Your message dated Sun, 13 Aug 2023 09:18:51 +0000
with message-id <e1qv7fl-00045u...@fasolo.debian.org>
and subject line Bug#1037662: fixed in flye 2.9.2+dfsg-2
has caused the Debian Bug report #1037662,
regarding flye: 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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--
1037662: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037662
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:flye
Version: 2.9.1+dfsg-1
Severity: normal
Tags: sid trixie
User: debian-...@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/flye_2.9.1+dfsg-1_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
[...]
16 | class Id
| ^~
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘size_t’ {aka ‘long unsigned int’} to ‘const
FastaRecord::Id&’
repeat_graph/../sequence/sequence_container.h:16:15: note: candidate:
‘constexpr FastaRecord::Id::Id(FastaRecord::Id&&)’
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘size_t’ {aka ‘long unsigned int’} to
‘FastaRecord::Id&&’
repeat_graph/graph_processing.cpp: In lambda function:
repeat_graph/graph_processing.cpp:334:62: error: no matching function for call
to ‘FastaRecord::Id::Id(size_t)’
334 | return FastaRecord::Id(nextEdgeId - 2);
| ^
repeat_graph/../sequence/sequence_container.h:19:17: note: candidate:
‘FastaRecord::Id::Id()’
19 | Id(): _id(std::numeric_limits<uint32_t>::max()) {}
| ^~
repeat_graph/../sequence/sequence_container.h:19:17: note: candidate expects
0 arguments, 1 provided
repeat_graph/../sequence/sequence_container.h:16:15: note: candidate:
‘constexpr FastaRecord::Id::Id(const FastaRecord::Id&)’
16 | class Id
| ^~
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘size_t’ {aka ‘long unsigned int’} to ‘const
FastaRecord::Id&’
repeat_graph/../sequence/sequence_container.h:16:15: note: candidate:
‘constexpr FastaRecord::Id::Id(FastaRecord::Id&&)’
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘size_t’ {aka ‘long unsigned int’} to
‘FastaRecord::Id&&’
repeat_graph/graph_processing.cpp:336:69: error: no matching function for call
to ‘FastaRecord::Id::Id(std::unordered_map<FastaRecord::Id, long unsigned
int>::mapped_type&)’
336 | return FastaRecord::Id(edgeIds[path.front()->edgeId]);
| ^
repeat_graph/../sequence/sequence_container.h:19:17: note: candidate:
‘FastaRecord::Id::Id()’
19 | Id(): _id(std::numeric_limits<uint32_t>::max()) {}
| ^~
repeat_graph/../sequence/sequence_container.h:19:17: note: candidate expects
0 arguments, 1 provided
repeat_graph/../sequence/sequence_container.h:16:15: note: candidate:
‘constexpr FastaRecord::Id::Id(const FastaRecord::Id&)’
16 | class Id
| ^~
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘std::unordered_map<FastaRecord::Id, long
unsigned int>::mapped_type’ {aka ‘long unsigned int’} to ‘const
FastaRecord::Id&’
repeat_graph/../sequence/sequence_container.h:16:15: note: candidate:
‘constexpr FastaRecord::Id::Id(FastaRecord::Id&&)’
repeat_graph/../sequence/sequence_container.h:16:15: note: no known
conversion for argument 1 from ‘std::unordered_map<FastaRecord::Id, long
unsigned int>::mapped_type’ {aka ‘long unsigned int’} to ‘FastaRecord::Id&&’
make[2]: *** [Makefile:40: repeat_graph/graph_processing.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [Makefile:33: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/setup.py", line 38, in run
subprocess.check_call(["make"])
File "/usr/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make']' returned non-zero exit status
2.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/setup.py", line 69, in <module>
setup(name='flye',
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 108, in
setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line
185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line
201, in run_commands
dist.run_commands()
File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line
969, in run_commands
self.run_command(cmd)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1213, in
run_command
super().run_command(command)
File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line
988, in run_command
cmd_obj.run()
File "/<<PKGBUILDDIR>>/setup.py", line 40, in run
sys.exit("Compilation error: ", e)
TypeError: exit expected at most 1 argument, got 2
E: pybuild pybuild:388: build: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py build
dh_auto_build: error: pybuild --build -i python{version} -p 3.11 returned exit
code 13
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: flye
Source-Version: 2.9.2+dfsg-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
flye, 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 1037...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated flye 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 13 Aug 2023 10:28:45 +0200
Source: flye
Architecture: source
Version: 2.9.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1037662
Changes:
flye (2.9.2+dfsg-2) unstable; urgency=medium
.
* gcc-13.patch: new: fix ftbfs with gcc-13. (Closes: #1037662)
* d/control: add myself to uploaders.
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Files:
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