+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/stacks-2.60nb3/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/stacks-2.60nb3/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for stacks-2.60nb3
/opt/pkg/bin/bmake all-recursive
Making all in htslib
depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT bcf_sr_sort.o -MD -MP -MF $depbase.Tpo -c -o bcf_sr_sort.o bcf_sr_sort.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo bgzf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT bgzf.o -MD -MP -MF $depbase.Tpo -c -o bgzf.o bgzf.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo bgzip.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT bgzip.o -MD -MP -MF $depbase.Tpo -c -o bgzip.o bgzip.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_codecs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_codecs.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_codecs.o cram/cram_codecs.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_decode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_decode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_decode.o cram/cram_decode.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_encode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_encode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_encode.o cram/cram_encode.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_external.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_external.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_external.o cram/cram_external.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_index.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_index.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_index.o cram/cram_index.c && mv -f $depbase.Tpo $depbase.Po
In file included from ./textutils_internal.h:32,
from ./hts_internal.h:31,
from cram/cram_index.c:65:
In function 'kputsn',
inlined from 'kputs' at ./htslib/kstring.h:156:9,
inlined from 'cram_index_build' at cram/cram_index.c:571:9:
./htslib/kstring.h:150:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
150 | s->s[s->l] = 0;
| ~~~~~~~~~~~^~~
./htslib/kstring.h:148:9: warning: 'memcpy' specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
148 | memcpy(s->s + s->l, p, l);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
depbase=`echo cram/cram_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_io.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_io.o cram/cram_io.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_samtools.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_samtools.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_samtools.o cram/cram_samtools.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_stats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/cram_stats.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_stats.o cram/cram_stats.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/files.o -MD -MP -MF $depbase.Tpo -c -o cram/files.o cram/files.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/mFILE.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/mFILE.o -MD -MP -MF $depbase.Tpo -c -o cram/mFILE.o cram/mFILE.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/open_trace_file.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/open_trace_file.o -MD -MP -MF $depbase.Tpo -c -o cram/open_trace_file.o cram/open_trace_file.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/pooled_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/pooled_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/pooled_alloc.o cram/pooled_alloc.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/rANS_static.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/rANS_static.o -MD -MP -MF $depbase.Tpo -c -o cram/rANS_static.o cram/rANS_static.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/sam_header.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/sam_header.o -MD -MP -MF $depbase.Tpo -c -o cram/sam_header.o cram/sam_header.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/string_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT cram/string_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/string_alloc.o cram/string_alloc.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT errmod.o -MD -MP -MF $depbase.Tpo -c -o errmod.o errmod.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo faidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT faidx.o -MD -MP -MF $depbase.Tpo -c -o faidx.o faidx.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo hfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT hfile.o -MD -MP -MF $depbase.Tpo -c -o hfile.o hfile.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo hfile_net.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT hfile_net.o -MD -MP -MF $depbase.Tpo -c -o hfile_net.o hfile_net.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo hts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT hts.o -MD -MP -MF $depbase.Tpo -c -o hts.o hts.c && mv -f $depbase.Tpo $depbase.Po
hts.c: In function 'hts_idx_init':
hts.c:1366:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow]
1366 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
| ^~~
depbase=`echo hts_os.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT hts_os.o -MD -MP -MF $depbase.Tpo -c -o hts_os.o hts_os.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo htsfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT htsfile.o -MD -MP -MF $depbase.Tpo -c -o htsfile.o htsfile.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT kfunc.o -MD -MP -MF $depbase.Tpo -c -o kfunc.o kfunc.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo knetfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT knetfile.o -MD -MP -MF $depbase.Tpo -c -o knetfile.o knetfile.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo kstring.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT kstring.o -MD -MP -MF $depbase.Tpo -c -o kstring.o kstring.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo multipart.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT probaln.o -MD -MP -MF $depbase.Tpo -c -o probaln.o probaln.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo realn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT realn.o -MD -MP -MF $depbase.Tpo -c -o realn.o realn.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo regidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT regidx.o -MD -MP -MF $depbase.Tpo -c -o regidx.o regidx.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo sam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT sam.o -MD -MP -MF $depbase.Tpo -c -o sam.o sam.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo synced_bcf_reader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT synced_bcf_reader.o -MD -MP -MF $depbase.Tpo -c -o synced_bcf_reader.o synced_bcf_reader.