installing dependencies ‘BGLR’

* 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’
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-gcc-14/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-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR
installing to /home/hornik/tmp/CRAN_special_donttest/Library/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
* DONE (BGLR)

checking PopVar_1.3.2.tar.gz ...

Depends:
Package: PopVar
  Depends: R (>= 3.5.0)
  Imports: BGLR, qtl, rrBLUP, stats, utils, methods, parallel

Timings:
          user system elapsed
PopVar 411.895  5.619 420.861

Results:
Check status summary:
                  NOTE
  Source packages    1

Check results summary:
PopVar ... NOTE
* checking CRAN incoming feasibility ... [4s/6s] NOTE
* checking for non-standard things in the check directory ... NOTE
* checking for detritus in the temp directory ... NOTE