From mboxrd@z Thu Jan 1 00:00:00 1970 From: Maxim Cournoyer Subject: bug#39872: python-anndata fails to build Date: Mon, 02 Mar 2020 14:29:44 -0500 Message-ID: <878ski5zdj.fsf@gmail.com> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:56531) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j8qlP-0000W8-ID for bug-guix@gnu.org; Mon, 02 Mar 2020 14:30:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j8qlO-00064t-F1 for bug-guix@gnu.org; Mon, 02 Mar 2020 14:30:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:60638) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j8qlO-00063z-Au for bug-guix@gnu.org; Mon, 02 Mar 2020 14:30:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1j8qlO-000611-4I for bug-guix@gnu.org; Mon, 02 Mar 2020 14:30:02 -0500 Sender: "Debbugs-submit" Resent-Message-ID: Received: from eggs.gnu.org ([2001:470:142:3::10]:56464) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j8qlB-0000ES-Ah for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j8ql9-0005y9-US for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:49 -0500 Received: from mail-qk1-x732.google.com ([2607:f8b0:4864:20::732]:44151) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j8ql9-0005xq-OH for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:47 -0500 Received: by mail-qk1-x732.google.com with SMTP id f198so818725qke.11 for ; Mon, 02 Mar 2020 11:29:47 -0800 (PST) Received: from raisin ([2607:fad8:4:6:235e:8579:8464:aacc]) by smtp.gmail.com with ESMTPSA id v82sm10641968qka.51.2020.03.02.11.29.45 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 02 Mar 2020 11:29:45 -0800 (PST) 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: 39872@debbugs.gnu.org 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.