--- Begin Message ---
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
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
find . -name "*.pyc" -delete
rm -rf /<<PKGBUILDDIR>>/debian/man_src/*.html
/<<PKGBUILDDIR>>/debian/man_src/*.?
rm -rf /<<PKGBUILDDIR>>/debian/man
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--sourcedirectory=assembler/src -O--buildsystem=cmake
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean -X.orig
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary
dh binary --sourcedirectory=assembler/src --buildsystem=cmake
dh_update_autotools_config -O--sourcedirectory=assembler/src
-O--buildsystem=cmake
dh_autoreconf -O--sourcedirectory=assembler/src -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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
project(ProjectName)
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
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "5.2")
-- Found OpenMP_CXX: -fopenmp (found version "5.2")
-- Found OpenMP: TRUE (found version "5.2")
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so
-- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found
-- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so
-- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found
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.
CMake Warning (dev) at cmake/deps.cmake:30 (find_package):
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
--
-- Looking for open
-- Looking for open - found
-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for signal.h
-- Looking for signal.h - found
-- Looking for sys/stat.h
-- Looking for sys/stat.h - found
-- Looking for cxxabi.h
-- Looking for cxxabi.h - not found
-- Looking for dlfcn.h
-- Looking for dlfcn.h - found
-- Looking for mach/mach.h
-- Looking for mach/mach.h - not found
-- Looking for link.h
-- Looking for link.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for sys/mman.h
-- Looking for sys/mman.h - found
-- Looking for fcntl.h
-- Looking for fcntl.h - found
-- Looking for malloc/malloc.h
-- Looking for malloc/malloc.h - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for sys/resource.h
-- Looking for sys/resource.h - found
-- Looking for backtrace
-- Looking for backtrace - found
-- backtrace facility detected in default set of libraries
-- Found Backtrace: /usr/include
-- Looking for futimens
-- Looking for futimens - found
-- Looking for futimes
-- Looking for futimes - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for getpagesize
-- Looking for getpagesize - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for mallinfo
-- Looking for mallinfo - found
-- Looking for mallctl
-- Looking for mallctl - not found
-- Looking for malloc_zone_statistics
-- Looking for malloc_zone_statistics - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Looking for pthread_getspecific in pthread
-- Looking for pthread_getspecific in pthread - found
-- Looking for pthread_rwlock_init in pthread
-- Looking for pthread_rwlock_init in pthread - found
-- Looking for pthread_mutex_lock in pthread
-- Looking for pthread_mutex_lock in pthread - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Performing Test HAVE_FFI_CALL
-- Performing Test HAVE_FFI_CALL - Success
-- Found FFI: /usr/lib/x86_64-linux-gnu/libffi.so
-- Could NOT find LibEdit (missing: LibEdit_INCLUDE_DIRS LibEdit_LIBRARIES)
-- Found zstd: /usr/lib/x86_64-linux-gnu/libzstd.so
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.15.3")
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.21.0")
-- Looking for include file endian.h
-- Looking for include file endian.h - found
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file strings.h
-- Looking for include file strings.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file sys/param.h
-- Looking for include file sys/param.h - found
-- Looking for include file sys/sysctl.h
-- Looking for include file sys/sysctl.h - not found
-- Looking for include file emmintrin.h
-- Looking for include file emmintrin.h - found
-- Looking for include file pmmintrin.h
-- Looking for include file pmmintrin.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Looking for chmod
-- Looking for chmod - found
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for fstat
-- Looking for fstat - found
-- Looking for getcwd
-- Looking for getcwd - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for mkstemp
-- Looking for mkstemp - found
-- Looking for popen
-- Looking for popen - found
-- Looking for putenv
-- Looking for putenv - found
-- Looking for stat
-- Looking for stat - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for sysctl
-- Looking for sysctl - not found
-- Looking for times
-- Looking for times - found
-- Looking for erfc
-- Looking for erfc - not found
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)
-- Generating done (0.2s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
FETCHCONTENT_FULLY_DISCONNECTED
PKGCONFIG_EXECUTABLE
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- all debruijn_test include_test
cd obj-x86_64-linux-gnu && make -j2 INSTALL="install
--strip-program=true" all debruijn_test include_test VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>>/assembler/src
-B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system
CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make
ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend
make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make
ext/bamtools/api/CMakeFiles/BamTools.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>>/assembler/src
/<<PKGBUILDDIR>>/assembler/ext/src/ConsensusCore
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake
"--color=" ConsensusCore
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>>/assembler/src
/<<PKGBUILDDIR>>/assembler/ext/src/bamtools/api
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake
"--color=" BamTools
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make
ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make
ext/bamtools/api/CMakeFiles/BamTools.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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[too-long-redacted] nsensusCore/AffineAlignment.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api &&
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[too-long-redacted] /src/ConsensusCore/Sequence.cpp
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ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/ext/bamtools/api &&
[too-long-redacted] s/api/SamSequenceDictionary.cpp
[ 3%] Building CXX object
ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o
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[too-long-redacted] ext/src/ConsensusCore/Utils.cpp
[ 3%] Building CXX object
ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o
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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
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[too-long-redacted] ternal/bam/BamMultiReader_p.cpp
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
--------------------------------------------------------------------------------
--- End Message ---
pgpqg8eINO8GN.pgp
