* installing *source* package ‘vcfppR’ ... ** package ‘vcfppR’ successfully unpacked and MD5 sums checked ** using staged installation Configuring HTSlib in src/htslib-1.21 checking for gcc... clang -arch arm64 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 clang -arch arm64 accepts -g... yes checking for clang -arch arm64 option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... unknown checking for clang -arch arm64 options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for pkg-config... /opt/R/arm64/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for clang -arch arm64 option to enable large file support... none needed checking shared library type for unknown-Darwin... Darwin dylib checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... aarch64-apple-darwin22.5.0 checking host system type... aarch64-apple-darwin22.5.0 checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... no checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing log... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o kfunc.o kfunc.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o kstring.o kstring.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o bcf_sr_sort.o bcf_sr_sort.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o bgzf.o bgzf.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o errmod.o errmod.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o faidx.o faidx.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o header.o header.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.21"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'clang -arch arm64' \ '-I/opt/R/arm64/include' \ '-O2 -fPIC -fvisibility=hidden' \ '-L/opt/R/arm64/lib -fvisibility=hidden ' \ '-llzma -lbz2 -lz -lcurl ' > config_vars.h clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hts.o hts.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hts_expr.o hts_expr.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hts_os.o hts_os.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o md5.o md5.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o multipart.o multipart.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o probaln.o probaln.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o realn.o realn.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o regidx.o regidx.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o region.o region.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o sam.o sam.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o sam_mods.o sam_mods.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o simd.o simd.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o synced_bcf_reader.o synced_bcf_reader.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o vcf_sweep.o vcf_sweep.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o tbx.o tbx.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o textutils.o textutils.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o thread_pool.o thread_pool.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o vcf.o vcf.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o vcfutils.o vcfutils.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_codecs.o cram/cram_codecs.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_decode.o cram/cram_decode.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_encode.o cram/cram_encode.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_external.o cram/cram_external.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_index.o cram/cram_index.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_io.o cram/cram_io.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/cram_stats.o cram/cram_stats.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/mFILE.o cram/mFILE.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/open_trace_file.o cram/open_trace_file.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o cram/string_alloc.o cram/string_alloc.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hfile_libcurl.o hfile_libcurl.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hfile_gcs.o hfile_gcs.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hfile_s3.o hfile_s3.c clang -arch arm64 -O2 -fPIC -fvisibility=hidden -I. -I/opt/R/arm64/include -c -o hfile_s3_write.o hfile_s3_write.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf-popgen.cpp -o vcf-popgen.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf-reader.cpp -o vcf-reader.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf-stats.cpp -o vcf-stats.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf-table.cpp -o vcf-table.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcf-writer.cpp -o vcf-writer.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o vcfppR.so RcppExports.o vcf-popgen.o vcf-reader.o vcf-stats.o vcf-table.o vcf-writer.o htslib-1.21/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/vcfppR.Rcheck/00LOCK-vcfppR/00new/vcfppR/libs ** generating debug symbols (dSYM) ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (vcfppR)