From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id moSFCB6Srl+ELwAA0tVLHw (envelope-from ) for ; Fri, 13 Nov 2020 14:03:10 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id UL7UAx6Srl8ZHgAA1q6Kng (envelope-from ) for ; Fri, 13 Nov 2020 14:03:10 +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 B78F9940719 for ; Fri, 13 Nov 2020 14:03:09 +0000 (UTC) Received: from localhost ([::1]:37300 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdZfQ-0005N9-O8 for larch@yhetil.org; Fri, 13 Nov 2020 09:03:08 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:60956) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdZeM-0004jI-RH for guix-patches@gnu.org; Fri, 13 Nov 2020 09:02:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35743) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kdZeM-0001Mm-DE for guix-patches@gnu.org; Fri, 13 Nov 2020 09:02:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kdZeM-0001fV-BY for guix-patches@gnu.org; Fri, 13 Nov 2020 09:02:02 -0500 Subject: bug#44613: [PATCH] Fix build for bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-To: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 14:02:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun Cc: 44613-done@debbugs.gnu.org Mail-Followup-To: 44613@debbugs.gnu.org, roel@gnu.org, roel@gnu.org Received: via spool by 44613-done@debbugs.gnu.org id=D44613.16052760716327 (code D ref 44613); Fri, 13 Nov 2020 14:02:02 +0000 Received: (at 44613-done) by debbugs.gnu.org; 13 Nov 2020 14:01:11 +0000 Received: from localhost ([127.0.0.1]:47285 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZdX-0001dz-44 for submit@debbugs.gnu.org; Fri, 13 Nov 2020 09:01:11 -0500 Received: from eggs.gnu.org ([209.51.188.92]:60626) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZdR-0001dK-PL for 44613-done@debbugs.gnu.org; Fri, 13 Nov 2020 09:01:09 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:59444) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdZdM-000148-Em; Fri, 13 Nov 2020 09:01:00 -0500 Received: from [143.121.239.14] (port=46298 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 1kdZdL-00056v-5C; Fri, 13 Nov 2020 09:00:59 -0500 Message-ID: From: Roel Janssen Date: Fri, 13 Nov 2020 15:00:57 +0100 In-Reply-To: <86k0upe5yp.fsf@gmail.com> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> <86k0upe5yp.fsf@gmail.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 Content-Transfer-Encoding: 7bit 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: -1.51 X-TUID: en4ef9QZM24N Hi Simon, On Fri, 2020-11-13 at 14:34 +0100, zimoun wrote: > Hi Roel, > > On Fri, 13 Nov 2020 at 13:55, Roel Janssen wrote: > > > I also tried removing the bundled htslib for bedtools, but didn't > > go > > this route for two reasons: > > - The bundled htslib for bedtools seems "slightly modified" (I > > didn't > > investigate further) > > - Replacing the references to libhts.a with $(pkg-config htslib -- > > cflags --libs) produced various linker errors. So I stopped right > > there. > > > > I'm sure more tools will likely have failed because of the htslib > > upgrade (sorry about this!), so having htslib-1.9 around for some > > time > > may be a good fallback for now. > > Thank for your explanations. > > > > Just to double-check: Is it OK to push the proposed patches? > > I have not tried them but they LGTM. > Thanks for the quick review. I pushed the patches in c3232fcc7785abc1057a0d4b5b1832f1e39c9c1b, da4a38edad52f7bb5a8d41465d09f3f0197fd0b7, and 3ede804f6d4c38ff0b9a5705544a8c35f6827ff1. Kind regards, Roel Janssen