/paml.h:25:31: warning: ‘s[0]’ may be used uninitialized [-Wmaybe-uninitialized]
   25 | #define min2(a,b) ((a)<(b)?(a):(b))
      |                   ~~~~~~~~~~~~^~~~~
paml_baseml/treespace.c:383:38: note: in expansion of macro ‘min2’
  383 |       k[nnode]=max2(s[0],s[1]); s[0]=min2(s[0],s[1]); s[1]=k[nnode];
      |                                      ^~~~
paml_baseml/treespace.c:375:52: note: ‘s[0]’ was declared here
  375 |    int index, i,j,k[NS+1], inode,nnode, nodea[NS], s[2];
      |                                                    ^
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c paml_baseml/R_paml_baseml_main.c -o paml_baseml/R_paml_baseml_main.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -D__HAVE_R_ -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c paml_baseml/tools.c -o paml_baseml/tools.o
paml_baseml/tools.c: In function ‘ScanFastaFile’:
paml_baseml/tools.c:967:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
  967 |    int tmp;             //WCC:add
      |        ^~~
paml_baseml/tools.c: In function ‘printsma’:
paml_baseml/tools.c:1019:9: warning: variable ‘codon’ set but not used [-Wunused-but-set-variable]
 1019 |    char codon[4]="   ";
      |         ^~~~~
In file included from paml_baseml/tools.c:3:
paml_baseml/tools.c: In function ‘strc’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:1106:4: note: in expansion of macro ‘FOR’
 1106 |    FOR (i,n) s[i]=(char)c;    s[n]=0;
      |    ^~~
paml_baseml/tools.c:1106:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1106 |    FOR (i,n) s[i]=(char)c;    s[n]=0;
      |                               ^
paml_baseml/tools.c: In function ‘gfopen’:
paml_baseml/tools.c:1130:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 1130 |    int tmp;             //WCC:add
      |        ^~~
paml_baseml/tools.c: In function ‘CDFBeta’:
paml_baseml/tools.c:2714:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 2714 |       if (q == (double)n)
      |       ^~
paml_baseml/tools.c:2716:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 2716 |          for(i=1 ; i<=n ; i++) {
      |          ^~~
paml_baseml/tools.c: In function ‘EigenTridagQLImplicit’:
paml_baseml/tools.c:4774:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 4774 |    for (i=1;i<n;i++) e[i-1]=e[i];  e[n-1]=0;
      |    ^~~
paml_baseml/tools.c:4774:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 4774 |    for (i=1;i<n;i++) e[i-1]=e[i];  e[n-1]=0;
      |                                    ^
paml_baseml/tools.c: In function ‘scanfile’:
paml_baseml/tools.c:4942:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 4942 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/tools.c: In function ‘DescriptiveStatistics’:
paml_baseml/tools.c:5228:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 5228 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/tools.c:5227:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 5227 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/tools.c: In function ‘DescriptiveStatisticsSimple’:
paml_baseml/tools.c:5457:10: warning: variable ‘tmp_c’ set but not used [-Wunused-but-set-variable]
 5457 |    char *tmp_c;         //WCC:add
      |          ^~~~~
paml_baseml/tools.c:5456:8: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
 5456 |    int tmp;                     //WCC:add
      |        ^~~
paml_baseml/tools.c: In function ‘Newton’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:6118:4: note: in expansion of macro ‘FOR’
 6118 |    FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]);       FPN (R_paml_baseml_file_pointer);
      |    ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/tools.c:6118:73: note: in expansion of macro ‘FPN’
 6118 |    FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]);       FPN (R_paml_baseml_file_pointer);
      |                                                                         ^~~
paml_baseml/tools.c: In function ‘ming2’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:6254:7: note: in expansion of macro ‘FOR’
 6254 |       FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][0]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/tools.c:6254:74: note: in expansion of macro ‘FPN’
 6254 |       FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][0]);  FPN(R_paml_baseml_file_pointer);
      |                                                                          ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:6255:7: note: in expansion of macro ‘FOR’
 6255 |       FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][1]);  FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/tools.c:6255:74: note: in expansion of macro ‘FPN’
 6255 |       FOR(j,n) fprintf(R_paml_baseml_file_pointer, " %9.5f", xb[j][1]);  FPN(R_paml_baseml_file_pointer);
      |                                                                          ^~~
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:6268:7: note: in expansion of macro ‘FOR’
 6268 |       FOR(i,n) fprintf(R_paml_baseml_file_pointer, " %8.5f", x[i]);   FPN(R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/tools.c:6268:71: note: in expansion of macro ‘FPN’
 6268 |       FOR(i,n) fprintf(R_paml_baseml_file_pointer, " %8.5f", x[i]);   FPN(R_paml_baseml_file_pointer);
      |                                                                       ^~~
paml_baseml/tools.c: In function ‘ming1’:
paml_baseml/paml.h:20:18: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   20 | #define FOR(i,n) for(i=0; i<n; i++)
      |                  ^~~
paml_baseml/tools.c:6440:7: note: in expansion of macro ‘FOR’
