Your message dated Tue, 20 Jun 2023 21:07:20 +0000
with message-id <[email protected]>
and subject line Bug#1037815: fixed in pbseqlib 5.3.5+dfsg-5
has caused the Debian Bug report #1037815,
regarding pbseqlib: ftbfs with GCC-13
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1037815: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037815
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:pbseqlib
Version: 5.3.5+dfsg-4
Severity: normal
Tags: sid trixie
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: pbseqlib
Source-Version: 5.3.5+dfsg-5
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pbseqlib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated pbseqlib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 20 Jun 2023 23:44:20 +0530
Source: pbseqlib
Architecture: source
Version: 5.3.5+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1037815
Changes:
pbseqlib (5.3.5+dfsg-5) unstable; urgency=medium
.
* Team upload.
* Annotate gtest with <!nocheck>
* Add patch to fix FTBFS with gcc-13 (Closes: #1037815)
* Disable salsa-CI for i386 due to pbbam not being available on 32 bit archs
* Mark libpbihdf-dev as MA: same
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pbseqlib_5.3.5+dfsg-5.debian.tar.xz
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Files:
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pbseqlib_5.3.5+dfsg-5.dsc
eb47630d4a22497b3e4f8b87641f74af 9904 science optional
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--- End Message ---
