From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001
From: "Robin H. Johnson" <robbat2@gentoo.org>
Date: Sat, 8 Aug 2015 13:49:04 -0700
Subject: proj/gentoo: Initial commit
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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
---
 sci-biology/blossoc/Manifest                       |  1 +
 sci-biology/blossoc/blossoc-1.4.0.ebuild           | 31 ++++++++++++++++++++++
 .../blossoc/files/blossoc-1.4.0-gcc43.patch        | 15 +++++++++++
 sci-biology/blossoc/metadata.xml                   |  5 ++++
 4 files changed, 52 insertions(+)
 create mode 100644 sci-biology/blossoc/Manifest
 create mode 100644 sci-biology/blossoc/blossoc-1.4.0.ebuild
 create mode 100644 sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
 create mode 100644 sci-biology/blossoc/metadata.xml

(limited to 'sci-biology/blossoc')

diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
new file mode 100644
index 000000000000..96859ca6bf5f
--- /dev/null
+++ b/sci-biology/blossoc/Manifest
@@ -0,0 +1 @@
+DIST blossoc-1.4.0.tar.gz 194885 SHA256 b23f51349f72f31263b8aca162c7590a5f52b72fd5e0d91b4a2591098ff5bdbe
diff --git a/sci-biology/blossoc/blossoc-1.4.0.ebuild b/sci-biology/blossoc/blossoc-1.4.0.ebuild
new file mode 100644
index 000000000000..7e5b6694d395
--- /dev/null
+++ b/sci-biology/blossoc/blossoc-1.4.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit autotools eutils
+
+DESCRIPTION="A linkage disequilibrium association mapping tool"
+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/"
+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="sci-libs/gsl
+	dev-libs/boost
+	sci-biology/snpfile"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	sed -i '/TESTS += first_test.sh/ d' "${S}/Makefile.am" || die
+	epatch "${FILESDIR}"/${P}-gcc43.patch
+	eautoreconf
+}
+
+src_install() {
+	emake install DESTDIR="${D}" || die "emake install failed"
+}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
new file mode 100644
index 000000000000..d8e354c1745f
--- /dev/null
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
@@ -0,0 +1,15 @@
+Fixes build with >=GCC-4.3
+
+http://bugs.gentoo.org/show_bug.cgi?id=292949
+
+Patch written by Sebastian Luther <SebastianLuther@gmx.de>
+--- pph.cc
++++ pph.cc
+@@ -23,6 +23,7 @@
+  */
+ 
+ #include "pph.hh"
++#include <cstdio>
+ #include <cmath>
+ #include <snpfile/matrix.hh>
+ using namespace BiRC::SNPFile;
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/blossoc/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>
-- 
cgit v1.2.3-65-gdbad