From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id gOY2HLlnrl/UNAAA0tVLHw (envelope-from ) for ; Fri, 13 Nov 2020 11:02:17 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id KPIJGLlnrl+lOAAAB5/wlQ (envelope-from ) for ; Fri, 13 Nov 2020 11:02:17 +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 2BC7594050F for ; Fri, 13 Nov 2020 11:02:15 +0000 (UTC) Received: from localhost ([::1]:45196 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWqM-0007J0-0M for larch@yhetil.org; Fri, 13 Nov 2020 06:02:14 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42908) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWqA-0007GT-2W for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35322) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kdWq9-0003Yd-Nh for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kdWq9-0001Jk-Kl for guix-patches@gnu.org; Fri, 13 Nov 2020 06:02:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 11:02:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44613@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16052652855014 (code B ref -1); Fri, 13 Nov 2020 11:02:01 +0000 Received: (at submit) by debbugs.gnu.org; 13 Nov 2020 11:01:25 +0000 Received: from localhost ([127.0.0.1]:46868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpY-0001Io-P0 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:25 -0500 Received: from lists.gnu.org ([209.51.188.17]:60528) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdWpX-0001Ig-1s for submit@debbugs.gnu.org; Fri, 13 Nov 2020 06:01:23 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:42704) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdWpP-0006a6-Nz for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:19 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:48998) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdWpL-0003H1-IN for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:14 -0500 Received: from [143.121.239.14] (port=45168 helo=[10.132.152.6]) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kdWpG-0002NT-Ip for guix-patches@gnu.org; Fri, 13 Nov 2020 06:01:10 -0500 Message-ID: From: Roel Janssen Date: Fri, 13 Nov 2020 12:01:04 +0100 Content-Type: multipart/mixed; boundary="=-A3Jh9HcEN31wwMB5f/Iy" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -3.3 (---) 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-Scanner: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; 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-Spam-Score: -0.41 X-TUID: gKgqbp0S7Z9+ --=-A3Jh9HcEN31wwMB5f/Iy Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Dear Guix, By updating samtools to 1.11, I introduced a build failure for bedtools. More precisely, the tests for intersect break in precisely this way: https://github.com/arq5x/bedtools2/issues/814 With the following patches, I'd like to add samtools-1.9, htslib-1.9 (samtools depends on that) to fix this problem with bedtools. Alternatively we could add a patch to disable the failing bedtools tests. I manually inspected the test results, and seem to match perfectly (indicating that there's no problem with bedtools). 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