* installing *source* package ‘pgenlibr’ ... ** package ‘pgenlibr’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /usr/bin/pkg-config 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 the compiler supports GNU C++... yes checking whether g++-13 -std=gnu++17 accepts -g... yes checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed configure: C++ compiler: g++-13 -std=gnu++17 configure: zstd 1.5.5 library detected -- skipping zstd compilation configure: libdeflate 1.9 library detected -- skipping libdeflate compilation configure: simde not detected by pkg-config; falling back on system header file check yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pgenlibr/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pvar_ffi_support.cpp -o pvar_ffi_support.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pvar.cpp -o pvar.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pgenlibr.cpp -o pgenlibr.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_base.cc -o include/plink2_base.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_bits.cc -o include/plink2_bits.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/pgenlib_misc.cc -o include/pgenlib_misc.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/pgenlib_read.cc -o include/pgenlib_read.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_bgzf.cc -o include/plink2_bgzf.o include/plink2_bgzf.cc:853:1: warning: embedding a directive within macro arguments is not portable 853 | # ifdef __cplusplus | ^ include/plink2_bgzf.cc:855:1: warning: embedding a directive within macro arguments is not portable 855 | # else | ^ include/plink2_bgzf.cc:857:1: warning: embedding a directive within macro arguments is not portable 857 | # endif | ^ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_string.cc -o include/plink2_string.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_text.cc -o include/plink2_text.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_thread.cc -o include/plink2_thread.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DTRY_SYSTEM_SIMDE -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c include/plink2_zstfile.cc -o include/plink2_zstfile.o gcc-ar rcs libPLINK2.a include/plink2_base.o include/plink2_bits.o include/pgenlib_misc.o include/pgenlib_read.o include/plink2_bgzf.o include/plink2_string.o include/plink2_text.o include/plink2_thread.o include/plink2_zstfile.o g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o pgenlibr.so pvar_ffi_support.o pgenlib_ffi_support.o pvar.o pgenlibr.o RcppExports.o -lPLINK2 -L. -lzstd -ldeflate -lz -lpthread make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pgenlibr/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pgenlibr/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pgenlibr/src' installing to /data/gannet/ripley/R/packages/tests-devel/pgenlibr.Rcheck/00LOCK-pgenlibr/00new/pgenlibr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (pgenlibr)