=> "/opt/pkg/bin/bmake" ["-C", "/Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks", "all", "PYTHON_VERSION_REQD=313", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] ===> Building for stacks-2.68 --- all --- /opt/pkg/bin/bmake all-recursive --- all-recursive --- Making all in htslib --- cram/.dirstamp --- --- cram/.deps/.dirstamp --- --- os/.dirstamp --- --- os/.deps/.dirstamp --- --- bcf_sr_sort.o --- --- bgzf.o --- --- bcf_sr_sort.o --- depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT bcf_sr_sort.o -MD -MP -MF $depbase.Tpo -c -o bcf_sr_sort.o bcf_sr_sort.c && mv -f $depbase.Tpo $depbase.Po --- bgzf.o --- depbase=`echo bgzf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT bgzf.o -MD -MP -MF $depbase.Tpo -c -o bgzf.o bgzf.c && mv -f $depbase.Tpo $depbase.Po --- bgzip.o --- depbase=`echo bgzip.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT bgzip.o -MD -MP -MF $depbase.Tpo -c -o bgzip.o bgzip.c && mv -f $depbase.Tpo $depbase.Po --- errmod.o --- depbase=`echo errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT errmod.o -MD -MP -MF $depbase.Tpo -c -o errmod.o errmod.c && mv -f $depbase.Tpo $depbase.Po --- faidx.o --- depbase=`echo faidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT faidx.o -MD -MP -MF $depbase.Tpo -c -o faidx.o faidx.c && mv -f $depbase.Tpo $depbase.Po --- hfile.o --- depbase=`echo hfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT hfile.o -MD -MP -MF $depbase.Tpo -c -o hfile.o hfile.c && mv -f $depbase.Tpo $depbase.Po --- hfile_net.o --- depbase=`echo hfile_net.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT hfile_net.o -MD -MP -MF $depbase.Tpo -c -o hfile_net.o hfile_net.c && mv -f $depbase.Tpo $depbase.Po --- hts.o --- depbase=`echo hts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT hts.o -MD -MP -MF $depbase.Tpo -c -o hts.o hts.c && mv -f $depbase.Tpo $depbase.Po --- hts_os.o --- depbase=`echo hts_os.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT hts_os.o -MD -MP -MF $depbase.Tpo -c -o hts_os.o hts_os.c && mv -f $depbase.Tpo $depbase.Po --- htsfile.o --- depbase=`echo htsfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT htsfile.o -MD -MP -MF $depbase.Tpo -c -o htsfile.o htsfile.c && mv -f $depbase.Tpo $depbase.Po --- kfunc.o --- depbase=`echo kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT kfunc.o -MD -MP -MF $depbase.Tpo -c -o kfunc.o kfunc.c && mv -f $depbase.Tpo $depbase.Po --- knetfile.o --- depbase=`echo knetfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT knetfile.o -MD -MP -MF $depbase.Tpo -c -o knetfile.o knetfile.c && mv -f $depbase.Tpo $depbase.Po --- kstring.o --- depbase=`echo kstring.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT kstring.o -MD -MP -MF $depbase.Tpo -c -o kstring.o kstring.c && mv -f $depbase.Tpo $depbase.Po --- md5.o --- depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c && mv -f $depbase.Tpo $depbase.Po --- multipart.o --- depbase=`echo multipart.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_codecs.o --- depbase=`echo cram/cram_codecs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_codecs.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_codecs.o cram/cram_codecs.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_decode.o --- depbase=`echo cram/cram_decode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_decode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_decode.o cram/cram_decode.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_encode.o --- depbase=`echo cram/cram_encode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_encode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_encode.o cram/cram_encode.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_external.o --- depbase=`echo cram/cram_external.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_external.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_external.o cram/cram_external.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_index.o --- depbase=`echo cram/cram_index.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_index.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_index.o cram/cram_index.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_io.o --- depbase=`echo cram/cram_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_io.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_io.o cram/cram_io.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_samtools.o --- depbase=`echo cram/cram_samtools.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_samtools.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_samtools.o cram/cram_samtools.c && mv -f $depbase.Tpo $depbase.Po --- cram/cram_stats.o --- depbase=`echo cram/cram_stats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/cram_stats.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_stats.o cram/cram_stats.c && mv -f $depbase.Tpo $depbase.Po --- cram/files.o --- depbase=`echo cram/files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/files.o -MD -MP -MF $depbase.Tpo -c -o cram/files.o cram/files.c && mv -f $depbase.Tpo $depbase.Po --- cram/mFILE.o --- depbase=`echo cram/mFILE.