* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’
* installing *source* package ‘MAGEE’ ...
** package ‘MAGEE’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for ZSTD_decompress in -lzstd... yes
checking zstd.h usability... yes
checking zstd.h presence... yes
checking for zstd.h... yes
configure: Will use system-wide zstd library
checking for libdeflate_zlib_decompress in -ldeflate... yes
checking libdeflate.h usability... yes
checking libdeflate.h presence... yes
checking for libdeflate.h... yes
configure: Will use system-wide libdeflate library
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/RtmpFR3oOK/R.INSTALL137c6d385cada/MAGEE/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fitglmm.cpp -o fitglmm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fitmagee.cpp -o fitmagee.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD -fpic  -g -O2 -Wall -pedantic -mtune=native   -c read_bgen.cpp -o read_bgen.o
gcc-13 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o MAGEE.so fitglmm.o fitmagee.o read_bgen.o registerDynamicSymbol.o -llapack -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lz -lbz2 -lzstd -ldeflate -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpFR3oOK/R.INSTALL137c6d385cada/MAGEE/src'
make[1]: Entering directory '/tmp/RtmpFR3oOK/R.INSTALL137c6d385cada/MAGEE/src'
make[1]: Leaving directory '/tmp/RtmpFR3oOK/R.INSTALL137c6d385cada/MAGEE/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-MAGEE/00new/MAGEE/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