From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:8:6d80::]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id Qa2eH+lriWA3nAAAgWs5BA (envelope-from ) for ; Wed, 28 Apr 2021 16:06:33 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id 4MsvGulriWCZbgAAbx9fmQ (envelope-from ) for ; Wed, 28 Apr 2021 14:06:33 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 075982BF6F for ; Wed, 28 Apr 2021 16:06:33 +0200 (CEST) Received: from localhost ([::1]:53600 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lbkpi-0001H0-L9 for larch@yhetil.org; Wed, 28 Apr 2021 10:06:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37928) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lbkpH-0001GD-0C for guix-patches@gnu.org; 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boundary="=-djLtlCJ59+uZ/z0rSwY4" User-Agent: Evolution 3.40.0 (3.40.0-1.fc34) MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1619618793; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post; bh=0+bO0YfCvtoVI1mTkb9M+p3Hr3THpPMhgFQ17CjTbvM=; b=exdJ+nMB2Op2JE4bhoVeIR0H9Xu2kskmklPkqOZXrnDaHSwK9LzB3BSkueNoAwDoLWABaK K6IWXt2rH6VoUbNCQfyoavRGdorCmMqk1+4BU27ORtI+/a9fh4iGqPqqGFzzgbWoTHKBRi hgYzLdVerA3uMpqQRXQP8SD9UADP1iJDTgvJswlV2qggLI+Vs5Xr5VWJNv00qAVU547VzM byGWtm/NAmQhfn3nv8PggeDnhhVhnyQtx1vdTWZ5o9y2E7kQpdEyWSf0lIbNVGIjgPTe5g vZCktIcXhVmNw1uyQYV2u81TDAiYEnS4wxcMbUeJwpyTvkf2h8Wt244HRPncnQ== ARC-Seal: i=1; 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charset="UTF-8" Content-Transfer-Encoding: 7bit On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote: > On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote: > > Hi Guix, > > > > The following patches update htslib, bcftools, samtools, and > > bedtools. > > I've succesfully built bedtools with the latest samtools instead of > > the > > 1.9 version. > > These look good and are ready for merging. Can you take a look at > python-pybedtools? There's a new version out which I hope builds with > the newer version of bedtools. > > Thanks. > I looked at python-pybedtools and came up with the following patch. The test phase is still not entirely happy because it ends with: --- ================ 497 passed, 3 xfailed, 426 warnings in 25.49s ================= Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/gnu/store/rz42ba0my9vrgbkjpkzr2drmnjk5ah50-python- 3.8.2/lib/python3.8/shutil.py", line 704, in rmtree orig_st = os.lstat(path) --- I attached the patch that I have that at least builds the newer version of python-pybedtools. I don't know how to further test it. Can I in the meantime already push the patches for updating htslib, bcftools, samtools and bedtools? 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