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###
### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneticsPed
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* checking for file ‘GeneticsPed/DESCRIPTION’ ... OK
* preparing ‘GeneticsPed’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘GeneticsPed’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c ainverse.cc -o ainverse.o
In file included from ../include/ainverse.h:20,
                 from ainverse.cc:9:
../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c eibd.cc -o eibd.o
gfortran  -fpic  -g -O2  -Wall -c ggmatmult.f -o ggmatmult.o
gfortran  -fpic  -g -O2  -Wall -c gpi.f -o gpi.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c inbreed.cc -o inbreed.o
In file included from ../include/inbreed.h:18,
                 from inbreed.cc:10:
../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c inverseAdditive.cc -o inverseAdditive.o
inverseAdditive.cc:1: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c meuwissen.cc -o meuwissen.o
meuwissen.cc:1: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c pedSort.cc -o pedSort.o
pedSort.cc:1: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c pedtemplate.cc -o pedtemplate.o
In file included from pedtemplate.cc:15:
../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
pedtemplate.cc: In member function ‘void Pedigree::ShowPed()’:
pedtemplate.cc:373:15: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘__gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type’ {aka ‘long int’} [-Wformat=]
  373 |     Rprintf("%d\t", p - pedigree.begin());
      |              ~^     ~~~~~~~~~~~~~~~~~~~~
      |               |       |
      |               int     __gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type {aka long int}
      |              %ld
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c register.cc -o register.o
In file included from ../include/../include/inbreed.h:18,
                 from ../include/meuwissen.h:7,
                 from register.cc:8:
../include/../include/pedtemplate.h:18: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:52:32: warning: ‘*Ped[S][0]’ may be used uninitialized [-Wmaybe-uninitialized]
   52 |       rPed[rN][0] = Link[Ped[S][0]];
      |                          ~~~~~~^~~
sargolzaei.c:53:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
   53 |       rPed[rN++][1] = Link[Ped[D][1]];
      |                            ~~~~~~^~~
sargolzaei.c:58:32: warning: ‘*Ped[D][0]’ may be used uninitialized [-Wmaybe-uninitialized]
   58 |       rPed[rN][0] = Link[Ped[D][0]];
      |                          ~~~~~~^~~
sargolzaei.c:59:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
   59 |       rPed[rN++][1] = Link[Ped[D][1]];
      |                            ~~~~~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c sortped.cc -o sortped.o
In file included from sortped.cc:1:
../include/sortped.h:5: warning: "R_NO_REMAP" redefined
    5 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
sortped.cc: In function ‘void SortPed(Pedigree&, TPedVec&)’:
sortped.cc:55:5: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
   55 |     error("Problems in pedigree.  Stopping inbreeding calculations\n");
      |     ^~~~~
      |     perror
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:200: sortped.o] Error 1
ERROR: compilation failed for package ‘GeneticsPed’
* removing ‘/tmp/RtmpBT5VVI/Rinst521a129efff69/GeneticsPed’
      -----------------------------------
ERROR: package installation failed