Groups > linux.debian.maint.python > #10657

Re: No clue yet for building snakemake since there are two dirs in .pybuild

Path	csiph.com!feeder.erje.net!2.eu.feeder.erje.net!news2.arglkargh.de!news.mixmin.net!aioe.org!bofh.it!news.nic.it!robomod
From	Stuart Prescott <stuart@debian.org>
Newsgroups	linux.debian.maint.python
Subject	Re: No clue yet for building snakemake since there are two dirs in .pybuild
Date	Tue, 26 Jun 2018 18:10:01 +0200
Message-ID	<w4YHv-2wC-3@gated-at.bofh.it> (permalink)
References	<w4SVr-7ns-1@gated-at.bofh.it>
X-Mailbox-Line	From debian-python-request@lists.debian.org Tue Jun 26 16:06:19 2018
Old-Return-Path	<debian-python@m.gmane.org>
X-Amavis-Spam-Status	No, score=-5.857 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, FOURLA=0.1, HEADER_FROM_DIFFERENT_DOMAINS=0.25, LDO_WHITELIST=-5, RDNS_NONE=0.793] autolearn=no autolearn_force=no
X-Policyd-Weight	using cached result; rate:hard: -6.1
X-Injected-Via-Gmane	http://gmane.org/
Lines	50
MIME-Version	1.0
Content-Type	text/plain; charset="ISO-8859-1"
Content-Transfer-Encoding	7Bit
User-Agent	KNode/4.14.10
X-Mailing-List	<debian-python@lists.debian.org> archive/latest/16066
List-ID	<debian-python.lists.debian.org>
List-URL	<https://lists.debian.org/debian-python/>
List-Archive	https://lists.debian.org/msgid-search/pgto4t$cde$1@blaine.gmane.org
Approved	robomod@news.nic.it
Organization	linux.* mail to news gateway
Sender	robomod@news.nic.it
X-Original-Date	Wed, 27 Jun 2018 02:05:50 +1000
X-Original-Message-ID	<pgto4t$cde$1@blaine.gmane.org>
X-Original-References	<20180626095124.2asvsuaoq6bilru5@an3as.eu>
X-Original-X-Complaints-To	usenet@blaine.gmane.org
Xref	csiph.com linux.debian.maint.python:10657

Show key headers only | View raw

Hi Andreas,

> 
"/build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build/tests/tests.py",
>   line 22, in <module>
>     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 0.227s
> 
> FAILED (errors=1)
> E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1:
> cd /build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build; python3.6
> -m nose tests
> 
> 
> 
> I think the cause of the issue is that there are two dirs in .pybuild:
> 
> 
> # ls -l /build/snakemake-5.1.5/.pybuild
> total 8
> drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6
> drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake
> 
> 
> and the latter contains all the installed files while the former is
> empty.  How can I prevent this?

Deleting PYBUILD_NAME from your debian/rules is sufficient to fix that. When 
set, that sets HOME to the above directory and the build system for some 
reason starts using that. 

And no, I can't explain why that is...

There are still 3 test failures; the one I glanced at was a missing build-
dep on python3-networkx (and I didn't look further).

cheers
Stuart


-- 
Stuart Prescott    http://www.nanonanonano.net/   stuart@nanonanonano.net
Debian Developer   http://www.debian.org/         stuart@debian.org
GPG fingerprint    90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7

Thread

Bug#894213: No clue yet for building snakemake since there are two dirs in .pybuild Andreas Tille <andreas@an3as.eu> - 2018-06-26 12:00 +0200
  Re: No clue yet for building snakemake since there are two dirs in .pybuild Stuart Prescott <stuart@debian.org> - 2018-06-26 18:10 +0200
    Re: No clue yet for building snakemake since there are two dirs in  .pybuild Piotr Ożarowski <piotr@debian.org> - 2018-06-27 11:10 +0200
      Re: No clue yet for building snakemake since there are two dirs in  .pybuild Piotr Ożarowski <piotr@debian.org> - 2018-06-27 14:40 +0200

csiph-web