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, 109 insertions, 0 deletions

diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest
new file mode 100644
index 000000000000..ec521a7104b3
--- /dev/null
+++ b/sci-biology/iqpnni/Manifest
@@ -0,0 +1,3 @@
+DIST iqpnni-3.2.tar.gz 638743 SHA256 0e97a03841e3460b9e0ddadbfa27393bf370ff82725a620c8d46a1ce85e4a20f
+DIST iqpnni-3.3.1.tar.gz 650395 SHA256 bdc5873c5dd59b07b8f8c9547e86120b53fa3cd802ec7acdad61bacc4c3ac7d9
+DIST iqpnni-3.3.2.tar.gz 646603 SHA256 e4ffc783c7444bfadd40c9d55e9fb0275fcf7dca80aa3217768c9bf63c28567f
diff --git a/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch
new file mode 100644
index 000000000000..c4f49284abc1
--- /dev/null
+++ b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch
@@ -0,0 +1,13 @@
+diff -rc iqpnni-3.3.1-orig/src/constant.h iqpnni-3.3.1/src/constant.h
+*** iqpnni-3.3.1-orig/src/constant.h	2009-01-04 19:33:35.000000000 -0500
+--- iqpnni-3.3.1/src/constant.h	2009-01-04 19:40:21.000000000 -0500
+***************
+*** 36,41 ****
+--- 36,42 ----
+  #include <stdio.h>
+  #include <math.h>
+  #include <string>
++ #include <string.h>
+  
+  using namespace std;
+  
diff --git a/sci-biology/iqpnni/iqpnni-3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.2.ebuild
new file mode 100644
index 000000000000..070e962fb311
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install() {
+	dobin src/iqpnni
+
+	dodoc ChangeLog AUTHORS README NEWS TODO
+	if use doc ; then
+		dohtml manual/iqpnni-manual.html
+		insinto /usr/share/doc/${P}
+		doins manual/iqpnni-manual.pdf
+	fi
+}
diff --git a/sci-biology/iqpnni/iqpnni-3.3.1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild
new file mode 100644
index 000000000000..8916e7e51608
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_install() {
+	dobin src/iqpnni
+
+	dodoc ChangeLog AUTHORS README NEWS TODO
+	if use doc ; then
+		dohtml manual/iqpnni-manual.html
+		insinto /usr/share/doc/${P}
+		doins manual/iqpnni-manual.pdf
+	fi
+}
diff --git a/sci-biology/iqpnni/iqpnni-3.3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild
new file mode 100644
index 000000000000..e9939ef0f506
--- /dev/null
+++ b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+DESCRIPTION="Important Quartet Puzzling and NNI Operation"
+HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
+SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install() {
+	dobin src/iqpnni
+
+	dodoc ChangeLog AUTHORS README NEWS TODO
+	if use doc ; then
+		dohtml manual/iqpnni-manual.html
+		insinto /usr/share/doc/${P}
+		doins manual/iqpnni-manual.pdf
+	fi
+}
diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/iqpnni/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>