* installing to library '/home/runner/R-patched/lib' * installing *source* package 'pgenlibr' ... ** this is package 'pgenlibr' version '0.5.3' ** 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++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed configure: C++ compiler: g++ -std=gnu++17 configure: zstd 1.5.7 library detected -- skipping zstd compilation configure: libdeflate 1.23 library detected -- skipping libdeflate compilation configure: simde not detected by pkg-config; falling back on system header file check no configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: 'g++ (Alpine 14.2.0) 14.2.0' make[1]: Entering directory '/var/local/PKGS/CRAN/pgenlibr/src' g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c pvar.cpp -o pvar.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c pgenlibr.cpp -o pgenlibr.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/plink2_base.cc -o ../inst/include/include/plink2_base.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/plink2_bits.cc -o ../inst/include/include/plink2_bits.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/pgenlib_ffi_support.cc -o ../inst/include/include/pgenlib_ffi_support.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/pgenlib_misc.cc -o ../inst/include/include/pgenlib_misc.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/pgenlib_read.cc -o ../inst/include/include/pgenlib_read.o g++ -std=gnu++17 -I"/home/runner/R-patched/build/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DIGNORE_BUNDLED_ZSTD -DIGNORE_BUNDLED_LIBDEFLATE -I../inst/include -I'/home/runner/R-patched/lib/Rcpp/include' -I/usr/local/include -fpic -O2 -mtune=native -Wno-ignored-attributes -D__MUSL__ -c ../inst/include/include/plink2_bgzf.cc -o ../inst/include/include/plink2_bgzf.o In file included from ../inst/include/include/plink2_bgzf.h:44, from ../inst/include/include/plink2_bgzf.cc:17: ../inst/include/include/plink2_string.h: In function 'const char* plink2::strnul(const char*)': ../inst/include/include/plink2_string.h:157:30: error: 'rawmemchr' was not declared in this scope; did you mean 'memchr'? 157 | return S_CAST(CXXCONST_CP, rawmemchr(str, 0)); | ^~~~~~~~~ ../inst/include/include/plink2_base.h:293:48: note: in definition of macro 'S_CAST' 293 | # define S_CAST(type, val) (static_cast(val)) | ^~~ ../inst/include/include/plink2_string.h: In function 'const char* plink2::AdvToDelim(const char*, char)': ../inst/include/include/plink2_string.h:1118:30: error: 'rawmemchr' was not declared in this scope; did you mean 'rawmemchr3'? 1118 | return S_CAST(CXXCONST_CP, rawmemchr(str_iter, delim)); | ^~~~~~~~~ ../inst/include/include/plink2_base.h:293:48: note: in definition of macro 'S_CAST' 293 | # define S_CAST(type, val) (static_cast(val)) | ^~~ make[1]: *** [/home/runner/R-patched/build/etc/Makeconf:209: ../inst/include/include/plink2_bgzf.o] Error 1 make[1]: Leaving directory '/var/local/PKGS/CRAN/pgenlibr/src' make[1]: Entering directory '/var/local/PKGS/CRAN/pgenlibr/src' make[1]: Leaving directory '/var/local/PKGS/CRAN/pgenlibr/src' ERROR: compilation failed for package 'pgenlibr' * removing '/home/runner/R-patched/lib/pgenlibr'