=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for htslib-1.12
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o kfunc.o kfunc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o kstring.o kstring.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o bgzf.o bgzf.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o errmod.o errmod.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o faidx.o faidx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o header.o header.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.12"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I/usr/include -I/usr/pkg/include -I/usr/include/krb5"' >> config_vars.h
echo '#define HTS_CFLAGS "-Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fvisibility=hidden "' >> config_vars.h
echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm   -lcurl -lcrypto"' >> config_vars.h
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hts_expr.o hts_expr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hts_os.o hts_os.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o md5.o md5.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o multipart.o multipart.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o probaln.o probaln.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o realn.o realn.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o regidx.o regidx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o region.o region.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o sam.o sam.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o tbx.o tbx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o textutils.o textutils.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o thread_pool.o thread_pool.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o vcf.o vcf.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o vcfutils.o vcfutils.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hfile_gcs.o hfile_gcs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hfile_s3.o hfile_s3.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hfile_s3_write.o hfile_s3_write.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o kfunc.pico kfunc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o kstring.pico kstring.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o bgzf.pico bgzf.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o errmod.pico errmod.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o faidx.pico faidx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o header.pico header.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hfile.pico hfile.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hts.pico hts.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hts_expr.pico hts_expr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hts_os.pico hts_os.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o md5.pico md5.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o multipart.pico multipart.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o probaln.pico probaln.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o realn.pico realn.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o regidx.pico regidx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o region.pico region.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o sam.pico sam.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o tbx.pico tbx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o textutils.pico textutils.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o thread_pool.pico thread_pool.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o vcf.pico vcf.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o vcfutils.pico vcfutils.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fpic -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o bgzip.o bgzip.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o htsfile.o htsfile.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o tabix.o tabix.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/hts_endian.o test/hts_endian.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/fieldarith.o test/fieldarith.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/hfile.o test/hfile.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/pileup.o test/pileup.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/sam.o test/sam.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_expr.o test/test_expr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_kfunc.o test/test_kfunc.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_kstring.o test/test_kstring.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_realn.o test/test_realn.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-regidx.o test/test-regidx.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_str2int.o test/test_str2int.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_view.o test/test_view.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_index.o test/test_index.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o test/test_introspection.o test/test_introspection.c
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
gcc -Wall -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden -I. -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fvisibility=hidden  -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
gcc -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fvisibility=hidden  -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm   -lcurl -lcrypto
gcc -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fvisibility=hidden  -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm   -lcurl -lcrypto
ld: kstring.pico: in function `kputd':
kstring.c:(.text+0x18): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: kstring.pico: in function `ksplit_core':
kstring.c:(.text+0x9e8): relocation truncated to fit: R_SPARC_GOT13 against symbol `_ctype_tab_' defined in .data section in /usr/lib/libc.so
ld: bcf_sr_sort.pico: in function `bcf_sr_sort_set':
bcf_sr_sort.c:(.text+0x2a34): relocation truncated to fit: R_SPARC_GOT13 against symbol `__sF' defined in .data section in /usr/lib/libc.so
ld: bgzf.pico: in function `mt_destroy':
bgzf.c:(.text+0x260): relocation truncated to fit: R_SPARC_GOT13 against symbol `__sF' defined in .data section in /usr/lib/libc.so
ld: bgzf.pico: in function `bgzf_check_EOF_common.isra.3':
bgzf.c:(.text+0x177c): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: bgzf.pico: in function `bgzf_read_init':
bgzf.c:(.text+0x1990): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: bgzf.pico: in function `bgzf_mt_read_block':
bgzf.c:(.text+0x26fc): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: bgzf.pico: in function `bgzf_is_bgzf':
bgzf.c:(.text+0x3290): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: bgzf.pico: in function `bgzf_read_block':
bgzf.c:(.text+0x3550): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so
ld: faidx.pico: in function `fai_retrieve.isra.4':
faidx.c:(.text+0x60): relocation truncated to fit: R_SPARC_GOT13 against symbol `_ctype_tab_' defined in .data section in /usr/lib/libc.so
ld: faidx.pico: in function `fai_build3_core':
faidx.c:(.text+0x570): additional relocation overflows omitted from the output
gmake: *** [Makefile:312: libhts.so] Error 1
gmake: *** Waiting for unfinished jobs....
*** Error code 2

Stop.
make[1]: stopped in /usr/pkgsrc/biology/htslib
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/biology/htslib