=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> 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-1.17nb5 gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 "1.17"' > 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' \ 'gcc' \ '-I/usr/include -I/usr/pkg/include -I/usr/include/krb5' \ '-Wall -O2 -I/usr/include -I/usr/pkg/include -I/usr/include/krb5 -fvisibility=hidden' \ '-L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -fvisibility=hidden ' \ '-llzma -lbz2 -lz -lm -lcurl -lcrypto' > config_vars.h gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -Wall -O2 -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 -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 -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 -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/utils.o htscodecs/htscodecs/utils.c gcc -Wall -O2 -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 -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 htscodecs/htscodecs/tokenise_name3.c: In function 'encode_name': htscodecs/htscodecs/tokenise_name3.c:766:16: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:772:35: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:772:55: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:822:34: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:867:23: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:873:34: warning: array subscript has type 'char' [-Wchar-subscripts] gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 distcc[26762] (dcc_select_for_write) ERROR: IO timeout distcc[26762] ERROR: timeout while connecting to 10.0.20.122:3742 distcc[26762] Warning: failed to distribute tbx.c to 10.0.20.122:3742, running locally instead gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c gcc -Wall -O2 -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 -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 -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 -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/utils.pico htscodecs/htscodecs/utils.c htscodecs/htscodecs/tokenise_name3.c: In function 'encode_name': htscodecs/htscodecs/tokenise_name3.c:766:16: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:772:35: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:772:55: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:822:34: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:867:23: warning: array subscript has type 'char' [-Wchar-subscripts] htscodecs/htscodecs/tokenise_name3.c:873:34: warning: array subscript has type 'char' [-Wchar-subscripts] gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_mod.o test/pileup_mod.c gcc -Wall -O2 -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 -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 -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 -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 -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_faidx.o test/test_faidx.c gcc -Wall -O2 -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 -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 -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_mod.o test/test_mod.c gcc -Wall -O2 -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 -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 -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 -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_time_funcs.o test/test_time_funcs.c gcc -Wall -O2 -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 -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 -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 -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 -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 -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 -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 -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 -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 gcc -Wall -O2 -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_set_variant_type.o test/test-bcf_set_variant_type.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 -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 -Wl,-version-script,htslib.map -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_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread kfunc.pico: in function `kt_fisher_exact': kfunc.c:(.text+0xb9c): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so 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 kstring.pico: in function `ksprintf': kstring.c:(.text+0x790): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so kstring.pico: in function `ksplit_core': kstring.c:(.text+0x9e0): relocation truncated to fit: R_SPARC_GOT13 against symbol `_ctype_tab_' defined in .data section in /usr/lib/libc.so bcf_sr_sort.pico: in function `bcf_sr_sort_next': bcf_sr_sort.c:(.text+0xad0): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so bcf_sr_sort.c:(.text+0x2f40): relocation truncated to fit: R_SPARC_GOT13 against symbol `__sF' defined in .data section in /usr/lib/libc.so bgzf.pico: in function `mt_destroy': bgzf.c:(.text+0x1d0): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so bgzf.c:(.text+0x2b8): relocation truncated to fit: R_SPARC_GOT13 against symbol `__sF' defined in .data section in /usr/lib/libc.so bgzf.pico: in function `bgzf_uncompress': bgzf.c:(.text+0xcd0): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so bgzf.pico: in function `inflate_gzip_block': bgzf.c:(.text+0x140c): relocation truncated to fit: R_SPARC_GOT13 against symbol `__stack_chk_guard' defined in .bss section in /usr/lib/libc.so bgzf.pico: in function `bgzf_check_EOF_common': bgzf.c:(.text+0x16d0): additional relocation overflows omitted from the output distcc[26482] ERROR: compile (null) on localhost failed gmake: *** [Makefile:358: 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