[Debian-med-packaging] Bug#1143706: spades: FTBFS: /usr/include/c++/16/bits/stl_tree.h:1402:72: error: static assertion failed: comparison object must be invocable with arguments of key_type
Santiago Vila
sanvila at debian.org
Wed Aug 5 12:25:30 BST 2026
Package: src:spades
Version: 4.0.0+really3.15.5+dfsg-3
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202608/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:spades, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --sourcedirectory=assembler/src --buildsystem=cmake
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dh binary --sourcedirectory=assembler/src --buildsystem=cmake
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dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_POLICY_VERSION_MINIMUM=3.5
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ../assembler/src
CMake Warning (dev) in CMakeLists.txt:
No project() command is present. The top-level CMakeLists.txt file must
contain a literal, direct call to the project() command. Add a line of
code such as
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near the top of the file, but after cmake_minimum_required().
CMake is pretending there is a "project(Project)" command on the first
line.
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) in CMakeLists.txt:
cmake_minimum_required() should be called prior to this top-level project()
call. Please see the cmake-commands(7) manual for usage documentation of
both commands.
This warning is for project developers. Use -Wno-dev to suppress it.
-- The C compiler identification is GNU 16.1.0
-- The CXX compiler identification is GNU 16.1.0
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CMake Warning (dev) at cmake/deps.cmake:30 (find_package):
Policy CMP0144 is not set: find_package uses upper-case <PACKAGENAME>_ROOT
variables. Run "cmake --help-policy CMP0144" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
CMake variable BOOST_ROOT is set to:
/<<PKGBUILDDIR>>/assembler/src/../ext/include
For compatibility, find_package is ignoring the variable, but code in a
.cmake module might still use it.
Call Stack (most recent call first):
CMakeLists.txt:55 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
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Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:55 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /<<PKGBUILDDIR>>/assembler/ext/include (found version "1.63.0")
Making Release Configuration...
Building SPAdes from N/A, sha: N/A
CMake Deprecation Warning at /<<PKGBUILDDIR>>/assembler/ext/src/mimalloc/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Override standard malloc (MI_OVERRIDE=ON)
-- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON)
-- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON)
-- Use the C++ compiler to compile (MI_USE_CXX=ON)
--
-- Library base name: mimalloc-none
-- Build type : none
-- Compiler : /usr/bin/x86_64-linux-gnu-g++
-- Install directory: /usr/lib/mimalloc-1.6
-- Build targets : object
--
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-- Found FFI: /usr/lib/x86_64-linux-gnu/libffi.so
-- Could NOT find LibEdit (missing: LibEdit_INCLUDE_DIRS LibEdit_LIBRARIES)
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-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.15.3")
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CMake Deprecation Warning at /<<PKGBUILDDIR>>/assembler/ext/src/googletest/CMakeLists.txt:4 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at /<<PKGBUILDDIR>>/assembler/ext/src/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Warning (dev) at /<<PKGBUILDDIR>>/assembler/ext/src/googletest/googletest/cmake/internal_utils.cmake:247 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
/<<PKGBUILDDIR>>/assembler/ext/src/googletest/googletest/CMakeLists.txt:91 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /usr/bin/python3 (found version "3.14.6")
CMake Deprecation Warning at projects/mts/CMakeLists.txt:8 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Configuring done (4.8s)
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CMake Warning:
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CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
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cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" all debruijn_test include_test VERBOSE=1
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In file included from /usr/include/c++/16/map:64,
from /<<PKGBUILDDIR>>/assembler/ext/include/bamtools/api/SamReadGroupDictionary.h:15,
from /<<PKGBUILDDIR>>/assembler/ext/include/bamtools/api/SamHeader.h:15,
from /<<PKGBUILDDIR>>/assembler/ext/include/bamtools/api/BamReader.h:16,
from /<<PKGBUILDDIR>>/assembler/ext/include/bamtools/api/BamMultiReader.h:14,
from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp:11:
/usr/include/c++/16/bits/stl_tree.h: In instantiation of 'bool std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_key_compare(const _Key1&, const _Key2&) const [with _Key1 = BamTools::Internal::MergeItem; _Key2 = BamTools::Internal::MergeItem; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>]':
/usr/include/c++/16/bits/stl_tree.h:2842:24: required from [too-long-redacted] BamTools::Internal::MergeItem]'
2842 | __x = _M_key_compare(__k, _S_key(__x)) ? _S_left(__x) : _S_right(__x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_tree.h:2940:4: required from 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_equal(_Arg&&) [with _Arg = const BamTools::Internal::MergeItem&; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>, std::allocator<BamTools::Internal::MergeItem> >::iterator]'
2940 | = _M_get_insert_equal_pos(_KeyOfValue()(__v));
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_multiset.h:528:36: required from 'std::multiset<_Key, _Compare, _Alloc>::iterator std::multiset<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = BamTools::Internal::MergeItem; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>, std::allocator<BamTools::Internal::MergeItem> >::const_iterator; value_type = BamTools::Internal::MergeItem]'
