downloading reverse dependencies ...
downloading BWGS_0.2.1.tar.gz ... ok
downloading GEmetrics_1.0.0.tar.gz ... ok
downloading predhy_2.1.1.tar.gz ... ok
downloading predhy.GUI_2.0.1.tar.gz ... ok
downloading BGGE_0.6.5.tar.gz ... ok
downloading GROAN_1.3.1.tar.gz ... ok
downloading MoBPS_1.6.64.tar.gz ... ok
downloading SFSI_1.4.1.tar.gz ... ok

installing dependencies ‘alstructure’, ‘BGLR’, ‘brnn’, ‘cPCG’, ‘doMPI’,
  ‘EMMREML’, ‘NAM’, ‘optiSel’, ‘phylogram’, ‘predhy’, ‘tensorEVD’

Warning: package ‘alstructure’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
also installing the dependencies ‘HaploSim’, ‘cccp’, ‘nadiv’, ‘pedigree’, ‘optiSolve’

begin installing package ‘HaploSim’
begin installing package ‘cccp’
begin installing package ‘nadiv’
begin installing package ‘BGLR’
begin installing package ‘brnn’
begin installing package ‘EMMREML’
begin installing package ‘doMPI’
begin installing package ‘NAM’
begin installing package ‘phylogram’
begin installing package ‘cPCG’
begin installing package ‘tensorEVD’
* installing *source* package ‘phylogram’ ...
** package ‘phylogram’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phylogram)
* installing *source* package ‘HaploSim’ ...
** package ‘HaploSim’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HaploSim)
begin installing package ‘pedigree’
* installing *source* package ‘brnn’ ...
** package ‘brnn’ 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/Rtmp3Mifja/R.INSTALL3c82fb46e74235/brnn/src'
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c Lanczos.c -o Lanczos.o
Lanczos.c: In function ‘extreme_eigenvalues’:
Lanczos.c:191:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  191 |     for (xx=0.0,zp=z,p0=zp+*n;zp<p0;zp++) xx += *zp * *zp;b[j]=sqrt(xx);
      |     ^~~
Lanczos.c:191:59: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  191 |     for (xx=0.0,zp=z,p0=zp+*n;zp<p0;zp++) xx += *zp * *zp;b[j]=sqrt(xx);
      |                                                           ^
Lanczos.c:285:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  285 |   for (i=0;i< *n+1;i++) if (q[i]) free(q[i]);free(q);
      |   ^~~
Lanczos.c:285:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  285 |   for (i=0;i< *n+1;i++) if (q[i]) free(q[i]);free(q);
      |                                              ^~~~
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c util.c -o util.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  -fopenmp -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.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  -fopenmp -I. -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c unix/util_unix.c -o unix/util_unix.o
gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o brnn.so Lanczos.o util.o init.o unix/util_unix.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3Mifja/R.INSTALL3c82fb46e74235/brnn/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-brnn/00new/brnn/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (brnn)
* installing *source* package ‘doMPI’ ...
** package ‘doMPI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (doMPI)
* installing *source* package ‘EMMREML’ ...
** package ‘EMMREML’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EMMREML)
* installing *source* package ‘tensorEVD’ ...
** package ‘tensorEVD’ 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/RtmpvRl1ku/R.INSTALL3c830a357027c/tensorEVD/src'
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 c_sum.c -o c_sum.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 c_tensor_evd.c -o c_tensor_evd.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 c_hadamard.c -o c_hadamard.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  -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 utils.c -o utils.o
gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o tensorEVD.so c_sum.o c_tensor_evd.o c_hadamard.o init.o utils.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
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvRl1ku/R.INSTALL3c830a357027c/tensorEVD/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-tensorEVD/00new/tensorEVD/libs
** R
** 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 (tensorEVD)
* installing *source* package ‘BGLR’ ...
** 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/RtmpIvLE5r/R.INSTALL3c830838a94d94/BGLR/src'
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
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIvLE5r/R.INSTALL3c830838a94d94/BGLR/src'
installing to /home/hornik/tmp/CRAN_recheck/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)
begin installing package ‘predhy’
* installing *source* package ‘pedigree’ ...
** package ‘pedigree’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpYiC84H/R.INSTALL3c84c91e3a8b9a/pedigree/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Pedigree.cpp -o Pedigree.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c pedigree_init.c -o pedigree_init.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o pedigree.so Pedigree.o pedigree_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpYiC84H/R.INSTALL3c84c91e3a8b9a/pedigree/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigree/00new/pedigree/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (pedigree)
* installing *source* package ‘cPCG’ ...
** package ‘cPCG’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqfNdSE/R.INSTALL3c83067222231/cPCG/src'
g++-14  -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
g++-14  -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -fopenmp  -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpparma_cPCG.cpp -o rcpparma_cPCG.o
g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cPCG.so RcppExports.o init.o rcpparma_cPCG.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqfNdSE/R.INSTALL3c83067222231/cPCG/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cPCG/00new/cPCG/libs
** R
** 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 (cPCG)
* installing *source* package ‘nadiv’ ...
** package ‘nadiv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGjE2m5/R.INSTALL3c82fd521eac93/nadiv/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Trow.cc -o Trow.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ainv.cc -o ainv.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_cumsum.c -o cs_cumsum.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_malloc.c -o cs_malloc.o
cs_malloc.c: In function ‘cs_realloc’:
cs_malloc.c:34:26: warning: pointer ‘p’ may be used after ‘realloc’ [-Wuse-after-free]
