proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 118 insertions, 0 deletions

diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
new file mode 100644
index 000000000000..d779bd4735c4
--- /dev/null
+++ b/sci-biology/recon/Manifest
@@ -0,0 +1 @@
+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
new file mode 100644
index 000000000000..29d220c7310d
--- /dev/null
+++ b/sci-biology/recon/files/1.06-buffer-overflow.patch
@@ -0,0 +1,13 @@
+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
new file mode 100644
index 000000000000..a02038d84784
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.06-respect.patch
@@ -0,0 +1,24 @@
+ 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/metadata.xml b/sci-biology/recon/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/recon/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/recon/recon-1.06-r1.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild
new file mode 100644
index 000000000000..86e820f49e9f
--- /dev/null
+++ b/sci-biology/recon/recon-1.06-r1.ebuild
@@ -0,0 +1,36 @@
+# 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
new file mode 100644
index 000000000000..12a9207c9f42
--- /dev/null
+++ b/sci-biology/recon/recon-1.06-r2.ebuild
@@ -0,0 +1,39 @@
+# 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
+}