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 CAEF1158094 for ; Thu, 7 Jul 2022 19:58:21 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 34135E0950; Thu, 7 Jul 2022 19:58:18 +0000 (UTC) Received: from smtp.gentoo.org (mail.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 1BA30E0950 for ; Thu, 7 Jul 2022 19:58:18 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (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 0514F340E43 for ; Thu, 7 Jul 2022 19:58:17 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id E81A0543 for ; Thu, 7 Jul 2022 19:58:13 +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: <1657223830.e00ee2933cf56d8a51e0abb0326ff4138e646cfe.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/recon/files/, sci-biology/recon/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch sci-biology/recon/recon-1.08-r1.ebuild sci-biology/recon/recon-1.08.ebuild X-VCS-Directories: sci-biology/recon/ sci-biology/recon/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: e00ee2933cf56d8a51e0abb0326ff4138e646cfe X-VCS-Branch: master Date: Thu, 7 Jul 2022 19:58:13 +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: e8b71744-5449-44f1-820c-8b58295e6080 X-Archives-Hash: e0b304227c8bb3d4e9f5107776982d38 commit: e00ee2933cf56d8a51e0abb0326ff4138e646cfe Author: David Seifert gentoo org> AuthorDate: Thu Jul 7 19:57:10 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Thu Jul 7 19:57:10 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e00ee293 sci-biology/recon: update EAPI 6 -> 8 Closes: https://bugs.gentoo.org/716082 Signed-off-by: David Seifert gentoo.org> .../recon-1.08-Wimplicit-function-declaration.patch | 20 ++++++++++++++++++++ .../{recon-1.08.ebuild => recon-1.08-r1.ebuild} | 16 ++++++++-------- 2 files changed, 28 insertions(+), 8 deletions(-) diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch new file mode 100644 index 000000000000..9eba16e4a410 --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch @@ -0,0 +1,20 @@ +--- a/src/bolts.h ++++ b/src/bolts.h +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + + + #define NAME_LEN 50 +--- a/src/seqlist.h ++++ b/src/seqlist.h +@@ -1,6 +1,7 @@ + + #include "bolts.h" + #include "string.h" ++#include + + #ifndef _seqlist_h + #define _seqlist_h diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild similarity index 75% rename from sci-biology/recon/recon-1.08.ebuild rename to sci-biology/recon/recon-1.08-r1.ebuild index a96403c812be..dd79dd43c496 100644 --- a/sci-biology/recon/recon-1.08.ebuild +++ b/sci-biology/recon/recon-1.08-r1.ebuild @@ -1,31 +1,31 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html" SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz" +S="${WORKDIR}/${P^^}" LICENSE="GPL-2" SLOT="0" -IUSE="examples" KEYWORDS="~amd64 ~x86" +IUSE="examples" RDEPEND="dev-lang/perl" -S=${WORKDIR}/${P^^} - PATCHES=( "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch + "${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch ) src_prepare() { default - sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die + sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die } src_compile() { @@ -35,13 +35,13 @@ src_compile() { src_install() { dobin scripts/* - exeinto /usr/libexec/${PN} + exeinto /usr/libexec/recon doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} newdoc {00,}README if use examples; then - insinto /usr/share/${PN} + insinto /usr/share/recon doins -r Demos fi }