From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 452BF15ACFB for ; Tue, 18 Apr 2023 10:04:48 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 86882E08F1; Tue, 18 Apr 2023 10:04:47 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 711D6E08F1 for ; Tue, 18 Apr 2023 10:04:47 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A25A5335D07 for ; Tue, 18 Apr 2023 10:04:46 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 11F90A1C for ; Tue, 18 Apr 2023 10:04:45 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1681812277.0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/bedtools/bedtools-2.30.0.ebuild sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch X-VCS-Directories: sci-biology/bedtools/ sci-biology/bedtools/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e X-VCS-Branch: master Date: Tue, 18 Apr 2023 10:04:45 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 4518a65a-2013-4703-adb8-c93040219e9e X-Archives-Hash: 00c7fe7708765f25077e4eac45f004fb commit: 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e Author: David Seifert gentoo org> AuthorDate: Tue Apr 18 10:04:37 2023 +0000 Commit: David Seifert gentoo org> CommitDate: Tue Apr 18 10:04:37 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f6ed95b sci-biology/bedtools: fix gcc 13 build Closes: https://bugs.gentoo.org/895860 Signed-off-by: David Seifert gentoo.org> sci-biology/bedtools/bedtools-2.30.0.ebuild | 1 + .../bedtools/files/bedtools-2.30.0-gcc13.patch | 25 ++++++++++++++++++++++ 2 files changed, 26 insertions(+) diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild index 5a8174fbdfe0..b86b87e72dc4 100644 --- a/sci-biology/bedtools/bedtools-2.30.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -34,6 +34,7 @@ BDEPEND=" PATCHES=( "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.30.0-gcc13.patch ) src_configure() { diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch new file mode 100644 index 000000000000..c63faf31c851 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch @@ -0,0 +1,25 @@ +https://github.com/arq5x/bedtools2/pull/1045 + +From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001 +From: David Seifert +Date: Tue, 18 Apr 2023 11:59:58 +0200 +Subject: [PATCH] Add missing include + +* breaks build with GCC 13: + https://bugs.gentoo.org/895860 +--- + src/utils/general/ParseTools.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h +index e056c149..3418eff1 100644 +--- a/src/utils/general/ParseTools.h ++++ b/src/utils/general/ParseTools.h +@@ -16,6 +16,7 @@ + #include "string.h" + #include + #include ++#include + + using namespace std; +