[Debian-med-packaging] Bug#1037595: blasr: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:22:06 BST 2023
Package: src:blasr
Version: 5.3.5+dfsg-6
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie 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-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/blasr_5.3.5+dfsg-6_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html
[...]
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
/usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=]
44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
/usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=]
44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
/usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=]
44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<std::__cxx11::basic_string<char> >’:
/usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray<std::__cxx11::basic_string<char> >’
/usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here
/usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=]
44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
| ^~~~~~~~~~
In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156:
/usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
70 | int BufferedHDF2DArray<T>::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength,
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7,
from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8,
from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3:
/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’:
/usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
/usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator<blasr::CompSeqAlignment>; value_type = blasr::CompSeqAlignment]’
/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here
/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy]
209 | class CompSeqAlignment : public Alignment
| ^~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’
103 | Alignment &operator=(const Alignment &rhs);
| ^~~~~~~~
/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy]
58 | class Alignment : public AlignmentStats
| ^~~~~~~~~
In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8:
/usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’
19 | AlignmentStats &operator=(const AlignmentStats &rhs);
| ^~~~~~~~
/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here
209 | class CompSeqAlignment : public Alignment
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33,
from /usr/include/c++/13/bits/allocator.h:46,
from /usr/include/c++/13/vector:63,
from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4,
from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1:
/usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here
187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -v returned exit code 1
make: *** [debian/rules:33: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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