* 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 13.2.0-23) 13.2.0’ using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’ make[1]: Entering directory '/tmp/RtmpYE9gAw/R.INSTALL18d82b73adf3cd/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 In file included from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26, from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29, from fitglmm.cpp:27: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’ 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’ 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’ 329 | #pragma message ("INFO: see the documentation for details") | ^ fitglmm.cpp: In function ‘SEXPREC* glmm_gei_bgen13(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: fitglmm.cpp:333:18: warning: unused variable ‘missRate’ [-Wunused-variable] 333 | double missRate = nmiss / (double)(n * 1.0); | ^~~~~~~~ fitglmm.cpp: In function ‘SEXPREC* glmm_gei_bgen11(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: fitglmm.cpp:877:16: warning: unused variable ‘missRate’ [-Wunused-variable] 877 | double missRate = nmiss / (double)(n * 1.0); | ^~~~~~~~ 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/RtmpYE9gAw/R.INSTALL18d82b73adf3cd/MAGEE/src' make[1]: Entering directory '/tmp/RtmpYE9gAw/R.INSTALL18d82b73adf3cd/MAGEE/src' make[1]: Leaving directory '/tmp/RtmpYE9gAw/R.INSTALL18d82b73adf3cd/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 * DONE (MAGEE)