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 qKr2EGqCrl+LHgAA0tVLHw (envelope-from ) for ; Fri, 13 Nov 2020 12:56:10 +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 YJXVDGqCrl8TcQAA1q6Kng (envelope-from ) for ; Fri, 13 Nov 2020 12:56:10 +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 A7B41940719 for ; Fri, 13 Nov 2020 12:56:09 +0000 (UTC) Received: from localhost ([::1]:55222 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdYca-0004U6-KV for larch@yhetil.org; Fri, 13 Nov 2020 07:56:08 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:44024) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kdYcU-0004Su-LT for guix-patches@gnu.org; Fri, 13 Nov 2020 07:56:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:35702) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kdYcU-00038A-Br for guix-patches@gnu.org; Fri, 13 Nov 2020 07:56:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kdYcU-0008VJ-AR for guix-patches@gnu.org; Fri, 13 Nov 2020 07:56:02 -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 12:56:02 +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: zimoun , 44613@debbugs.gnu.org Received: via spool by 44613-submit@debbugs.gnu.org id=B44613.160527214132660 (code B ref 44613); Fri, 13 Nov 2020 12:56:02 +0000 Received: (at 44613) by debbugs.gnu.org; 13 Nov 2020 12:55:41 +0000 Received: from localhost ([127.0.0.1]:47248 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdYc8-0008Ui-OY for submit@debbugs.gnu.org; Fri, 13 Nov 2020 07:55:40 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43840) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kdYc6-0008UU-EC for 44613@debbugs.gnu.org; Fri, 13 Nov 2020 07:55:39 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56966) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kdYc1-0002yi-26; Fri, 13 Nov 2020 07:55:33 -0500 Received: from [143.121.239.14] (port=45972 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 1kdYby-00059k-SX; Fri, 13 Nov 2020 07:55:32 -0500 Message-ID: <695715d9f08a7ec06b6dfe8bcf71173829a0d029.camel@gnu.org> From: Roel Janssen Date: Fri, 13 Nov 2020 13:55:29 +0100 In-Reply-To: <86v9e9e8gz.fsf@gmail.com> References: <86v9e9e8gz.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: 8bit 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: psaBlczlmYBl Hi Simon, On Fri, 2020-11-13 at 13:39 +0100, zimoun wrote: > Hi Roel, > > On Fri, 13 Nov 2020 at 12:01, Roel Janssen wrote: > > > 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. > > Recently, investigating why the substitute of ’python-pysam’ was not > available, I decided then to give a try at fixing the TODO: > > --8<---------------cut here---------------start------------->8--- >               (snippet '(begin >                           ;; Drop bundled htslib. TODO: Also remove > samtools >                           ;; and bcftools. >                           (delete-file-recursively "htslib") >                           #t)))) > --8<---------------cut here---------------end--------------->8--- > > And the bundled version is 1.9 (if I remember correctly), therefore > because of: > > --8<---------------cut here---------------start------------->8--- >     (native-inputs >      `(("python-cython" ,python-cython) >        ;; Dependencies below are are for tests only. >        ("samtools" ,samtools) >        ("bcftools" ,bcftools) >        ("python-nose" ,python-nose))) > --8<---------------cut here---------------end--------------->8--- > > some tests are unhappy. > > That’s said, these additions seem fine with me. :-) > 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. Just to double-check: Is it OK to push the proposed patches? Kind regards, Roel Janssen