Re: q2-types=2019.10.0: FTBFS: build dependencies conflict
Hi Liubov,
On Sun, Dec 15, 2019 at 03:34:13PM +0100, Liubov Chuprikova wrote:
> Hi Andreas,
>
> I was updating q2-types and had faced the following error:
>
> -
> conflict:
> pkg1:
> package: python3-pandas
> version: 0.25.3+dfsg-4
> architecture: all
> unsat-conflict: python3-skbio:amd64 (< 0.5.5-2.1)
> pkg2:
> package: python3-skbio
> version: 0.5.5-2
> architecture: amd64
> depchain1:
> -
> ...
> E: Package build dependencies not satisfied; skipping
> zsh: exit 3 sbuild -d sid --extra-package=../qiime_2019.10.0-1_all.deb
>
> So, python3-skbio breaks python3-pandas in unstable [1]. I saw that you've
> started updating it to 0.5.5-3. Is there something that hampers its release
> at the moment?
There are build time test suite errors:
...
AssertionError:.
Arrays are not almost equal to 7 decimals
x and y nan location mismatch:
x: array([[-2.5170346e-02, -3.8742000e-02, 3.7030794e-02, -1.8248587e-02,
-1.2974103e-03, 8.1410679e-04, -1.7370121e-02, 3.6121106e-02,
nan],...
y: array([[-2.5170346e-02, -3.8742000e-02, 3.7030794e-02, -1.8248587e-02,
-1.2974103e-03, 8.1410679e-04, -1.7370121e-02, 3.6121106e-02,
0.0000000e+00],...
======================================================================
FAIL: test__identify_sample_groups_not_strict (skbio.stats.tests.test_power.PowerAnalysisTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build/skbio/stats/tests/test_power.py", line 496, in test__identify_sample_groups_not_strict
npt.assert_array_equal(known_pairs[k][i], test_pairs[k][i])
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 917, in assert_array_equal
assert_array_compare(operator.__eq__, x, y, err_msg=err_msg,
File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 841, in assert_array_compare
raise AssertionError(msg)
AssertionError:.
Arrays are not equal
Mismatch: 100%
x: array(['MM', 'WM'], dtype=object)
y: array(['WM', 'MM'], dtype=object)
----------------------------------------------------------------------
Ran 2340 tests in 68.250s
FAILED (SKIP=30, errors=2, failures=2)
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /build/python-skbio-0.5.5/.pybuild/cpython3_3.8_skbio/build; python3.8 -m nose -v.
which are discussed with upstream here:
https://github.com/biocore/scikit-bio/issues/1681
https://github.com/biocore/scikit-bio/issues/1678
Any help is welcome.
Kind regards
Andreas.
> [1]
> https://salsa.debian.org/science-team/pandas/commit/387037efcb9744258e20965548ebe88823f11fea
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