Groups | Search | Server Info | Keyboard shortcuts | Login | Register [http] [https] [nntp] [nntps]

Groups > linux.debian.maint.python > #14988 > unrolled thread

Bug#1032120: Tiledb-py fails to build (Was: tiledb: uses atomic operations, but is not linked to libatomic)

Back to article view | Back to linux.debian.maint.python

This discussion starts older than the indexed window; earlier articles aren't shown. The article labeled Started by below is the oldest one visible, not the original post.

Contents

  Bug#1032120: Tiledb-py fails to build (Was: tiledb: uses atomic operations, but is not linked to libatomic) Adam Cecile <acecile@le-vert.net> - 2023-03-25 15:20 +0100

#14988 — Bug#1032120: Tiledb-py fails to build (Was: tiledb: uses atomic operations, but is not linked to libatomic)

[Multipart message — attachments visible in raw view] — view raw

Hello,

It seems unittests are running against very new pandas version that wants pyarrow (but it does not seems to be available in the archive).
Can you check while self.use_arrow evaluate to True ? That's mostly the root cause of the failure.
I'll try to have a look when I'll be in front of my computer.

Regards, Adam.

On March 25, 2023 2:55:39 PM GMT+01:00, Andreas Tille <andreas@an3as.eu> wrote:
>Hi,
>
>as you can read in the bug log, there was an upload of a new version of
>tiledb a couple of hours before it has migrated to testing.  Thus the
>package remains affected by a testing removal (together with its two
>reverse dependencies tiledb and genomicsdb).  To follow the freeze
>policy I reverted the version bump and NMUed tiledb
>2.15.0really2.14.1-0.1 to experimental (since the maintainer did not
>responded).
>
>As we can see tiledb-py does not build against tiledb 2.15.0[1]
>
>I've now forced (Build-)Depends to
>   tibtiledb-dev (>= 2.15.0really2.14.1~)
>but it seems Salsa CI autopkgtest does not respect the setting
>
>variables:
>  # Build against tiledb in experimental
>  RELEASE: 'experimental'
>
>and thus the autopkgtest log does not reproduce the error I've got
>in my local build:
>
>...
>
>=================================== FAILURES ===================================
>_______________ TestNumpyToArray.test_from_numpy_empty_str[1-0] ________________
>
>self = <tests.test_libtiledb.TestNumpyToArray object at 0x7fe177722710>
>empty_str = '', num_strs = 1
>
>    @pytest.mark.parametrize("empty_str", ["", b""])
>    @pytest.mark.parametrize("num_strs", [1, 1000])
>    def test_from_numpy_empty_str(self, empty_str, num_strs):
>        uri = self.path("test_from_numpy_empty_str")
>        np_array = np.asarray([empty_str] * num_strs, dtype="O")
>        tiledb.from_numpy(uri, np_array)
>....
>        with tiledb.open(uri, "r") as A:
>            assert_array_equal(A[:], np_array)
>            if has_pandas():
>>               assert_array_equal(A.query(use_arrow=True).df[:][""], np_array)
>
>tests/test_libtiledb.py:3356:
>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
>/usr/lib/python3/dist-packages/tiledb/multirange_indexing.py:192: in __getitem__
>    return self if self.return_incomplete else self._run_query()
>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
>
>self = <tiledb.multirange_indexing.DataFrameIndexer object at 0x7fe1779ef150>
>
>    def _run_query(self) -> Union[DataFrame, Table]:
>        if self.pyquery is not None:
>            self.pyquery.submit()
>....
>        if self.pyquery is None:
>            df = DataFrame(self._empty_results)
>        elif self.use_arrow:
>            with timing("buffer_conversion_time"):
>>               table = self.pyquery._buffers_to_pa_table()
>E               ModuleNotFoundError: No module named 'pyarrow'
>
>/usr/lib/python3/dist-packages/tiledb/multirange_indexing.py:329: ModuleNotFoundError
>_______________ TestNumpyToArray.test_from_numpy_empty_str[1-1] ________________
>
>self = <tests.test_libtiledb.TestNumpyToArray object at 0x7fe177722490>
>empty_str = b'', num_strs = 1
>
>    @pytest.mark.parametrize("empty_str", ["", b""])
>    @pytest.mark.parametrize("num_strs", [1, 1000])
>    def test_from_numpy_empty_str(self, empty_str, num_strs):
>        uri = self.path("test_from_numpy_empty_str")
>        np_array = np.asarray([empty_str] * num_strs, dtype="O")
>        tiledb.from_numpy(uri, np_array)
>....
>        with tiledb.open(uri, "r") as A:
>            assert_array_equal(A[:], np_array)
>            if has_pandas():
>>               assert_array_equal(A.query(use_arrow=True).df[:][""], np_array)
>
>tests/test_libtiledb.py:3356:
>/usr/lib/python3/dist-packages/tiledb/multirange_indexing.py:192: in __getitem__
>    return self if self.return_incomplete else self._run_query()
>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
>
>self = <tiledb.multirange_indexing.DataFrameIndexer object at 0x7fe177a16ed0>
>
>variables:
>  # Build against tiledb in experimental
>  RELEASE: 'experimental'
>    def _run_query(self) -> Union[DataFrame, Table]:
>        if self.pyquery is not None:
>            self.pyquery.submit()
>....
>        if self.pyquery is None:
>            df = DataFrame(self._empty_results)
>        elif self.use_arrow:
>            with timing("buffer_conversion_time"):
>>               table = self.pyquery._buffers_to_pa_table()
>E               ModuleNotFoundError: No module named 'pyarrow'
>
>/usr/lib/python3/dist-packages/tiledb/multirange_indexing.py:329: ModuleNotFoundError
>______________ TestNumpyToArray.test_from_numpy_empty_str[1000-0] ______________
>
>self = <tests.test_libtiledb.TestNumpyToArray object at 0x7fe177722510>
>empty_str = '', num_strs = 1000
>
>    @pytest.mark.parametrize("empty_str", ["", b""])
>    @pytest.mark.parametrize("num_strs", [1, 1000])
>    def test_from_numpy_empty_str(self, empty_str, num_strs):
>        uri = self.path("test_from_numpy_empty_str")
>        np_array = np.asarray([empty_str] * num
>
>=================================== FAILURES ===================================
>_______________ TestNumpyToArray.test_from_numpy_empty_str[1-0] ________________
>
>self = <tests.test_libtiledb.TestNumpyToArray object at 0x7fe177722710>
>empty_str = '', num_strs = 1
>
>    @pytest.mark.parametrize("empty_str", ["", b""])
>    @pytest.mark.parametrize("num_strs", [1, 1000])
>    def test_from_numpy_empty_str(self, empty_str, num_strs):
>        uri = self.path("test_from_numpy_empty_str")
>        np_array = np.asarray([empty_str] * num_strs, dtype="O")
>        tiledb.from_numpy(uri, np_array)
>....
>        with tiledb.open(uri, "r") as A:
>            assert_array_equal(A[:], np_array)
>            if has_pandas():
>>               assert_array_equal(A.query(use_arrow=True).df[:][""], np_array)
>
>tests/test_libtiledb.py:3356:
>...
>
>
>I admit I'm a bit astonished since when tiledb 2.14.1 was available
>in unstable the autopkgtest used to work.  Any idea how to fix this
>issue would be welcome.
>
>Kind regards,
>   Andreas
>
>[1] https://salsa.debian.org/python-team/packages/tiledb-py/-/pipelines/514328
>
>-- 
>http://fam-tille.de

[toc] | [standalone]

Back to top | Article view | linux.debian.maint.python

csiph-web