Install log for 'MAGEE'

* 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 clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -arch x86_64 -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... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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... no
configure: Will build libdeflate library from the package
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2  -c fitglmm.cpp -o fitglmm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2  -c fitmagee.cpp -o fitmagee.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include   -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2  -c read_bgen.cpp -o read_bgen.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/adler32.c -o libdeflate/lib/adler32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/deflate_decompress.c -o libdeflate/lib/deflate_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/utils.c -o libdeflate/lib/utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/crc32.c -o libdeflate/lib/crc32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/gzip_compress.c -o libdeflate/lib/gzip_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/zlib_compress.c -o libdeflate/lib/zlib_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/deflate_compress.c -o libdeflate/lib/deflate_compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/gzip_decompress.c -o libdeflate/lib/gzip_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/zlib_decompress.c -o libdeflate/lib/zlib_decompress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/arm/cpu_features.c -o libdeflate/lib/arm/cpu_features.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c libdeflate/lib/x86/cpu_features.c -o libdeflate/lib/x86/cpu_features.o
In file included from fitglmm.cpp:27:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo:26:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
  #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
          ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
    #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
            ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
  #pragma message ("INFO: see the documentation for details")
          ^
fitglmm.cpp:333:18: warning: unused variable 'missRate' [-Wunused-variable]
          double missRate = nmiss / (double)(n * 1.0);
                 ^
fitglmm.cpp:877:16: warning: unused variable 'missRate' [-Wunused-variable]
        double missRate = nmiss / (double)(n * 1.0);
               ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MAGEE.so fitglmm.o fitmagee.o read_bgen.o registerDynamicSymbol.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -lz -lbz2 -lzstd libdeflate/lib/adler32.o libdeflate/lib/deflate_decompress.o libdeflate/lib/utils.o libdeflate/lib/crc32.o libdeflate/lib/gzip_compress.o libdeflate/lib/zlib_compress.o libdeflate/lib/deflate_compress.o libdeflate/lib/gzip_decompress.o libdeflate/lib/zlib_decompress.o libdeflate/lib/arm/cpu_features.o libdeflate/lib/x86/cpu_features.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/MAGEE.Rcheck/00LOCK-MAGEE/00new/MAGEE/libs
** generating debug symbols (dSYM)
** 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 (MAGEE)