   34 |     return ((*ok) ? pnew : p) ;             /* return original p if failure */
      |            ~~~~~~~~~~~~~~^~~~
cs_malloc.c:32:12: note: call to ‘realloc’ here
   32 |     pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_multiply.c -o cs_multiply.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_norm.c -o cs_norm.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_scatter.c -o cs_scatter.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_transpose.c -o cs_transpose.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c cs_util.c -o cs_util.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dfc.cc -o dfc.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c diif.cc -o diif.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dij.cc -o dij.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dsim.cc -o dsim.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ga.cc -o ga.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c genedrop.cc -o genedrop.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   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c minv.cc -o minv.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c reT.cc -o reT.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sdsim.cc -o sdsim.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG   -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sinv.cc -o sinv.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o nadiv.so Trow.o ainv.o cs_cumsum.o cs_malloc.o cs_multiply.o cs_norm.o cs_scatter.o cs_transpose.o cs_util.o dfc.o diif.o dij.o dsim.o ga.o genedrop.o init.o minv.o reT.o sdsim.o sinv.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGjE2m5/R.INSTALL3c82fd521eac93/nadiv/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nadiv/00new/nadiv/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (nadiv)
* installing *source* package ‘predhy’ ...
** package ‘predhy’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (predhy)
* installing *source* package ‘NAM’ ...
** package ‘NAM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpAf1nIN/R.INSTALL3c83025a80e/NAM/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Functions.cpp -o Functions.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c c.c -o c.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o NAM.so Functions.o RcppExports.o c.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpAf1nIN/R.INSTALL3c83025a80e/NAM/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-NAM/00new/NAM/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 (NAM)
* installing *source* package ‘cccp’ ...
** package ‘cccp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWKXWXC/R.INSTALL3c82f863420a34/cccp/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c CONEC.cpp -o CONEC.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c DCP.cpp -o DCP.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c DLP.cpp -o DLP.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c DNL.cpp -o DNL.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c DQP.cpp -o DQP.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GPP.cpp -o GPP.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Modules.cpp -o Modules.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RPP.cpp -o RPP.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SOPS.cpp -o SOPS.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cccp.so CONEC.o DCP.o DLP.o DNL.o DQP.o GPP.o Modules.o RPP.o RcppExports.o SOPS.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
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWKXWXC/R.INSTALL3c82f863420a34/cccp/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cccp/00new/cccp/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (cccp)
begin installing package ‘optiSolve’
* installing *source* package ‘optiSolve’ ...
** package ‘optiSolve’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (optiSolve)
begin installing package ‘optiSel’
* installing *source* package ‘optiSel’ ...
** package ‘optiSel’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp2tTSTX/R.INSTALL3c88aa11db0ef3/optiSel/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_completeness.cpp -o rcpp_completeness.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_genecont.cpp -o rcpp_genecont.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_haplofreq.cpp -o rcpp_haplofreq.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_makeA.cpp -o rcpp_makeA.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_makeA_lowMem.cpp -o rcpp_makeA_lowMem.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segBreedComp.cpp -o rcpp_segBreedComp.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segIBD.cpp -o rcpp_segIBD.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segIBDandN.cpp -o rcpp_segIBDandN.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segIBDandNVersion2.cpp -o rcpp_segIBDandNVersion2.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segInbreeding.cpp -o rcpp_segInbreeding.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_segN.cpp -o rcpp_segN.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o optiSel.so RcppExports.o rcpp_completeness.o rcpp_genecont.o rcpp_haplofreq.o rcpp_makeA.o rcpp_makeA_lowMem.o rcpp_segBreedComp.o rcpp_segIBD.o rcpp_segIBDandN.o rcpp_segIBDandNVersion2.o rcpp_segInbreeding.o rcpp_segN.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
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp2tTSTX/R.INSTALL3c88aa11db0ef3/optiSel/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-optiSel/00new/optiSel/libs
** R
** data
** 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 (optiSel)

checking BGLR_1.1.3.tar.gz ...
checking BWGS_0.2.1.tar.gz ...
checking GEmetrics_1.0.0.tar.gz ...
checking predhy_2.1.1.tar.gz ...
checking predhy.GUI_2.0.1.tar.gz ...
checking BGGE_0.6.5.tar.gz ...
checking GROAN_1.3.1.tar.gz ...
checking MoBPS_1.6.64.tar.gz ...
checking SFSI_1.4.1.tar.gz ...

Depends:
Package: BGLR
  Depends: R (>= 3.5.0)
  Imports: truncnorm, MASS, methods

Timings:
       user system elapsed
BGLR 43.801  4.501  49.704

Results:
Check status summary:
                  NOTE OK
  Source packages    0  1
  Reverse depends    2  6

Check results summary:
BGLR ... OK
rdepends_BGGE ... OK
rdepends_BWGS ... NOTE
* checking Rd files ... [0s/0s] NOTE
rdepends_GEmetrics ... OK
rdepends_GROAN ... OK
rdepends_MoBPS ... NOTE
* checking Rd files ... [1s/1s] NOTE
rdepends_predhy.GUI ... OK
rdepends_predhy ... OK
rdepends_SFSI ... OK