[Debian-med-packaging] Bug#1012919: fast5: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:08:30 BST 2022
Package: src:fast5
Version: 0.6.5-6
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12
[This bug is targeted to the upcoming bookworm release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/fast5_0.6.5-6_unstable_gcc12.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2298:70: required from here
/usr/include/c++/12/type_traits:1135:52: error: static assertion failed: template argument must be a complete class or an unbounded array
1135 | static_assert(std::__is_complete_or_unbounded(__type_identity<_Tp>{}),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/type_traits:1135:52: note: ‘std::__is_complete_or_unbounded<__type_identity<array<char, 1> > >((std::__type_identity<std::array<char, 1> >(), std::__type_identity<std::array<char, 1> >()))’ evaluates to false
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In instantiation of ‘_ForwardIterator std::__uninitialized_default_n(_ForwardIterator, _Size) [with _ForwardIterator = array<char, 1>*; _Size = long unsigned int]’:
/usr/include/c++/12/bits/stl_uninitialized.h:766:44: required from ‘_ForwardIterator std::__uninitialized_default_n_a(_ForwardIterator, _Size, allocator<_Tp>&) [with _ForwardIterator = array<char, 1>*; _Size = long unsigned int; _Tp = array<char, 1>]’
/usr/include/c++/12/bits/stl_vector.h:1713:36: required from ‘void std::vector<_Tp, _Alloc>::_M_default_initialize(size_type) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; size_type = long unsigned int]’
/usr/include/c++/12/bits/stl_vector.h:553:9: required from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; size_type = long unsigned int; allocator_type = std::allocator<std::array<char, 1> >]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2298:70: required from here
/usr/include/c++/12/bits/stl_uninitialized.h:699:42: error: invalid use of incomplete type ‘std::iterator_traits<std::array<char, 1>*>::value_type’ {aka ‘struct std::array<char, 1>’}
699 | return __uninitialized_default_n_1<__is_trivial(_ValueType)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/tuple:1595:45: note: declaration of ‘std::iterator_traits<std::array<char, 1>*>::value_type’ {aka ‘struct std::array<char, 1>’}
1595 | template<typename _Tp, size_t _Nm> struct array;
| ^~~~~
/usr/include/c++/12/bits/stl_vector.h: In instantiation of ‘std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; size_type = long unsigned int]’:
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:1807:29: required from ‘void hdf5_tools::detail::Writer<std::vector<_Tp> >::operator()(hid_t, const std::string&, bool, const std::vector<_Tp>&, Args&& ...) const [with Args = {}; In_Data_Type = std::array<char, 1>; hid_t = long int; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2038:42: required from ‘void hdf5_tools::File::write(const std::string&, bool, const In_Data_Storage&, Args&& ...) const [with In_Data_Storage = std::vector<std::array<char, 1> >; Args = {}; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2062:14: required from ‘void hdf5_tools::File::write_attribute(const std::string&, const In_Data_Storage&, Args&& ...) const [with In_Data_Storage = std::vector<std::array<char, 1> >; Args = {}; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2303:42: required from here
/usr/include/c++/12/bits/stl_vector.h:988:50: error: invalid use of incomplete type ‘struct std::array<char, 1>’
988 | { return size_type(this->_M_impl._M_finish - this->_M_impl._M_start); }
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/tuple:1595:45: note: declaration of ‘struct std::array<char, 1>’
1595 | template<typename _Tp, size_t _Nm> struct array;
| ^~~~~
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp: In instantiation of ‘void hdf5_tools::detail::Writer_Helper<2, In_Data_Type>::operator()(hid_t, const std::string&, bool, hid_t, size_t, const In_Data_Type*, hid_t) const [with In_Data_Type = std::array<char, 1>; hid_t = long int; std::string = std::__cxx11::basic_string<char>; size_t = long unsigned int]’:
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:1811:75: required from ‘void hdf5_tools::detail::Writer<std::vector<_Tp> >::operator()(hid_t, const std::string&, bool, const std::vector<_Tp>&, Args&& ...) const [with Args = {}; In_Data_Type = std::array<char, 1>; hid_t = long int; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2038:42: required from ‘void hdf5_tools::File::write(const std::string&, bool, const In_Data_Storage&, Args&& ...) const [with In_Data_Storage = std::vector<std::array<char, 1> >; Args = {}; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2062:14: required from ‘void hdf5_tools::File::write_attribute(const std::string&, const In_Data_Storage&, Args&& ...) const [with In_Data_Storage = std::vector<std::array<char, 1> >; Args = {}; std::string = std::__cxx11::basic_string<char>]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2303:42: required from here
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:1559:55: error: invalid application of ‘sizeof’ to incomplete type ‘std::array<char, 1>’
1559 | mem_dtype_id_holder = Util::make_str_type(sizeof(In_Data_Type));
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:1578:38: error: invalid use of incomplete type ‘struct std::array<char, 1>’
1578 | charptr_buff[i] = &in[i][0];
| ~~^
/usr/include/c++/12/tuple:1595:45: note: declaration of ‘struct std::array<char, 1>’
1595 | template<typename _Tp, size_t _Nm> struct array;
| ^~~~~
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:1578:41: error: no match for ‘operator[]’ (operand types are ‘const std::array<char, 1>’ and ‘int’)
1578 | charptr_buff[i] = &in[i][0];
| ~~~~~^
In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/string:41:
/usr/include/c++/12/bits/new_allocator.h: In instantiation of ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = std::array<char, 1>; size_type = long unsigned int]’:
/usr/include/c++/12/bits/alloc_traits.h:464:28: required from ‘static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = std::array<char, 1>; pointer = std::array<char, 1>*; allocator_type = std::allocator<std::array<char, 1> >; size_type = long unsigned int]’
/usr/include/c++/12/bits/stl_vector.h:378:33: required from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; pointer = std::array<char, 1>*; std::size_t = long unsigned int]’
/usr/include/c++/12/bits/stl_vector.h:395:33: required from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; std::size_t = long unsigned int]’
/usr/include/c++/12/bits/stl_vector.h:332:9: required from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; std::size_t = long unsigned int; allocator_type = std::allocator<std::array<char, 1> >]’
/usr/include/c++/12/bits/stl_vector.h:552:47: required from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = std::array<char, 1>; _Alloc = std::allocator<std::array<char, 1> >; size_type = long unsigned int; allocator_type = std::allocator<std::array<char, 1> >]’
/<<PKGBUILDDIR>>/src/../include/fast5/hdf5_tools.hpp:2298:70: required from here
/usr/include/c++/12/bits/new_allocator.h:117:24: error: invalid application of ‘sizeof’ to incomplete type ‘std::array<char, 1>’
117 | static_assert(sizeof(_Tp) != 0, "cannot allocate incomplete types");
| ^~~~~~~~~~~
/usr/include/c++/12/bits/new_allocator.h:124:42: error: invalid application of ‘sizeof’ to incomplete type ‘std::array<char, 1>’
124 | if (__n > (std::size_t(-1) / sizeof(_Tp)))
| ^~~~~~~~~~~
/usr/include/c++/12/bits/new_allocator.h:137:62: error: invalid application of ‘sizeof’ to incomplete type ‘std::array<char, 1>’
137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^~~~~~~~~~~
make[2]: *** [Makefile:58: hdf5-mod] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [debian/rules:23: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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