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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id A795E139694 for ; Sat, 25 Feb 2017 16:15:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 69FFBE0D12; Sat, 25 Feb 2017 16:15:24 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 38042E0D12 for ; Sat, 25 Feb 2017 16:15:24 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 77BA0340FC8 for ; Sat, 25 Feb 2017 16:15:22 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id E0C8A5440 for ; Sat, 25 Feb 2017 16:15:20 +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: <1488039273.960abf9442aca3794235dc9f15e92005e9d0d77d.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/Manifest sci-biology/recon/files/recon-1.08-buffer-overflow.patch sci-biology/recon/files/recon-1.08-perl-shebangs.patch sci-biology/recon/recon-1.08.ebuild X-VCS-Directories: sci-biology/recon/files/ sci-biology/recon/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 960abf9442aca3794235dc9f15e92005e9d0d77d X-VCS-Branch: master Date: Sat, 25 Feb 2017 16:15:20 +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-Archives-Salt: 7d2688d0-ceb6-4f82-b338-0dadfa59f737 X-Archives-Hash: c3b0b348b6a7ab35a368c74662246acf commit: 960abf9442aca3794235dc9f15e92005e9d0d77d Author: David Seifert gentoo org> AuthorDate: Sat Feb 25 16:14:33 2017 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Feb 25 16:14:33 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=960abf94 sci-biology/recon: Version bump to 1.08 Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/recon/Manifest | 1 + .../recon/files/recon-1.08-buffer-overflow.patch | 11 +++++ .../recon/files/recon-1.08-perl-shebangs.patch | 19 +++++++++ sci-biology/recon/recon-1.08.ebuild | 48 ++++++++++++++++++++++ 4 files changed, 79 insertions(+) diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest index d779bd4735..c27ca97b51 100644 --- a/sci-biology/recon/Manifest +++ b/sci-biology/recon/Manifest @@ -1 +1,2 @@ +DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL e9a60353e4f6bbe37883c648a7c8f5d363c780d03a681dd2d6803d2e65a1eb5f9b8fb02a85721636e7a792b53628a00f21d57d1c4066fb8b91b2fb1d4c383763 DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec diff --git a/sci-biology/recon/files/recon-1.08-buffer-overflow.patch b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch new file mode 100644 index 0000000000..e6bf54e7c2 --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch @@ -0,0 +1,11 @@ +--- a/src/eledef.c ++++ b/src/eledef.c +@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp, + + void img_charge(IPROT_t **shadow, int ct, FILE *input) { + int i=0, pos=0; +- char line[151]; ++ char line[256]; + int scan_flag; + MSP_t msp; + diff --git a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch new file mode 100644 index 0000000000..769fe4a93c --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch @@ -0,0 +1,19 @@ +Make Perl shebangs Prefix friendly +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/scripts/MSPCollect.pl ++++ b/scripts/MSPCollect.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + if (!@ARGV) { + die "usage: MSPCollect BLAST_output_file\n"; +--- a/scripts/recon.pl ++++ b/scripts/recon.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $path = ""; + diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08.ebuild new file mode 100644 index 0000000000..8d934d014f --- /dev/null +++ b/sci-biology/recon/recon-1.08.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +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/${P^^}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="examples" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl" + +S=${WORKDIR}/${P^^} + +PATCHES=( + "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch + "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch +) + +src_prepare() { + default + sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die +} + +src_compile() { + emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -C src +} + +src_install() { + dobin scripts/* + + exeinto /usr/libexec/${PN} + doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} + + newdoc {00,}README + + if use examples; then + insinto /usr/share/${PN} + doins -r Demos + fi +}