############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ cd "htslib-1.18" && make -f "Makefile.Rhtslib" echo '/* Default config.h generated by Makefile */' > config.h echo '#ifndef _XOPEN_SOURCE' >> config.h echo '#define _XOPEN_SOURCE 600' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h if [ "x" != "x" ] && \ [ "x" != "x" ] && \ [ "x" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> config.h ; \ echo '#define HAVE_SSE4_1 1' >> config.h ; \ echo '#define HAVE_SSSE3 1' >> config.h ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \ echo '#define UBSAN 1' >> config.h ; \ echo '#endif' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> config.h ; \ fi clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > 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 -D_FILE_OFFSET_BITS=64' \ '-falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden' \ '-L/opt/R/arm64/lib -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.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 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 ranlib libhts.a clang -arch arm64 -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.18 -compatibility_version 3.1.18 -L/opt/R/arm64/lib -fvisibility=hidden -o libhts.dylib 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 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 -lz -lm -lbz2 -llzma -lcurl ln -sf libhts.dylib libhts.3.dylib sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib" cd "htslib-1.18/htslib" && cp * "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include/htslib" clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include" -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib" cd "htslib-1.18" && cp libhts.a "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib" clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Rhtslib.so R_init_Rhtslib.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/testdata/tabix" cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/libs ** R ** 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 * DONE (Rhtslib)