[gentoo-commits] repo/gentoo:master commit in: sci-biology/recon/files/, sci-biology/recon/

[David Seifert]

commit:     adeefddadbab83e8ab35a0a7d6dcf1e6f2698b05
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 16:35:43 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 17:13:02 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=adeefdda

sci-biology/recon: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/4076

 sci-biology/recon/Manifest                         |  1 -
 sci-biology/recon/files/1.06-buffer-overflow.patch | 13 --------
 sci-biology/recon/files/recon-1.06-respect.patch   | 24 -------------
 sci-biology/recon/recon-1.06-r1.ebuild             | 36 --------------------
 sci-biology/recon/recon-1.06-r2.ebuild             | 39 ----------------------
 5 files changed, 113 deletions(-)

diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index c27ca97b51..2e55e8cb1e 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1,2 +1 @@
 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/1.06-buffer-overflow.patch b/sci-biology/recon/files/1.06-buffer-overflow.patch
deleted file mode 100644
index 29d220c731..0000000000
--- a/sci-biology/recon/files/1.06-buffer-overflow.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/eledef.c b/src/eledef.c
-index 964890b..a001ec4 100644
---- 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[100];
-+  char line[256];
-   int scan_flag;
-   MSP_t msp;
- 

diff --git a/sci-biology/recon/files/recon-1.06-respect.patch b/sci-biology/recon/files/recon-1.06-respect.patch
deleted file mode 100644
index a02038d847..0000000000
--- a/sci-biology/recon/files/recon-1.06-respect.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- src/Makefile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/Makefile b/src/Makefile
-index 36ef59b..e45a0f2 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -13,14 +13,14 @@ MANDIR  = $(HOME)/man
- #SRCDIR = .
- 
- ## your compiler
--CC = gcc
-+CC ?= gcc
- #CC = cc    # for SGI Origin200 compiler#
- 
- ## any special compiler flags you want
- #  -pedantic clashes with -DMEMDEBUG??
- #
- #CFLAGS = -g -Wall -pedantic
--CFLAGS = -O
-+CFLAGS ?= -O
- #CFLAGS = -g
- #CFLAGS = -TARG:exc_max -64 -Ofast=ip27   #specific SGI Origin200  compiler#
- 

diff --git a/sci-biology/recon/recon-1.06-r1.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild
deleted file mode 100644
index 86e820f49e..0000000000
--- a/sci-biology/recon/recon-1.06-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit eutils
-
-DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
-SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/RECON${PV}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-buffer-overflow.patch
-	sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_install() {
-	dobin scripts/*
-	exeinto /usr/libexec/${PN}
-	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
-	dodoc 00README
-	insinto /usr/share/${PN}
-	use examples && doins -r Demos
-}

diff --git a/sci-biology/recon/recon-1.06-r2.ebuild b/sci-biology/recon/recon-1.06-r2.ebuild
deleted file mode 100644
index 12a9207c9f..0000000000
--- a/sci-biology/recon/recon-1.06-r2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="4"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
-SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/RECON${PV}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-buffer-overflow.patch \
-		"${FILESDIR}"/${P}-respect.patch
-	sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
-	tc-export CC
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_install() {
-	dobin scripts/*
-	exeinto /usr/libexec/${PN}
-	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
-	dodoc 00README
-	insinto /usr/share/${PN}
-	use examples && doins -r Demos
-}