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo tabix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT tabix.o -MD -MP -MF $depbase.Tpo -c -o tabix.o tabix.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo tbx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT tbx.o -MD -MP -MF $depbase.Tpo -c -o tbx.o tbx.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo textutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT textutils.o -MD -MP -MF $depbase.Tpo -c -o textutils.o textutils.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo thread_pool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT thread_pool.o -MD -MP -MF $depbase.Tpo -c -o thread_pool.o thread_pool.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT vcf.o -MD -MP -MF $depbase.Tpo -c -o vcf.o vcf.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf_sweep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT vcf_sweep.o -MD -MP -MF $depbase.Tpo -c -o vcf_sweep.o vcf_sweep.c && mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c && mv -f $depbase.Tpo $depbase.Po
rm -f libhts.a
ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o
ranlib libhts.a
depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/aln_utils.o -MD -MP -MF $depbase.Tpo -c -o src/aln_utils.o src/aln_utils.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/BamI.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/BamI.o -MD -MP -MF $depbase.Tpo -c -o src/BamI.o src/BamI.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/catalog_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/catalog_utils.o -MD -MP -MF $depbase.Tpo -c -o src/catalog_utils.o src/catalog_utils.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/cmb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/cmb.o -MD -MP -MF $depbase.Tpo -c -o src/cmb.o src/cmb.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/constants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/constants.o -MD -MP -MF $depbase.Tpo -c -o src/constants.o src/constants.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNANSeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/DNANSeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNANSeq.o src/DNANSeq.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNASeq4.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/DNASeq4.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq4.o src/DNASeq4.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNASeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/DNASeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq.o src/DNASeq.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/gzFasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/gzFasta.o -MD -MP -MF $depbase.Tpo -c -o src/gzFasta.o src/gzFasta.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/input.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/input.o -MD -MP -MF $depbase.Tpo -c -o src/input.o src/input.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/kmers.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/kmers.o -MD -MP -MF $depbase.Tpo -c -o src/kmers.o src/kmers.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/locus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/locus.o -MD -MP -MF $depbase.Tpo -c -o src/locus.o src/locus.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/log_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/log_utils.o -MD -MP -MF $depbase.Tpo -c -o src/log_utils.o src/log_utils.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/MetaPopInfo.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/MetaPopInfo.o -MD -MP -MF $depbase.Tpo -c -o src/MetaPopInfo.o src/MetaPopInfo.cc && mv -f $depbase.Tpo $depbase.Po
src/MetaPopInfo.cc: In member function 'void MetaPopInfo::fill_pop_indexes(std::map<int, std::pair<int, int> >&) const':
src/MetaPopInfo.cc:427:30: warning: narrowing conversion of 'i' from 'size_t' {aka 'long unsigned int'} to 'int' [-Wnarrowing]
427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} );
| ^
depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fopenmp -I/usr/include -I/opt/pkg/include/python3.11 -I/opt/pkg/include -MT src/models.o -MD -MP -MF $depbase.Tpo -c -o src/models.o src/models.cc && mv -f $depbase.Tpo $depbase.Po
src/models.cc: In member function 'double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const':
src/models.cc:736:30: error: 'numeric_limits' is not a member of 'std'
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ^~~~~~~~~~~~~~
src/models.cc:736:45: error: expected primary-expression before 'double'
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ^~~~~~
src/models.cc:736:45: error: expected ')' before 'double'
736 | if (weighted_sum >= std::numeric_limits<double>::min()) {
| ~ ^~~~~~
| )
src/models.cc: In member function 'virtual SiteCall MarukiLowModel::call(const SiteCounts&) const':
src/models.cc:865:31: error: 'numeric_limits' is not a member of 'std'
865 | double lnl_dimorph = std::numeric_limits<double>::lowest();
| ^~~~~~~~~~~~~~
src/models.cc:865:46: error: expected primary-expression before 'double'
865 | double lnl_dimorph = std::numeric_limits<double>::lowest();
| ^~~~~~
In file included from /opt/tools/gcc13/include/c++/13.2.0/cassert:44,
from src/constants.h:39,
from src/models.h:24,
from src/models.cc:30:
src/models.cc:883:31: error: 'numeric_limits' is not a member of 'std'
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~~~~~~~~~
src/models.cc:883:46: error: expected primary-expression before 'double'
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~
src/models.cc:883:46: error: expected ')' before 'double'
src/models.cc:883:5: note: to match this '('
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~
src/models.cc:883:64: error: expected ')' before ';' token
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^
src/models.cc:883:5: note: to match this '('
883 | assert(lnl_dimorph > std::numeric_limits<double>::lowest());
| ^~~~~~
src/models.cc: In member function 'double MarukiLowModel::calc_ln_weighted_sum(double, double, double, const LikData&) const':
src/models.cc:744:1: warning: control reaches end of non-void function [-Wreturn-type]
744 | }
| ^
*** [src/models.o] Error code 1
bmake[2]: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
1 error
bmake[2]: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
*** [all-recursive] Error code 1
bmake[1]: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
1 error
bmake[1]: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
*** [all] Error code 2
bmake: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
1 error
bmake: stopped in /home/pbulk/build/biology/stacks/work/stacks-2.60
*** Error code 2
Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/stacks
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/stacks