From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:bcc0::]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id uAdGLNeIimDOGQAAgWs5BA (envelope-from ) for ; Thu, 29 Apr 2021 12:22:15 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id cJX1J9eIimBBOAAAbx9fmQ (envelope-from ) for ; Thu, 29 Apr 2021 10:22:15 +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 4EC4A1BFB3 for ; Thu, 29 Apr 2021 12:22:15 +0200 (CEST) Received: from localhost ([::1]:40420 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc3oE-0001T9-0A for larch@yhetil.org; Thu, 29 Apr 2021 06:22:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43616) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lc3o3-0001Rs-DU for guix-patches@gnu.org; Thu, 29 Apr 2021 06:22:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43349) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lc3o2-0007K3-I6 for guix-patches@gnu.org; Thu, 29 Apr 2021 06:22:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lc3o2-0007zn-Dx for guix-patches@gnu.org; Thu, 29 Apr 2021 06:22:02 -0400 Subject: bug#47821: [PATCH] Update htslib, bcftools, samtools, bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-To: guix-patches@gnu.org Resent-Date: Thu, 29 Apr 2021 10:22:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 47821 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner Cc: 47821-done@debbugs.gnu.org Mail-Followup-To: 47821@debbugs.gnu.org, roel@gnu.org, roel@gnu.org Received: via spool by 47821-done@debbugs.gnu.org id=D47821.161969171930723 (code D ref 47821); Thu, 29 Apr 2021 10:22:02 +0000 Received: (at 47821-done) by debbugs.gnu.org; 29 Apr 2021 10:21:59 +0000 Received: from localhost ([127.0.0.1]:54894 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc3ny-0007zT-VG for submit@debbugs.gnu.org; Thu, 29 Apr 2021 06:21:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:35238) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lc3nx-0007zI-Ik for 47821-done@debbugs.gnu.org; Thu, 29 Apr 2021 06:21:58 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:39444) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lc3nq-0007GD-C7; Thu, 29 Apr 2021 06:21:51 -0400 Received: from [143.121.198.253] (port=56914) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1lc3no-0005ws-Eo; Thu, 29 Apr 2021 06:21:50 -0400 References: <9345d6a11fd99f1a8eefeb3664508938255e1287.camel@gnu.org> <63890b0475ea51a1215713195d929ff76b639630.camel@gnu.org> From: Roel Janssen Message-ID: <42f9d1f0-88d6-beb7-81c1-ef1b0e501ff2@gnu.org> Date: Thu, 29 Apr 2021 12:21:37 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.7.1 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Content-Language: en-US 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=1619691735; 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: content-transfer-encoding:content-transfer-encoding:resent-to: 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=wRUtJavJ9lgZTXwbeLVKbl8X6mnEYV4H3a+6QHEcG1A=; 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dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 4EC4A1BFB3 X-Spam-Score: -2.95 X-Migadu-Scanner: scn0.migadu.com X-TUID: 3kIP2FgT2Rur On 4/29/21 8:43 AM, Efraim Flashner wrote: > On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote: >> 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? >> > Yeah, those patches LGTM. Thanks. I pushed these. For python-pybedtools, I think a little bit more testing is required.  I can take a look at it in the second week of May, so hopefully someone beats me to it. :) Kind regards, Roel Janssen