[Debian-med-packaging] Bug#956220: FTBFS: FileNotFoundError

[Frédéric Bonnard]

Package: src:q2-cutadapt
Version: 2019.10.0-1
Control: tags -1 ftbfs

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Dear maintainer,
trying to reproduce the ppc64el specific failure : https://buildd.debian.org/status/fetch.php?pkg=q2-cutadapt&arch=ppc64el&ver=2019.10.0-1&stamp=1582306016&raw=0

I actually found out that q2-cutadapt fails to build on ppc64el as well
as on amd64 and maybe more currently. Maybe something related with qiime ?

--
q2_cutadapt/tests/test_demux.py FFFFFFFFFFFFFFF..........                                                                         [ 73%]
q2_cutadapt/tests/test_trim.py FFFF.....                                                                                          [100%]

=============================================================== FAILURES ================================================================
___________________________________________________ TestDemuxSingle.test_all_matched ____________________________________________________

self = <q2_cutadapt.tests.test_demux.TestDemuxSingle testMethod=test_all_matched>

    def test_all_matched(self):
        metadata = CategoricalMetadataColumn(
            pd.Series(['AAAA', 'CCCC', 'GGGG'], name='Barcode',
                      index=pd.Index(['sample_a', 'sample_b', 'sample_c'],
                                     name='id')))

        with redirected_stdio(stderr=os.devnull):
            obs_demuxed_art, obs_untrimmed_art = \
>               self.demux_single_fn(self.muxed_sequences, metadata)

q2_cutadapt/tests/test_demux.py:82:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
<decorator-gen-125>:2: in demux_single
    ???
/usr/lib/python3/dist-packages/qiime2/sdk/action.py:215: in bound_callable
    provenance.add_input(name, artifact)
/usr/lib/python3/dist-packages/qiime2/core/archive/provenance.py:406: in add_input
    self.inputs[name] = self.add_ancestor(input)
/usr/lib/python3/dist-packages/qiime2/core/archive/provenance.py:157: in add_ancestor
    shutil.copytree(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

src = '/tmp/qiime2-archive-v4zvnm2n/c361bb75-7dcd-4a97-976e-629b57020e7c/provenance'
dst = '/tmp/qiime2-provenance-pnb_bn2t/artifacts/c361bb75-7dcd-4a97-976e-629b57020e7c', symlinks = False
ignore = <function ignore_patterns.<locals>._ignore_patterns at 0x7f76a7814310>, copy_function = <function copy2 at 0x7f76c55688b0>
ignore_dangling_symlinks = False, dirs_exist_ok = False

    def copytree(src, dst, symlinks=False, ignore=None, copy_function=copy2,
                 ignore_dangling_symlinks=False, dirs_exist_ok=False):
        """Recursively copy a directory tree and return the destination directory.

        dirs_exist_ok dictates whether to raise an exception in case dst or any
        missing parent directory already exists.

        If exception(s) occur, an Error is raised with a list of reasons.

        If the optional symlinks flag is true, symbolic links in the
        source tree result in symbolic links in the destination tree; if
        it is false, the contents of the files pointed to by symbolic
        links are copied. If the file pointed by the symlink doesn't
        exist, an exception will be added in the list of errors raised in
        an Error exception at the end of the copy process.

        You can set the optional ignore_dangling_symlinks flag to true if you
        want to silence this exception. Notice that this has no effect on
        platforms that don't support os.symlink.

        The optional ignore argument is a callable. If given, it
        is called with the `src` parameter, which is the directory
        being visited by copytree(), and `names` which is the list of
        `src` contents, as returned by os.listdir():

            callable(src, names) -> ignored_names

        Since copytree() is called recursively, the callable will be
        called once for each directory that is copied. It returns a
        list of names relative to the `src` directory that should
        not be copied.

        The optional copy_function argument is a callable that will be used
        to copy each file. It will be called with the source path and the
        destination path as arguments. By default, copy2() is used, but any
        function that supports the same signature (like copy()) can be used.

        """
        sys.audit("shutil.copytree", src, dst)
>       with os.scandir(src) as itr:
E       FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2-archive-v4zvnm2n/c361bb75-7dcd-4a97-976e-629b57020e7c/provenance'

/usr/lib/python3.8/shutil.py:552: FileNotFoundError
--

Regards,


F.
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