Path: csiph.com!news.mixmin.net!aioe.org!bofh.it!news.nic.it!robomod From: Gordon Ball Newsgroups: linux.debian.maint.python Subject: Re: Bug#878498: snakemake FTBFS with Python 3.6 as default Date: Thu, 07 Dec 2017 23:00:01 +0100 Message-ID: References: X-Mailbox-Line: From debian-python-request@lists.debian.org Thu Dec 7 21:57:51 2017 Old-Return-Path: X-Amavis-Spam-Status: No, score=-7.2 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, FOURLA=0.1, LDO_WHITELIST=-5, MEDS2=2, RCVD_IN_DNSWL_MED=-2.3] autolearn=ham autolearn_force=no X-Policyd-Weight: NOT_IN_SBL_XBL_SPAMHAUS=-1.5 NOT_IN_BL_NJABL=-1.5 CL_IP_EQ_FROM_MX=-3.1; rate: -6.1 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Thunderbird/52.5.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Language: en-AU Content-Transfer-Encoding: 8bit X-Mailing-List: archive/latest/15384 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/80b67c5a-df81-43d7-042b-27f2be69175e@chronitis.net Approved: robomod@news.nic.it Lines: 87 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Date: Thu, 7 Dec 2017 22:57:31 +0100 X-Original-Message-ID: <80b67c5a-df81-43d7-042b-27f2be69175e@chronitis.net> X-Original-References: <150794840271.14303.2296024578220978868.reportbug@localhost> <20171206211445.w5ouhoxcvwpgi23p@an3as.eu> Xref: csiph.com linux.debian.maint.python:9993 On 06/12/17 22:14, Andreas Tille wrote: > control: tags -1 help > > Hi, > > I've upgraded snakemake in Git to latest upstream but its featuring the > same issue. I'm pretty sure you Python people know a simple answer for > this issue. To first order, the issue with the `export PATH` line can be fixed by changing it to `export PATH:=$(CURDIR)/bin:$(PATH)` (since the `build` step generates `bin/snakemake` and the PYBUILD_BEFORE_TEST just copies it into the build directory). However, having done this still about half of the tests fail, with various errors. Some are related to build dependencies (google-cloud-sdk, boto3) but others are less obvious. Quite a few refer to a stacktrace within scheduler.py; if this is trying to run a multiprocess scheduler as part of a build-time test this sounds likely to be an ongoing source of pain. This also occurs if you make the temporary (but guaranteed to fail in future) fix of just changing `pythonX.Y_3.5` to `3.6`, so I think there are deeper issues with how the test suite needs to be run, which probably need input from someone familiar with the package in question. > > Any help would be welcome > > Andreas. > > On Sat, Oct 14, 2017 at 05:33:22AM +0300, Adrian Bunk wrote: >> Source: snakemake >> Version: 3.10.0-1 >> Severity: serious >> Tags: buster sid >> >> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html >> >> ... >> ====================================================================== >> ERROR: Failure: Exception (snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).) >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest >> raise self.exc_val.with_traceback(self.tb) >> File "/usr/lib/python3/dist-packages/nose/loader.py", line 418, in loadTestsFromName >> addr.filename, addr.module) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath >> return self.importFromDir(dir_path, fqname) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir >> mod = load_module(part_fqname, fh, filename, desc) >> File "/usr/lib/python3.6/imp.py", line 235, in load_module >> return load_source(name, filename, file) >> File "/usr/lib/python3.6/imp.py", line 172, in load_source >> module = _load(spec) >> File "", line 684, in _load >> File "", line 665, in _load_unlocked >> File "", line 678, in exec_module >> File "", line 219, in _call_with_frames_removed >> File "/build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build/tests/tests.py", line 21, in >> raise Exception("snakemake not in PATH. For testing, install snakemake with " >> Exception: snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv). >> >> ---------------------------------------------------------------------- >> Ran 4 tests in 0.535s >> >> FAILED (errors=1) >> E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose tests >> dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13 >> debian/rules:18: recipe for target 'build' failed >> make: *** [build] Error 25 >> >> >> >> The problem is the the following line in debian/rules: >> >> export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH) >> >> _______________________________________________ >> Debian-med-packaging mailing list >> Debian-med-packaging@lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >> >