[Debian-med-packaging] Bug#1037662: flye: ftbfs with GCC-13

[Matthias Klose]

Package: src:flye
Version: 2.9.1+dfsg-1
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/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