528 | { return _M_t._M_insert_equal(__x); }
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:130:18: required from 'void BamTools::Internal::MultiMerger<Compare>::Add(BamTools::Internal::MergeItem) [with Compare = BamTools::Algorithms::Sort::ByName]'
130 | m_data.insert(item);
| ~~~~~~~~~~~~~^~~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:123:13: required from here
123 | inline void MultiMerger<Compare>::Add(MergeItem item) {
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_tree.h:1402:72: error: static assertion failed: comparison object must be invocable with arguments of key_type
1402 | __is_invocable<const _Compare&, const _Key&, const _Key&>::value,
| ^~~~~
• 'std::integral_constant<bool, false>::value' evaluates to false
/usr/include/c++/16/bits/stl_tree.h:1406:40: error: no match for call to '(const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>) (const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&)'
1406 | return _M_impl._M_key_compare(__k1, __k2);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.h:25,
from /<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp:14:
• there is 1 candidate
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:57:8:
57 | struct MergeItemSorter : public std::binary_function<MergeItem, MergeItem, bool> {
| ^~~~~~~~~~~~~~~
• candidate 1: 'bool BamTools::Internal::MergeItemSorter<Compare>::operator()(const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&) [with Compare = BamTools::Algorithms::Sort::ByName]' (near match)
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:64:14:
64 | bool operator()(const MergeItem& lhs, const MergeItem& rhs) {
| ^~~~~~~~
• passing 'const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>*' as 'this' argument discards qualifiers
/usr/include/c++/16/bits/stl_tree.h: In instantiation of 'bool std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_key_compare(const _Key1&, const _Key2&) const [with _Key1 = BamTools::Internal::MergeItem; _Key2 = BamTools::Internal::MergeItem; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>]':
/usr/include/c++/16/bits/stl_tree.h:2842:24: required from [too-long-redacted] BamTools::Internal::MergeItem]'
2842 | __x = _M_key_compare(__k, _S_key(__x)) ? _S_left(__x) : _S_right(__x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_tree.h:2940:4: required from 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_equal(_Arg&&) [with _Arg = const BamTools::Internal::MergeItem&; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>, std::allocator<BamTools::Internal::MergeItem> >::iterator]'
2940 | = _M_get_insert_equal_pos(_KeyOfValue()(__v));
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_multiset.h:528:36: required from 'std::multiset<_Key, _Compare, _Alloc>::iterator std::multiset<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = BamTools::Internal::MergeItem; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>, std::allocator<BamTools::Internal::MergeItem> >::const_iterator; value_type = BamTools::Internal::MergeItem]'
528 | { return _M_t._M_insert_equal(__x); }
| ~~~~~~~~~~~~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:130:18: required from 'void BamTools::Internal::MultiMerger<Compare>::Add(BamTools::Internal::MergeItem) [with Compare = BamTools::Algorithms::Sort::ByPosition]'
130 | m_data.insert(item);
| ~~~~~~~~~~~~~^~~~~~
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:123:13: required from here
123 | inline void MultiMerger<Compare>::Add(MergeItem item) {
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/16/bits/stl_tree.h:1402:72: error: static assertion failed: comparison object must be invocable with arguments of key_type
1402 | __is_invocable<const _Compare&, const _Key&, const _Key&>::value,
| ^~~~~
• 'std::integral_constant<bool, false>::value' evaluates to false
/usr/include/c++/16/bits/stl_tree.h:1406:40: error: no match for call to '(const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>) (const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&)'
1406 | return _M_impl._M_key_compare(__k1, __k2);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
• there is 1 candidate
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:57:8:
57 | struct MergeItemSorter : public std::binary_function<MergeItem, MergeItem, bool> {
| ^~~~~~~~~~~~~~~
• candidate 1: 'bool BamTools::Internal::MergeItemSorter<Compare>::operator()(const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&) [with Compare = BamTools::Algorithms::Sort::ByPosition]' (near match)
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api/internal/bam/BamMultiMerger_p.h:64:14:
64 | bool operator()(const MergeItem& lhs, const MergeItem& rhs) {
| ^~~~~~~~
• passing 'const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>*' as 'this' argument discards qualifiers
make[4]: *** [ext/bamtools/api/CMakeFiles/BamTools.dir/build.make:250: ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:1611: ext/bamtools/api/CMakeFiles/BamTools.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore & [too-long-redacted] nsusCore/Matrix/DenseMatrix.cpp
[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore & [too-long-redacted] susCore/Matrix/SparseMatrix.cpp
[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore & [too-long-redacted] ConsensusCore/Poa/PoaConfig.cpp
[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore & [too-long-redacted] sensusCore/Poa/PoaConsensus.cpp
[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore & [too-long-redacted] /ConsensusCore/Poa/PoaGraph.cpp
[ 4%] Linking CXX static library libConsensusCore.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1
/usr/bin/x86_64-linux-gnu-ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o
/usr/bin/x86_64-linux-gnu-ranlib libConsensusCore.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 4%] Built target ConsensusCore
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 -j2 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 failed with exit status 2
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