[Debian-med-packaging] Bug#1015668: spades: ftbfs with LTO (link time optimization) enabled
Matthias Klose
doko at debian.org
Tue Jul 19 18:01:02 BST 2022
Package: src:spades
Version: 3.15.4+dfsg-2
Severity: minor
Tags: sid bookworm
User: debian-gcc at lists.debian.org
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/spades_3.15.4+dfsg-2_unstable_dpkglto.log
The last lines of the build log are at the end of this report.
[...]
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so
[ 91%] Linking CXX executable ../../bin/spades-read-filter
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector<long unsigned int>&, std::vector<std::vector<long unsigned int> >&)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
357 | for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) << (unsigned)getQual(kms, j) << " "; std::cout << "\n";
| ^~~
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:357:101: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
357 | for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) << (unsigned)getQual(kms, j) << " "; std::cout << "\n";
| ^~~
[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/hammer -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_data.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-kmer-estimating
[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/hammer -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/hammer/config_struct_hammer.cpp
[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/hammer -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_corrector.cpp
[ 91%] Linking CXX executable ../../bin/spades-core
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm
[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/corrector -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/corrector/config_struct.cpp
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const string&, const string&, size_t)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion]
72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1;
| ~~~~~~~~~~^~~~~~~~~~~
[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/corrector -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/corrector/main.cpp
In file included from /<<PKGBUILDDIR>>/assembler/src/projects/hammer/globals.hpp:11,
from /<<PKGBUILDDIR>>/assembler/src/projects/hammer/hammer_tools.hpp:19,
from /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:11:
In member function 'NibbleString<21u, 6u, unsigned long>::set(unsigned long, unsigned char)',
inlined from 'NibbleString<21u, 6u, unsigned long>::NibbleString(unsigned char const*)' at /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:62:16,
inlined from 'KMerStat::KMerStat(unsigned int, float, unsigned char const*)' at /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:121:96,
inlined from 'KMerClustering::SubClusterSingle(std::vector<unsigned long, std::allocator<unsigned long> > const&, std::vector<std::vector<unsigned long, std::allocator<unsigned long> >, std::allocator<std::vector<unsigned long, std::allocator<unsigned long> > > >&)' at /<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:433:81:
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_stat.hpp:69:40: warning: 'MEM <const long unsigned int[2]> [(value_type &)&kms + 8][0]' may be used uninitialized [-Wmaybe-uninitialized]
69 | storage_[idx] = (storage_[idx] & ~(MaxValue << offset)) | ((value & MaxValue) << offset);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'KMerClustering::SubClusterSingle(std::vector<unsigned long, std::allocator<unsigned long> > const&, std::vector<std::vector<unsigned long, std::allocator<unsigned long> >, std::allocator<std::vector<unsigned long, std::allocator<unsigned long> > > >&)':
/<<PKGBUILDDIR>>/assembler/src/projects/hammer/kmer_cluster.cpp:433:22: note: 'kms' declared here
433 | KMerStat kms(0 /* cnt */, 1.0 /* total quality */, NULL /*quality */);
| ^~~
[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/assembler/src/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/include -I/<<PKGBUILDDIR>>/assembler/src -I/<<PKGBUILDDIR>>/assembler/src/common -I/<<PKGBUILDDIR>>/assembler/src/projects/hammer -I/<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/include -isystem /<<PKGBUILDDIR>>/assembler/src/../ext/include -isystem /<<PKGBUILDDIR>>/assembler/ext/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /<<PKGBUILDDIR>>/assembler/src/projects/hammer/expander.cpp
[ 91%] Linking CXX executable ../../bin/spades-corrector-core
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-kmercount
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-read-filter
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 91%] Built target spades-corrector-core
[ 93%] Linking CXX executable ../../bin/spades-hammer
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target spades-hammer
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target spades-core
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:29: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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