* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘APIS’ ...
** package ‘APIS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDDSXDP/R.INSTALL395682539415a4/APIS/src'
gcc-14 -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 APIS_init_Recom.c -o APIS_init_Recom.o
gcc-14 -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 calculate_likelihood.c -o calculate_likelihood.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o APIS.so APIS_init_Recom.o calculate_likelihood.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDDSXDP/R.INSTALL395682539415a4/APIS/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDDSXDP/R.INSTALL395682539415a4/APIS/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDDSXDP/R.INSTALL395682539415a4/APIS/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-APIS/00new/APIS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘APIS’
    finding HTML links ... done
    APIS_2n                                 html  
    APIS_3n                                 html  
    APIS_dam                                html  
    APIS_offspring                          html  
    APIS_offspring3n                        html  
    APIS_sire                               html  
    assignment_power                        html  
    import_from_ped                         html  
    import_from_vcf                         html  
    launch_APIShiny                         html  
    plot_delta                              html  
    plot_mismatches                         html  
    plot_probabilities                      html  
    simulate_offspring                      html  
** 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 (APIS)