From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: bug#39872: python-anndata fails to build Date: Wed, 04 Mar 2020 14:27:03 +0100 Message-ID: <140f49bf93cd1d27a8111b3ab588177fc379af99.camel@gnu.org> References: <878ski5zdj.fsf@gmail.com> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-YPSo1wMfUwcY01Bn/HzX" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:42780) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j9U4C-00062I-7p for bug-guix@gnu.org; Wed, 04 Mar 2020 08:28:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j9U4A-0005pN-BT for bug-guix@gnu.org; Wed, 04 Mar 2020 08:28:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34530) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j9U4A-0005p3-7M for bug-guix@gnu.org; Wed, 04 Mar 2020 08:28:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1j9U4A-0007Pb-3t for bug-guix@gnu.org; Wed, 04 Mar 2020 08:28:02 -0500 Sender: "Debbugs-submit" Resent-Message-ID: In-Reply-To: <878ski5zdj.fsf@gmail.com> List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+gcggb-bug-guix=m.gmane-mx.org@gnu.org Sender: "bug-Guix" To: Maxim Cournoyer , 39872@debbugs.gnu.org --=-YPSo1wMfUwcY01Bn/HzX Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote: > 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 > 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 > 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: > error: Test failed: > 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. I sent an e-mail from another address that doesn't seem to have made the guix- patches mailing list. The attached patches updates the version of python- anndata, and fixes the build. Note that for python-zarr I disabled the tests because the majority of the tests need external packages. We could add all dependencies to make the test suite work, but that requires a significant amount of work (for example, the Azure SDK for Python is one of the external dependencies). Is it OK to move forward with the disabled test suite for python-zarr? 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