[Debian-med-packaging] Bug#1119732: cyvcf2: FTBFS: cyvcf2/cyvcf2.pyx:400:122: Unicode objects only support coercion to Py_UNICODE*.

[Santiago Vila]

Package: src:cyvcf2
Version: 0.31.1-2
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202510/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:cyvcf2, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
	pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean 

Error compiling Cython file:
------------------------------------------------------------
...
        number: str
             valid VCF number
        description: str
             description of added line.
        """
        ret = bcf_hdr_append(self.hdr, "##INFO=<ID={id},Number={number},Type={type},Description=\"{description}\">".format(id=id, type=type, number=number, description=description))
                                                                                                                          ^
------------------------------------------------------------

cyvcf2/cyvcf2.pyx:400:122: Unicode objects only support coercion to Py_UNICODE*.
warning: cyvcf2/cyvcf2.pyx:1377:36: Assigning to 'char *' from 'const char *' discards const qualifier
warning: cyvcf2/cyvcf2.pyx:2079:12: Assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards const qualifier
warning: cyvcf2/cyvcf2.pyx:2278:29: Assigning to 'char *' from 'const char *' discards const qualifier
warning: cyvcf2/cyvcf2.pyx:2350:15: Assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards const qualifier
Compiling cyvcf2/cyvcf2.pyx because it changed.
[1/1] Cythonizing cyvcf2/cyvcf2.pyx
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/setup.py", line 270, in <module>
    extensions = cythonize(extensions, compiler_directives=compiler_directives)
  File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1150, in cythonize
    cythonize_one(*args)
    ~~~~~~~~~~~~~^^^^^^^
  File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1294, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: cyvcf2/cyvcf2.pyx
E: pybuild pybuild:389: clean: plugin distutils failed with: exit code=1: python3.13 setup.py clean 
dh_auto_clean: error: pybuild --clean -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:17: clean] Error 25
dpkg-buildpackage: error: debian/rules clean subprocess returned exit status 2
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