Path: csiph.com!news.mixmin.net!aioe.org!bofh.it!news.nic.it!robomod From: Ken Yamaguchi Newsgroups: linux.debian.bugs.dist,linux.debian.maint.python Subject: Bug#980005: lumpy-sv: lumpyexpress fails with no args Date: Wed, 13 Jan 2021 00:10:01 +0100 Message-ID: References: X-Mailbox-Line: From debian-bugs-dist-request@lists.debian.org Tue Jan 12 23:09:08 2021 Old-Return-Path: X-Spam-Flag: NO X-Spam-Score: -2.028 Reply-To: Ken Yamaguchi , 980005@bugs.debian.org Resent-To: debian-bugs-dist@lists.debian.org Resent-Cc: Debian Med Packaging Team X-Debian-Pr-Message: followup 980005 X-Debian-Pr-Package: lumpy-sv X-Debian-Pr-Keywords: help confirmed X-Debian-Pr-Source: lumpy-sv X-Spam-Bayes: score:0.0000 Tokens: new, 35; hammy, 149; neutral, 39; spammy, 1. spammytokens:0.987-1--H*r:sk:ip-10-0 hammytokens:0.000-+--H*UA:1.10.1, 0.000-+--H*u:1.10.1, 0.000-+--H*UA:2018-07-13, 0.000-+--H*u:2018-07-13, 0.000-+--UD:patch Dkim-Signature: v=1; a=rsa-sha256; c=simple/simple; d=knowledgesynthesis.com; s=201812; t=1610492201; bh=egOA6qNHHYYmrt2r4phNfU/HFC6Qh4NRBlvcVBA+VvI=; h=Date:From:To:Cc:Subject:References:In-Reply-To:From; b=QiVSBMR3JGp3sNBS164H1kUaFpy38fTlb0FSzt5o7RfGOKRDLenofBo6mMrt5u1iA V8iNPIqLupdHN6md16mkNzDJsM61evnD6up/YXpB7CT1lLcmBhQChnPAx5XYjhbo8Y CSpIGwriTA2di1AcjmMp6k01Jh8vh5MdiZUl0qP4mf75sm0ycYeyHtgX96JCF91Nff hYOksvh3b5mL1xru9Haz4xYRB78SqqaKkrQp9xqjPndpkToPkDwS1/JomdhdR8AEBH IkaEj4X3xKNKBaszhe44/X4992yzYycAhgCic8+MEdep4fxDHqoTBxsnf9GOufyqLw CzSceD7lXSH7Q== MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.10.1 (2018-07-13) X-Greylist: delayed 528 seconds by postgrey-1.36 at buxtehude; Tue, 12 Jan 2021 23:05:33 UTC X-Debian-Message: from BTS X-Mailing-List: archive/latest/1644355 List-ID: List-URL: Approved: robomod@news.nic.it Lines: 39 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Andreas Tille , 980005@bugs.debian.org, Debian Python X-Original-Date: Tue, 12 Jan 2021 22:56:41 +0000 X-Original-Message-ID: <20210112225641.GA10978@knowledgesynthesis.com> X-Original-References: <161048192648.3215.17832019956441998304.reportbug@2fa8301b1b93> <20210112210821.GE5326@an3as.eu> <161048192648.3215.17832019956441998304.reportbug@2fa8301b1b93> Xref: csiph.com linux.debian.bugs.dist:1042274 linux.debian.maint.python:13106 On Wed, Jan 13, 2021 at 12:04:08AM +0200, Juhani Numminen wrote: > It's a change made in debian/patches/lumpyexpress.config.patch. > https://salsa.debian.org/med-team/lumpy-sv/-/commit/e64a65545fbf60c5c98965bc1d00d416b2f9582c#6864ced7557ec33a7ee70c7b0c75b076f84f4fac_24_30 > > - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" > - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" > + $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')" > + $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')" > > It's not entirely correct even if it worked: the original causes > a visible error message to alert if one of the required modules does > not exist. The current patch will not cause error messages or the > python check to exit non-zero. > > Because it's a Debian context we could rely on dpkg dependencies i.e. > just don't perform this check and comment out the two lines. > > -- > Juhani There's a discussion of the issue at https://stackoverflow.com/questions/39660934/error-when-using-importlib-util-to-check-for-library/39661116 To remove the error, - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" + $PYTHON_TEST -c "from importlib import util; util.find_spec('pysam')" + $PYTHON_TEST -c "from importlib import util; util.find_spec('numpy')" To print an error message, perhaps the awkward-looking - $PYTHON_TEST -c "import imp; imp.find_module('pysam')" - $PYTHON_TEST -c "import imp; imp.find_module('numpy')" + $PYTHON_TEST -c "from importlib import util; print('pysam not found') if util.find_spec('pysam') is None else None" + $PYTHON_TEST -c "from importlib import util; print('numpy not found') if util.find_spec('numpy') is None else None" Ken