* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘BGLR’ ...
** package ‘BGLR’ 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/RtmpY78dXZ/R.INSTALL10639e378d2d/BGLR/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c util_sample.c -o util_sample.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c util_plink.c -o util_plink.o
util_plink.c: In function ‘read_string’:
util_plink.c:39:25: warning: pointer ‘buffer’ may be used after ‘realloc’ [-Wuse-after-free]
   39 |                         free(buffer);
      |                         ^~~~~~~~~~~~
util_plink.c:36:43: note: call to ‘realloc’ here
   36 |                      char *tmp = (char *) realloc(buffer, buf_size);
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
util_plink.c: In function ‘read_ped_’:
util_plink.c:190:23: warning: ‘Line_copy’ may be used uninitialized [-Wmaybe-uninitialized]
  190 |                 token=strtok(Line_copy,"\t ");
      |                       ^~~~~~~~~~~~~~~~~~~~~~~
util_plink.c:105:15: note: ‘Line_copy’ was declared here
  105 |         char *Line_copy;
      |               ^~~~~~~~~
util_plink.c:263:17: warning: ‘Line’ may be used uninitialized [-Wmaybe-uninitialized]
  263 |                 free(Line);
      |                 ^~~~~~~~~~
util_plink.c:104:15: note: ‘Line’ was declared here
  104 |         char *Line;
      |               ^~~~
util_plink.c:229:51: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized]
  229 |                                                 if(tmp=='0' && token[0]=='0')
      |                                                   ^
util_plink.c:114:14: note: ‘tmp’ was declared here
  114 |         char tmp;
      |              ^~~
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c util_sample_cross.c -o util_sample_cross.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sampler_multitrait.c -o sampler_multitrait.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3  -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o BGLR.so util_sample.o util_plink.o util_sample_cross.o sampler_multitrait.o init.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpY78dXZ/R.INSTALL10639e378d2d/BGLR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpY78dXZ/R.INSTALL10639e378d2d/BGLR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpY78dXZ/R.INSTALL10639e378d2d/BGLR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-BGLR/00new/BGLR/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘BGLR’
    finding HTML links ... done
    BFDR                                    html  
    BGLR                                    html  
    BLR                                     html  
    BLRCross                                html  
    BLRXy                                   html  
    Multitrait                              html  
    getGCovar                               html  
    getVariances                            html  
    mice.A                                  html  
    mice                                    html  
    mice.X                                  html  
    mice.map                                html  
    mice.pheno                              html  
    plot.BGLR                               html  
    predict.BGLR                            html  
    readBinMat                              html  
    readBinMatMultitrait                    html  
    read_bed                                html  
    read_ped                                html  
    residuals.BGLR                          html  
    simulated3t                             html  
    simulated3t.X                           html  
    simulated3t.pheno                       html  
    summary.BGLR                            html  
    vech                                    html  
    wheat.A                                 html  
    wheat                                   html  
    wheat.X                                 html  
    wheat.Y                                 html  
    wheat.sets                              html  
    write_bed                               html  
    xpnd                                    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 (BGLR)