##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL bgx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘bgx’ ...
** using staged installation
checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking for gcc architecture flag... 
checking for gcc architecture flag... unknown
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
tar: Ignoring unknown extended header keyword 'SCHILY.fflags'
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -g -O2 -Wall -Werror=format-security  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
In file included from bgx.cc:32:
rand.hh:51:11: warning: "R_NO_REMAP" redefined
   51 |   #define R_NO_REMAP
      |           ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
rand.hh: In member function ‘RealType Rand<GenType, RealType>::Normal()’:
rand.hh:399:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  399 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:399:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  399 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:406:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  406 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:406:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  406 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:413:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  413 |       if(u0<.5) return y; return -y;
      |       ^~
rand.hh:413:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  413 |       if(u0<.5) return y; return -y;
      |                           ^~~~~~
rand.hh:420:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  420 |     if(u0<.5) return y; return -y;
      |     ^~
rand.hh:420:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  420 |     if(u0<.5) return y; return -y;
      |                         ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -g -O2 -Wall -Werror=format-security  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
bgx_frontend.cc:49:11: warning: "R_NO_REMAP" redefined
   49 |   #define R_NO_REMAP
      |           ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -g -O2 -Wall -Werror=format-security  -ffast-math -O3 -c qnorm.c -o qnorm.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -g -O2 -Wall -Werror=format-security  -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I ../boostIncl -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -g -O2 -Wall -Werror=format-security  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
sokal.cc:46:11: warning: "R_NO_REMAP" redefined
   46 |   #define R_NO_REMAP
      |           ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -L/home/biocbuild/R/R/lib -lR
rm -r ../boostIncl
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-bgx/00new/bgx/libs
** R
** 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 (bgx)