 6440 |       FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]);       FPN (R_paml_baseml_file_pointer);
      |       ^~~
paml_baseml/paml.h:22:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   22 | #define FPN(file) fputc('\n', file)
      |                   ^~~~~
paml_baseml/tools.c:6440:76: note: in expansion of macro ‘FPN’
 6440 |       FOR (i,n) fprintf(R_paml_baseml_file_pointer, "%8.4f", x0[i]);       FPN (R_paml_baseml_file_pointer);
      |                                                                            ^~~
gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o phyclust.so R_phyclust.o R_phyclust_edist.o R_phyclust_em_step.o R_phyclust_find_consensus.o R_phyclust_label.o R_phyclust_logL.o R_phyclust_logPt.o R_phyclust_qmatrix.o R_phyclust_se.o R_phyclust_se_update.o R_phyclust_struct.o R_phyclust_update.o RRand.o R_RRand.o zzz.o phyclust/phyclust_ape_nj.o phyclust/phyclust_edist.o phyclust/phyclust_em_control.o phyclust/phyclust_em_fp.o phyclust/phyclust_em_phyclust_struct.o phyclust/phyclust_em_step.o phyclust/phyclust_em_tool.o phyclust/phyclust_file_input.o phyclust/phyclust_init_method.o phyclust/phyclust_init_method_ex.o phyclust/phyclust_init_method_kmed.o phyclust/phyclust_init_method_nj.o phyclust/phyclust_init_method_pam.o phyclust/phyclust_init_procedure.o phyclust/phyclust_label.o phyclust/phyclust_logpL.o phyclust/phyclust_optim_nmmin.o phyclust/phyclust_pam.o phyclust/phyclust_qmatrix_array.o phyclust/phyclust_qmatrix.o phyclust/phyclust_se_convolution_em_step.o phyclust/phyclust_se_convolution_em_tool.o phyclust/phyclust_se_convolution_logpL.o phyclust/phyclust_se_em_fp.o phyclust/phyclust_se_em_phyclust_struct.o phyclust/phyclust_se_em_tool.o phyclust/phyclust_se_pmatrix.o phyclust/phyclust_se_struct.o phyclust/phyclust_struct.o phyclust/phyclust_tool.o msdir/ms.o msdir/ms_main.o msdir/R_ms_main.o msdir/R_rand.o msdir/streec.o seq-gen/aamodels.o seq-gen/eigen.o seq-gen/evolve.o seq-gen/gamma.o seq-gen/global.o seq-gen/model.o seq-gen/nucmodels.o seq-gen/R_seq-gen_main.o seq-gen/seq-gen.o seq-gen/treefile.o seq-gen/twister.o paml_baseml/baseml.o paml_baseml/R_paml_baseml_main.o paml_baseml/tools.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNRnMiH/R.INSTALL13e5446635db6/phyclust/src'
installing to /home/hornik/tmp/CRAN_recheck/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)
* installing *source* package ‘scrm’ ...
** package ‘scrm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwRtdSv/R.INSTALL13e5630ef4090/scrm/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrmr.cpp -o scrmr.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c test_exports.cpp -o test_exports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/forest.cc -o scrm/forest.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/model.cc -o scrm/model.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/node.cc -o scrm/node.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/node_container.cc -o scrm/node_container.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/param.cc -o scrm/param.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/time_interval.cc -o scrm/time_interval.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/tree_point.cc -o scrm/tree_point.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/random/random_generator.cc -o scrm/random/random_generator.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/random/fastfunc.cc -o scrm/random/fastfunc.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/summary_statistics/frequency_spectrum.cc -o scrm/summary_statistics/frequency_spectrum.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/summary_statistics/newick_tree.cc -o scrm/summary_statistics/newick_tree.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/summary_statistics/oriented_forest.cc -o scrm/summary_statistics/oriented_forest.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/summary_statistics/seg_sites.cc -o scrm/summary_statistics/seg_sites.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DVERSION="\"R\"" -DRBUILD -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c scrm/summary_statistics/tmrca.cc -o scrm/summary_statistics/tmrca.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o scrm.so scrmr.o test_exports.o RcppExports.o scrm/forest.o scrm/model.o scrm/node.o scrm/node_container.o scrm/param.o scrm/time_interval.o scrm/tree_point.o scrm/random/random_generator.o scrm/random/fastfunc.o scrm/summary_statistics/frequency_spectrum.o scrm/summary_statistics/newick_tree.o scrm/summary_statistics/oriented_forest.o scrm/summary_statistics/seg_sites.o scrm/summary_statistics/tmrca.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwRtdSv/R.INSTALL13e5630ef4090/scrm/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-scrm/00new/scrm/libs
** 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
** 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 (scrm)

checking abc_2.2.2.tar.gz ...
checking abctools_1.1.7.tar.gz ...
checking EasyABC_1.5.2.tar.gz ...
checking ecolottery_1.0.0.tar.gz ...
checking MaxWiK_1.0.5.tar.gz ...
checking poems_1.3.1.tar.gz ...
checking coala_0.7.2.tar.gz ...

Depends:
Package: abc
  Depends: R (>= 2.10), abc.data, nnet, quantreg, MASS, locfit

Timings:
       user system elapsed
abc 104.939   5.52   111.4

Results:
Check status summary:
                  NOTE OK
  Source packages    0  1
  Reverse depends    2  4

Check results summary:
abc ... OK
rdepends_abctools ... NOTE
* checking Rd cross-references ... NOTE
rdepends_coala ... OK
rdepends_EasyABC ... OK
rdepends_ecolottery ... NOTE
* checking Rd cross-references ... NOTE
rdepends_MaxWiK ... OK
rdepends_poems ... OK