* installing *source* package 'MAGEE' ...
** this is package 'MAGEE' version '1.4.4'
** package 'MAGEE' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.3.0'
using C++ compiler: 'g++.exe (GCC) 14.3.0'
make[1]: Entering directory '/d/temp/2025_11_01_00_52_33_4216/RtmpuUquqM/R.INSTALL5c5859e497a/MAGEE/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitglmm.cpp -o fitglmm.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from fitglmm.cpp:26:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitmagee.cpp -o fitmagee.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from fitmagee.cpp:26:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -DARMA_64BIT_WORD -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_bgen.cpp -o read_bgen.o
In file included from D:/RCompile/recent/R-4.5.2/include/R.h:73,
from read_bgen.cpp:1:
D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/exceptions.h: In function 'void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]':
D:/RCompile/recent/R-4.5.2/include/R_ext/Error.h:85:17: warning: infinite recursion detected [-Winfinite-recursion]
85 | #define warning Rf_warning
| ^~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/exceptions.h:190:17: note: in expansion of macro 'warning'
190 | inline void warning(const char* fmt, Args&&... args ) {
| ^~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/RcppCommon.h:133,
from D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp.h:27,
from read_bgen.cpp:2:
D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/exceptions.h:191:19: note: recursive call
191 | Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/arm/cpu_features.c -o libdeflate/lib/arm/cpu_features.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/x86/cpu_features.c -o libdeflate/lib/x86/cpu_features.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/adler32.c -o libdeflate/lib/adler32.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/crc32.c -o libdeflate/lib/crc32.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/deflate_compress.c -o libdeflate/lib/deflate_compress.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/deflate_decompress.c -o libdeflate/lib/deflate_decompress.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/gzip_compress.c -o libdeflate/lib/gzip_compress.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/gzip_decompress.c -o libdeflate/lib/gzip_decompress.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/utils.c -o libdeflate/lib/utils.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/zlib_compress.c -o libdeflate/lib/zlib_compress.o
gcc -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c libdeflate/lib/zlib_decompress.c -o libdeflate/lib/zlib_decompress.o
g++ -std=gnu++17 -shared -s -static-libgcc -o MAGEE.dll tmp.def fitglmm.o fitmagee.o read_bgen.o registerDynamicSymbol.o -LD:/RCompile/recent/R-4.5.2/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.5.2/bin/x64 -lRblas -lgfortran -lquadmath -lz -lbz2 -lzstd libdeflate/lib/arm/cpu_features.o libdeflate/lib/x86/cpu_features.o libdeflate/lib/adler32.o libdeflate/lib/crc32.o libdeflate/lib/deflate_compress.o libdeflate/lib/deflate_decompress.o libdeflate/lib/gzip_compress.o libdeflate/lib/gzip_decompress.o libdeflate/lib/utils.o libdeflate/lib/zlib_compress.o libdeflate/lib/zlib_decompress.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.5.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_11_01_00_52_33_4216/RtmpuUquqM/R.INSTALL5c5859e497a/MAGEE/src'
make[1]: Entering directory '/d/temp/2025_11_01_00_52_33_4216/RtmpuUquqM/R.INSTALL5c5859e497a/MAGEE/src'
make[1]: Leaving directory '/d/temp/2025_11_01_00_52_33_4216/RtmpuUquqM/R.INSTALL5c5859e497a/MAGEE/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-MAGEE/00new/MAGEE/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'MAGEE' as MAGEE_1.4.4.zip
* DONE (MAGEE)