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/mFILE.o -MD -MP -MF $depbase.Tpo -c -o cram/mFILE.o cram/mFILE.c && mv -f $depbase.Tpo $depbase.Po --- cram/open_trace_file.o --- depbase=`echo cram/open_trace_file.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -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 $depbase.Po --- cram/pooled_alloc.o --- depbase=`echo cram/pooled_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/pooled_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/pooled_alloc.o cram/pooled_alloc.c && mv -f $depbase.Tpo $depbase.Po --- cram/rANS_static.o --- depbase=`echo cram/rANS_static.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/rANS_static.o -MD -MP -MF $depbase.Tpo -c -o cram/rANS_static.o cram/rANS_static.c && mv -f $depbase.Tpo $depbase.Po --- cram/sam_header.o --- depbase=`echo cram/sam_header.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/sam_header.o -MD -MP -MF $depbase.Tpo -c -o cram/sam_header.o cram/sam_header.c && mv -f $depbase.Tpo $depbase.Po --- cram/string_alloc.o --- depbase=`echo cram/string_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT cram/string_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/string_alloc.o cram/string_alloc.c && mv -f $depbase.Tpo $depbase.Po --- probaln.o --- depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT probaln.o -MD -MP -MF $depbase.Tpo -c -o probaln.o probaln.c && mv -f $depbase.Tpo $depbase.Po --- realn.o --- depbase=`echo realn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT realn.o -MD -MP -MF $depbase.Tpo -c -o realn.o realn.c && mv -f $depbase.Tpo $depbase.Po --- regidx.o --- depbase=`echo regidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT regidx.o -MD -MP -MF $depbase.Tpo -c -o regidx.o regidx.c && mv -f $depbase.Tpo $depbase.Po --- sam.o --- depbase=`echo sam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT sam.o -MD -MP -MF $depbase.Tpo -c -o sam.o sam.c && mv -f $depbase.Tpo $depbase.Po --- synced_bcf_reader.o --- depbase=`echo synced_bcf_reader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT synced_bcf_reader.o -MD -MP -MF $depbase.Tpo -c -o synced_bcf_reader.o synced_bcf_reader.c && mv -f $depbase.Tpo $depbase.Po --- tabix.o --- depbase=`echo tabix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT tabix.o -MD -MP -MF $depbase.Tpo -c -o tabix.o tabix.c && mv -f $depbase.Tpo $depbase.Po --- tbx.o --- --- textutils.o --- --- tbx.o --- depbase=`echo tbx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT tbx.o -MD -MP -MF $depbase.Tpo -c -o tbx.o tbx.c && mv -f $depbase.Tpo $depbase.Po --- textutils.o --- depbase=`echo textutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT textutils.o -MD -MP -MF $depbase.Tpo -c -o textutils.o textutils.c && mv -f $depbase.Tpo $depbase.Po --- thread_pool.o --- --- vcf.o --- --- thread_pool.o --- depbase=`echo thread_pool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT thread_pool.o -MD -MP -MF $depbase.Tpo -c -o thread_pool.o thread_pool.c && mv -f $depbase.Tpo $depbase.Po --- vcf.o --- depbase=`echo vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT vcf.o -MD -MP -MF $depbase.Tpo -c -o vcf.o vcf.c && mv -f $depbase.Tpo $depbase.Po --- vcf_sweep.o --- depbase=`echo vcf_sweep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT vcf_sweep.o -MD -MP -MF $depbase.Tpo -c -o vcf_sweep.o vcf_sweep.c && mv -f $depbase.Tpo $depbase.Po --- vcfutils.o --- depbase=`echo vcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c && mv -f $depbase.Tpo $depbase.Po --- os/rand.o --- depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang -DHAVE_CONFIG_H -I. -I.. -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c && mv -f $depbase.Tpo $depbase.Po --- libhts.a --- rm -f libhts.a ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o ranlib libhts.a --- src/.dirstamp --- --- src/.deps/.dirstamp --- --- src/clean.o --- --- src/kmers.o --- --- src/file_io.o --- --- src/clean.o --- depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/clean.o -MD -MP -MF $depbase.Tpo -c -o src/clean.o src/clean.cc && mv -f $depbase.Tpo $depbase.Po --- src/kmers.o --- depbase=`echo src/kmers.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/kmers.o -MD -MP -MF $depbase.Tpo -c -o src/kmers.o src/kmers.cc && mv -f $depbase.Tpo $depbase.Po --- src/file_io.o --- depbase=`echo src/file_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -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 --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:35: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:30: --- src/kmers.o --- /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/clean.o --- In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/kmers.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' --- src/clean.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ --- src/kmers.o --- 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/clean.o --- /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:35: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] --- src/file_io.o --- 426 | sprintf(buf, "%d", i); | ^ --- src/kmers.o --- 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/file_io.o --- /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/kmers.