* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘BGLR’ ...
** package ‘BGLR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0CB02w/R.INSTALLb2e6a65b487b4/BGLR/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-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-13 -I"/home/hornik/tmp/R.check/r-devel-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-13 -I"/home/hornik/tmp/R.check/r-devel-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-13 -I"/home/hornik/tmp/R.check/r-devel-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-13 -I"/home/hornik/tmp/R.check/r-devel-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-13 -shared -L/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0CB02w/R.INSTALLb2e6a65b487b4/BGLR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0CB02w/R.INSTALLb2e6a65b487b4/BGLR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0CB02w/R.INSTALLb2e6a65b487b4/BGLR/src'
installing to /home/hornik/tmp/R.check/r-devel-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
** 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
* creating tarball
packaged installation of ‘BGLR’ as ‘BGLR_1.1.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (BGLR)