From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id YLfPE3+Mrl8kawAA0tVLHw (envelope-from ) for ; Fri, 13 Nov 2020 13:39:11 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id 6Ni7D3+Mrl8jFQAAbx9fmQ (envelope-from ) for ; Fri, 13 Nov 2020 13:39:11 +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 D36ED9401BD for ; Fri, 13 Nov 2020 13:39:10 +0000 (UTC) Received: from localhost ([::1]:52498 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdZID-0004Oz-Lo for larch@yhetil.org; Fri, 13 Nov 2020 08:39:09 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:55496) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdZI6-0004Of-QD for guix-patches@gnu.org; Fri, 13 Nov 2020 08:39:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35718) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kdZI6-0001BW-GY for guix-patches@gnu.org; Fri, 13 Nov 2020 08:39:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kdZI6-000149-DD for guix-patches@gnu.org; Fri, 13 Nov 2020 08:39:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#44613] [PATCH] Fix build for bedtools Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Nov 2020 13:39:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44613 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen , 44613@debbugs.gnu.org Received: via spool by 44613-submit@debbugs.gnu.org id=B44613.16052747044039 (code B ref 44613); Fri, 13 Nov 2020 13:39:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 13:38:24 +0000 Received: from localhost ([127.0.0.1]:47264 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZHU-000135-AJ for submit@debbugs.gnu.org; Fri, 13 Nov 2020 08:38:24 -0500 Received: from mail-wm1-f66.google.com ([209.85.128.66]:39610) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdZHS-00012q-MR for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 08:38:23 -0500 Received: by mail-wm1-f66.google.com with SMTP id s13so8519478wmh.4 for <44613@debbugs.gnu.org>; Fri, 13 Nov 2020 05:38:22 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:in-reply-to:references:date:message-id:mime-version :content-transfer-encoding; bh=zSw2QQZW4vWDV71p5cy8617NNxK3pYBbvybT3A5l1pw=; b=o6ZG2qDtjYYz132girfkQ87dHWfjY4KPm7b+iUJO23N9/vu3Of0tadDTSbmFpMm6RS pRngdVqH1DWF7TIRfjRIUPeWaGb/WfyShBgVzTTb3Ucr6u9WVoh+k7MpTSieEAwXJX0z p/SUdsUwy6OkClFYtIB18jpoE6KxBPwOBp0RZyOwu0H7QQMTdOdgJGt8DkL3wx81kqFm GZ/KD0GcZn3epqDkiu+bqSw2TLOWZA/kkfkzgUs/5yRr8z9yNgrXNEUDlGXxl4Nfgktu I1UX6onZf3uM4+GP0vjvnVKBXZCGF8q7zWm9B0f+qqxSKjoWdgfbldNEXX4OXgGxX6j6 7mWQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:in-reply-to:references:date :message-id:mime-version:content-transfer-encoding; bh=zSw2QQZW4vWDV71p5cy8617NNxK3pYBbvybT3A5l1pw=; b=DRRoi/IHNeiZCKrO7ChKn9D6wJZA8bu8IFiTsPJOLuYrILEQBR2uiwjiXy5LmdCFJV ygqBCT8XkfM5SAhOFJ9BuaEfAX3IdVL+JFBIRXKmw0cfocyrLOuOqp3LyK8V/EDs2SdB lfKSBD3iGMNgp+mPeEnA1MB3jcxkke2REvv0jNuagD40sieusBWG5rbUxP+UGRSkJ6RE MqbbfuvNBKMnAaUkd4EFXaKIhlXy4isgnYObsVQ7nDh6Rd9ZAzsS/NbdC+IhN5XNHy1U xmJNJVI/9tpiNDAKG+QYeyDSci1SQMdIcGVndSL8wBKd9W+qVXNSZqup1IUgEmk7nLTo HWbQ== X-Gm-Message-State: AOAM5304b44H8sqxE465FhFhWwK5M1SUZe19ZG0pxMnJzlhuckA2dejz WVpc+HGFlFpDmC1zoAuhnioRbw0fajeZjQ== X-Google-Smtp-Source: ABdhPJwxE8D0usZk6mDVSt1bPBQnvnxAHmCYkoxedsDJSW1luhi0DmXUAicy5UsxF/WChR0iK2OA/Q== X-Received: by 2002:a1c:230e:: with SMTP id j14mr2534530wmj.187.1605274696332; Fri, 13 Nov 2020 05:38:16 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id d3sm11971436wrg.16.2020.11.13.05.38.15 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 13 Nov 2020 05:38:15 -0800 (PST) From: zimoun In-Reply-To: <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> References: <86v9e9e8gz.fsf@gmail.com> <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> Date: Fri, 13 Nov 2020 14:34:06 +0100 Message-ID: <86k0upe5yp.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) 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=fail (headers rsa verify failed) header.d=gmail.com header.s=20161025 header.b=o6ZG2qDt; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); 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: 0.09 X-TUID: kS05xgsXIQ+z 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. All the best, simon PS: I am always confused if the removal should be done in =E2=80=99origin=E2=80= =99 or in the =E2=80=99add-after 'unpack=E2=80=99 phase; especially when the bundle is fr= ee software. Other said, what should an user expect when fetching with =E2=80=9Cguix bui= ld -S=E2=80=9D? Anyway! :-)