GNU bug report logs - #39872
python-anndata fails to build

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: bug-guix <bug-guix <at> gnu.org>
Subject: python-anndata fails to build
Date: Mon, 02 Mar 2020 14:29:44 -0500

Build log extract:

--8<---------------cut here---------------start------------->8---
starting phase `check'
running "python setup.py" with command "test" and parameters ()
running test
running egg_info
writing anndata.egg-info/PKG-INFO
writing dependency_links to anndata.egg-info/dependency_links.txt
writing requirements to anndata.egg-info/requires.txt
writing top-level names to anndata.egg-info/top_level.txt
reading manifest file 'anndata.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'anndata.egg-info/SOURCES.txt'
running build_ext
anndata (unittest.loader._FailedTest) ... ERROR

======================================================================
ERROR: anndata (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: anndata
Traceback (most recent call last):
  File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
    package = self._get_module_from_name(name)
  File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/__init__.py", line 1, in <module>
    from .base import AnnData
  File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/base.py", line 21, in <module>
    from scipy.sparse.sputils import IndexMixin
ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py)


----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1
builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed with exit code 1
build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv failed
View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv.bz2'.
guix build: error: build of
`/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv'
failed
--8<---------------cut here---------------end--------------->8---

On master c1febbbf94ee794d7a97dbde12102634f2b13529.

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