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/clean.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:35: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] --- src/file_io.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ --- src/kmers.o --- 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here --- src/file_io.o --- /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' --- src/clean.o --- 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/file_io.o --- 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/kmers.o --- 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:35: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/kmers.o --- 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: --- src/file_io.o --- 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:35: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: --- src/kmers.o --- src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: --- src/file_io.o --- src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: --- src/clean.o --- src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: --- src/kmers.o --- src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: --- src/clean.o --- src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} --- src/kmers.o --- src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: --- src/clean.o --- | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: --- src/file_io.o --- src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: --- src/clean.o --- src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: --- src/kmers.o --- src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: --- src/file_io.o --- src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: --- src/kmers.o --- src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: --- src/file_io.o --- src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: --- src/clean.o --- src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: --- src/kmers.o --- In file included from src/kmers.cc:24: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: --- src/file_io.o --- In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/kmers.o --- src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/file_io.o --- 92 | , utags (move(o.utags)) | ^ | std:: --- src/kmers.o --- 99 | , loc (move(o.loc)) | ^ | std:: --- src/file_io.o --- src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: --- src/kmers.o --- src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: --- src/file_io.o --- src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: --- src/clean.o --- In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:37: --- src/kmers.o --- src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/clean.o --- src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] --- src/kmers.o --- 101 | , alleles (move(o.alleles)) | ^ | std:: --- src/file_io.o --- src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ --- src/clean.o --- 92 | , utags (move(o.utags)) | ^ | std:: --- src/file_io.o --- | std:: --- src/clean.o --- src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: --- src/kmers.o --- src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: --- src/file_io.o --- src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: --- src/clean.o --- src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: --- src/file_io.o --- src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: --- src/clean.o --- src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 28 warnings generated. --- src/write.o --- depbase=`echo src/write.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc && mv -f $depbase.Tpo $depbase.Po --- src/kmers.o --- 28 warnings generated. --- src/aln_utils.o --- depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/aln_utils.o -MD -MP -MF $depbase.Tpo -c -o src/aln_utils.o src/aln_utils.cc && mv -f $depbase.Tpo $depbase.Po --- src/file_io.o --- 28 warnings generated. --- src/BamI.o --- depbase=`echo src/BamI.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/BamI.o -MD -MP -MF $depbase.Tpo -c -o src/BamI.o src/BamI.cc && mv -f $depbase.Tpo $depbase.Po --- src/write.o --- In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: src/write.cc:34:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 34 | sprintf(tile, "%04d", href->tile); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ src/write.cc:63:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 63 | sprintf(tile, "%04d", href->tile); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ src/write.cc:120:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 120 | sprintf(tile, "%04d", href->tile); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ src/write.cc:156:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 156 | sprintf(tile, "%04d", href->tile); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ 32 warnings generated. --- src/catalog_utils.o --- depbase=`echo src/catalog_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/catalog_utils.o -MD -MP -MF $depbase.Tpo -c -o src/catalog_utils.o src/catalog_utils.cc && mv -f $depbase.Tpo $depbase.Po --- src/cmb.o --- depbase=`echo src/cmb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/cmb.o -MD -MP -MF $depbase.Tpo -c -o src/cmb.o src/cmb.cc && mv -f $depbase.Tpo $depbase.Po --- src/BamI.o --- In file included from src/BamI.cc:6: In file included from src/BamI.h:36: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/BamI.cc:6: In file included from src/BamI.h:36: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/BamI.cc:6: In file included from src/BamI.h:36: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/BamI.cc:6: In file included from src/BamI.h:36: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/BamI.cc:6: In file included from src/BamI.h:36: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/BamI.cc:157:9: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 157 | hdr(move(header)), | ^ | std:: 8 warnings generated. --- src/constants.o --- depbase=`echo src/constants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/constants.o -MD -MP -MF $depbase.Tpo -c -o src/constants.o src/constants.cc && mv -f $depbase.Tpo $depbase.Po --- src/catalog_utils.o --- In file included from src/catalog_utils.cc:30: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/catalog_utils.cc:30: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/catalog_utils.cc:30: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:30: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:30: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:31: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:31: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:32: In file included from src/PopMap.h:39: src/Vcf.h:374:18: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 374 | size_t len = sprintf(s, "%zu", pos0 + 1); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:32: In file included from src/PopMap.h:39: src/Vcf.h:413:22: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 413 | size_t len = sprintf(s, "%ld", phred_qual); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: --- src/cmb.o --- In file included from src/cmb.cc:30: In file included from src/cmb.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/cmb.cc:30: In file included from src/cmb.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/cmb.cc:30: In file included from src/cmb.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/constants.o --- In file included from src/constants.cc:5: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/constants.cc:5: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/constants.cc:5: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ --- src/cmb.o --- 3 warnings generated. --- src/DNANSeq.o --- depbase=`echo src/DNANSeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/DNANSeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNANSeq.o src/DNANSeq.cc && mv -f $depbase.Tpo $depbase.Po --- src/catalog_utils.o --- 24 warnings generated. --- src/DNASeq4.o --- depbase=`echo src/DNASeq4.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/DNASeq4.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq4.o src/DNASeq4.cc && mv -f $depbase.Tpo $depbase.Po --- src/constants.o --- 3 warnings generated. --- src/DNASeq.o --- depbase=`echo src/DNASeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/DNASeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq.o src/DNASeq.cc && mv -f $depbase.Tpo $depbase.Po --- src/gzFasta.o --- depbase=`echo src/gzFasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/gzFasta.o -MD -MP -MF $depbase.Tpo -c -o src/gzFasta.o src/gzFasta.cc && mv -f $depbase.Tpo $depbase.Po --- src/DNASeq4.o --- In file included from src/DNASeq4.cc:1: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: src/DNASeq4.cc:96:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | *this = move(seq); | ^ | std:: 3 warnings generated. --- src/input.o --- depbase=`echo src/input.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/input.o -MD -MP -MF $depbase.Tpo -c -o src/input.o src/input.cc && mv -f $depbase.Tpo $depbase.Po --- src/locus.o --- depbase=`echo src/locus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/locus.o -MD -MP -MF $depbase.Tpo -c -o src/locus.o src/locus.cc && mv -f $depbase.Tpo $depbase.Po --- src/gzFasta.o --- In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 7 warnings generated. --- src/log_utils.o --- depbase=`echo src/log_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -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 --- src/input.o --- In file included from src/input.cc:25: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/input.cc:25: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/input.cc:25: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/input.cc:25: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/input.cc:25: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 7 warnings generated. --- src/MetaPopInfo.o --- depbase=`echo src/MetaPopInfo.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/MetaPopInfo.o -MD -MP -MF $depbase.Tpo -c -o src/MetaPopInfo.o src/MetaPopInfo.cc && mv -f $depbase.Tpo $depbase.Po --- src/locus.o --- In file included from src/locus.cc:24: In file included from src/locus.h:32: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/locus.cc:24: In file included from src/locus.h:32: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/locus.cc:24: In file included from src/locus.h:32: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/locus.cc:24: In file included from src/locus.h:32: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/locus.cc:24: In file included from src/locus.h:32: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/locus.cc:24: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/locus.cc:24: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: src/locus.cc:519:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 519 | *r1 = SAlnRead(AlnRead::merger_of(move(*r1), move(*r2)), r1->sample); | ^ | std:: src/locus.cc:519:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 519 | *r1 = SAlnRead(AlnRead::merger_of(move(*r1), move(*r2)), r1->sample); | ^ | std:: src/locus.cc:668:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 668 | CLocAlnSet merged (move(left)); | ^ | std:: src/locus.cc:691:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 691 | merged.add(move(r)); | ^ | std:: src/locus.cc:727:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 727 | merged.add(move(r)); | ^ | std:: --- src/log_utils.o --- In file included from src/log_utils.cc:27: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/log_utils.cc:27: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/log_utils.cc:27: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ 3 warnings generated. --- src/models.o --- depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; clang++ -DHAVE_CONFIG_H -I. -I./htslib -I/opt/pkg/include -I/opt/pkg/include/python3.13 -pipe -Os -Xpreprocessor -fopenmp -I/opt/pkg/include -I/opt/pkg/include/python3.13 -MT src/models.o -MD -MP -MF $depbase.Tpo -c -o src/models.o src/models.cc && mv -f $depbase.Tpo $depbase.Po --- src/MetaPopInfo.o --- In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: In file included from src/stacks.h:36: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/MetaPopInfo.cc:427:30: error: non-constant-expression cannot be narrowed from type 'size_t' (aka 'unsigned long') to 'const int' in initializer list [-Wc++11-narrowing-const-reference] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); | ^ 7 warnings and 1 error generated. *** [src/MetaPopInfo.o] Error code 1 bmake[2]: stopped making "all-am" in /var/tmp/work/biology/stacks/work/stacks-2.68 --- src/locus.o --- 25 warnings generated. --- src/models.o --- In file included from src/models.cc:30: In file included from src/models.h:25: src/utils.h:426:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 426 | sprintf(buf, "%d", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/models.cc:30: In file included from src/models.h:25: src/utils.h:438:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 438 | sprintf(buf, "%ld", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/models.cc:30: In file included from src/models.h:25: src/utils.h:450:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] 450 | sprintf(buf, "%zu", i); | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here 278 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") | ^ /Applications/Xcode-16.4.0.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX15.5.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' 218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) | ^ In file included from src/models.cc:30: In file included from src/models.h:26: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:27: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:28: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:28: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:29: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/models.cc:30: src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 115 | : alleles_(move(alleles)) | ^ | std:: src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 117 | , sample_calls_(move(sample_calls)) | ^ | std:: src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.cc:515:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 515 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:515:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 515 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:709:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 709 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:709:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 709 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:1007:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls)); | ^ | std:: src/models.cc:1007:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls)); | ^ | std:: 38 warnings generated. bmake[2]: 1 error bmake[2]: stopped making "all-am" in /var/tmp/work/biology/stacks/work/stacks-2.68 bmake[1]: stopped making "all-recursive" in /var/tmp/work/biology/stacks/work/stacks-2.68 bmake: stopped making "all" in /var/tmp/work/biology/stacks/work/stacks-2.68 *** Error code 2 Stop. bmake[1]: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks *** Error code 1 Stop. bmake: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks