Debian Bug report logs - #1015699
vg: ftbfs with LTO (link time optimization) enabled

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Message #5 received at [email protected] (full text, mbox, reply):

From: Matthias Klose <[email protected]>

To: [email protected]

Subject: vg: ftbfs with LTO (link time optimization) enabled

Date: Tue, 19 Jul 2022 17:02:09 +0000

Package: src:vg
Version: 1.30.0+ds-1
Severity: minor
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-lto

This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled.  For a background
for LTO please see

https://wiki.debian.org/ToolChain/LTO

The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures.  The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.

To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:

export DEB_BUILD_MAINT_OPTIONS = optimize=+lto

Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:

export DEB_BUILD_MAINT_OPTIONS = optimize=-lto

or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/vg_1.30.0+ds-1_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp 
. ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp 
rm -f lib/libvg.a
ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o
ar: creating lib/libvg.a
. ./source_me.sh && g++ -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/<<PKGBUILDDIR>>/lib /<<PKGBUILDDIR>>/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic 
rm -f lib/vg_is_static
. ./source_me.sh && g++ -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o  -lvg -L/<<PKGBUILDDIR>>/lib /<<PKGBUILDDIR>>/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lm -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lm -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 
lto1: fatal error: multiple prevailing defs for ‘_ZTIN4sdsl14rank_support_vILh1ELh1EEE’
compilation terminated.
lto-wrapper: fatal error: g++ returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:368: test/build_graph] Error 1
make[2]: *** Waiting for unfinished jobs....
src/subcommand/../algorithms/walk.hpp:22: warning: type ‘struct walk_t’ violates the C++ One Definition Rule [-Wodr]
   22 | struct walk_t {
      | 
src/algorithms/prune.cpp:12: note: a different type is defined in another translation unit
   12 | struct walk_t {
      | 
src/subcommand/../algorithms/walk.hpp:29: note: the first difference of corresponding definitions is field ‘path’
   29 |     std::vector<handle_t> path;
      | 
src/algorithms/prune.cpp:20: note: a field with different name is defined in another translation unit
   20 |     pos_t begin;
      | 
deps/vowpal_wabbit/vowpalwabbit/comp_io.h:19: warning: type ‘struct comp_io_buf’ violates the C++ One Definition Rule [-Wodr]
   19 | class comp_io_buf : public io_buf
      | 
deps/vowpal_wabbit/vowpalwabbit/comp_io.h:19: note: a different type is defined in another translation unit
   19 | class comp_io_buf : public io_buf
      | 
deps/vowpal_wabbit/vowpalwabbit/comp_io.h:22: note: the first difference of corresponding definitions is field ‘gz_files’
   22 |   std::vector<gzFile> gz_files;
      | 
deps/vowpal_wabbit/vowpalwabbit/comp_io.h:22: note: a field of same name but different type is defined in another translation unit
   22 |   std::vector<gzFile> gz_files;
      | 
/usr/include/c++/11/bits/stl_vector.h:389: note: type name ‘std::vector<void*, std::allocator<void*> >’ should match type name ‘std::vector<gzFile_s*, std::allocator<gzFile_s*> >’
  389 |     class vector : protected _Vector_base<_Tp, _Alloc>
      | 
deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:19: warning: type ‘struct update_data’ violates the C++ One Definition Rule [-Wodr]
   19 | struct update_data
      | 
deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:18: note: a different type is defined in another translation unit
   18 | struct update_data
      | 
deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:21: note: the first difference of corresponding definitions is field ‘update’
   21 |   float update;
      | 
deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:20: note: a field with different name is defined in another translation unit
   20 |   struct OjaNewton *ON;
      | 
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf returned exit code 2
make[1]: *** [debian/rules:40: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

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