* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘adephylo’ ...
** this is package ‘adephylo’ version ‘1.1-17’
** package ‘adephylo’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwQ59zF/R.INSTALL2c47cc3b5d4616/adephylo/src'
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c adesub.c -o adesub.o
adesub.c: In function ‘getpermutation’:
adesub.c:479:15: warning: unused variable ‘seed’ [-Wunused-variable]
  479 |     int i, n, seed;
      |               ^~~~
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c distPhylo.c -o distPhylo.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c misc.c -o misc.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phylog.c -o phylog.o
gcc-14 -std=gnu23 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sptips.c -o sptips.o
gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o adephylo.so adesub.o distPhylo.o init.o misc.o phylog.o sptips.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwQ59zF/R.INSTALL2c47cc3b5d4616/adephylo/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwQ59zF/R.INSTALL2c47cc3b5d4616/adephylo/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwQ59zF/R.INSTALL2c47cc3b5d4616/adephylo/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adephylo/00new/adephylo/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘adephylo’
    finding HTML links ... done
    abouheif                                html  
    adephylo-package                        html  
    bullseye                                html  
    carni19                                 html  
    carni70                                 html  
    distRoot                                html  
    distTips                                html  
    listDD                                  html  
    listTips                                html  
    lizards                                 html  
    maples                                  html  
    miscUtils                               html  
    mjrochet                                html  
    moranIdx                                html  
    orthobasis                              html  
    orthogram                               html  
    palm                                    html  
    ppca                                    html  
    procella                                html  
    proxTips                                html  
    sp.tips                                 html  
    table.phylo4d                           html  
    tithonia                                html  
    treePart                                html  
    ungulates                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (adephylo)