+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/stacks-2.60/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/stacks-2.60/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for stacks-2.60
/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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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 $depbase.Po
depbase=`echo cram/cram_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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 $depbase.Po
depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -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 $depbase.Po
depbase=`echo src/mstack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/mstack.o -MD -MP -MF $depbase.Tpo -c -o src/mstack.o src/mstack.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mst.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/mst.o -MD -MP -MF $depbase.Tpo -c -o src/mst.o src/mst.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/nucleotides.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/nucleotides.o -MD -MP -MF $depbase.Tpo -c -o src/nucleotides.o src/nucleotides.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/renz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/renz.o -MD -MP -MF $depbase.Tpo -c -o src/renz.o src/renz.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Seq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/Seq.o -MD -MP -MF $depbase.Tpo -c -o src/Seq.o src/Seq.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sql_utilities.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/sql_utilities.o -MD -MP -MF $depbase.Tpo -c -o src/sql_utilities.o src/sql_utilities.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/stacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/stacks.o -MD -MP -MF $depbase.Tpo -c -o src/stacks.o src/stacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/Vcf.o -MD -MP -MF $depbase.Tpo -c -o src/Vcf.o src/Vcf.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/clean.o -MD -MP -MF $depbase.Tpo -c -o src/clean.o src/clean.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/file_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/file_io.o -MD -MP -MF $depbase.Tpo -c -o src/file_io.o src/file_io.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/write.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/bootstrap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/bootstrap.o -MD -MP -MF $depbase.Tpo -c -o src/bootstrap.o src/bootstrap.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/export_formats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/export_formats.o -MD -MP -MF $depbase.Tpo -c -o src/export_formats.o src/export_formats.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mapping_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/mapping_utils.o -MD -MP -MF $depbase.Tpo -c -o src/mapping_utils.o src/mapping_utils.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/genotype_dictionaries.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/genotype_dictionaries.o -MD -MP -MF $depbase.Tpo -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/PopSum.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/PopSum.o -MD -MP -MF $depbase.Tpo -c -o src/PopSum.o src/PopSum.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Hwp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/Hwp.o -MD -MP -MF $depbase.Tpo -c -o src/Hwp.o src/Hwp.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/ustacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/ustacks.o -MD -MP -MF $depbase.Tpo -c -o src/ustacks.o src/ustacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/cstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/cstacks.o -MD -MP -MF $depbase.Tpo -c -o src/cstacks.o src/cstacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/sstacks.o -MD -MP -MF $depbase.Tpo -c -o src/sstacks.o src/sstacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/process_radtags.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/process_radtags.o -MD -MP -MF $depbase.Tpo -c -o src/process_radtags.o src/process_radtags.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/process_shortreads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/process_shortreads.o -MD -MP -MF $depbase.Tpo -c -o src/process_shortreads.o src/process_shortreads.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/kmer_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/kmer_filter.o -MD -MP -MF $depbase.Tpo -c -o src/kmer_filter.o src/kmer_filter.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/clone_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/clone_filter.o -MD -MP -MF $depbase.Tpo -c -o src/clone_filter.o src/clone_filter.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/populations.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/populations.o -MD -MP -MF $depbase.Tpo -c -o src/populations.o src/populations.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/phasedstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/phasedstacks.o -MD -MP -MF $depbase.Tpo -c -o src/phasedstacks.o src/phasedstacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/tsv2bam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/tsv2bam.o -MD -MP -MF $depbase.Tpo -c -o src/tsv2bam.o src/tsv2bam.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/gstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/gstacks.o -MD -MP -MF $depbase.Tpo -c -o src/gstacks.o src/gstacks.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/debruijn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/debruijn.o -MD -MP -MF $depbase.Tpo -c -o src/debruijn.o src/debruijn.cc && mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/SuffixTree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; g++ -DHAVE_CONFIG_H -I. -I./htslib -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -MT src/SuffixTree.o -MD -MP -MF $depbase.Tpo -c -o src/SuffixTree.o src/SuffixTree.cc && mv -f $depbase.Tpo $depbase.Po
rm -f libcore.a
ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o
ranlib libcore.a
rm -f libclean.a
ar cru libclean.a src/clean.o src/file_io.o src/write.o
ranlib libclean.a
rm -f libpop.a
ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o
ranlib libpop.a
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp
g++ -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -fopenmp -D_FORTIFY_SOURCE=2 -I/usr/include -I/opt/pkg/include/python3.9 -I/opt/pkg/include -lsocket -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp