[Debian-med-packaging] Bug#1037815: pbseqlib: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:29:57 BST 2023
Package: src:pbseqlib
Version: 5.3.5+dfsg-4
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/pbseqlib_5.3.5+dfsg-4_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
[...]
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<short int>’:
../hdf/BufferedHDF2DArray.hpp:127:1: required from here
../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);
| ^~~~~~~~~~
../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,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<float>’:
../hdf/BufferedHDF2DArray.hpp:128:1: required from here
../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);
| ^~~~~~~~~~
../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,
| ^~~~~~~~~~
../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray<char>’:
../hdf/BufferedHDF2DArray.hpp:137:1: required from here
../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);
| ^~~~~~~~~~
../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,
| ^~~~~~~~~~
In file included from ../hdf/HDFBasReader.hpp:14:
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader<T_Sequence>::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’
../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader<T_Sequence>::InitializeCommon() [with T_Sequence = SMRTSequence]’
../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader<T_Sequence>::Initialize() [with T_Sequence = SMRTSequence]’
../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader<T_Sequence>::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string<char>]’
../alignment/files/ReaderAgglomerate.cpp:250:47: required from here
../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy]
33 | attribute = object.openAttribute(attributeName.c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf5/serial/H5Cpp.h:34,
from ../hdf/HDFData.hpp:6:
/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’
32 | Attribute(const Attribute &original);
| ^~~~~~~~~
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string<char>]’
../hdf/HDFAtom.hpp:38:9: required from here
../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy]
33 | attribute = object.openAttribute(attributeName.c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’
32 | Attribute(const Attribute &original);
| ^~~~~~~~~
../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom<T>::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom<T>::Initialize(HDFGroup&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>]’
../hdf/HDFAtom.hpp:38:9: required from here
../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy]
33 | attribute = object.openAttribute(attributeName.c_str());
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’
32 | Attribute(const Attribute &original);
| ^~~~~~~~~
[89/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.cpp
[90/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp
[91/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp
[92/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp
[93/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp
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:24: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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