From 61b8654f706e0c48f79a631ee797be9ba5135b2c Mon Sep 17 00:00:00 2001
From: Ted Tanberry <ted.tanberry@gmail.com>
Date: Thu, 24 Dec 2015 21:12:54 +0100
Subject: sci-biology/mcl: Version bump, fix bug 569040 and QA issues.

Package-Manager: portage-2.2.26
---
 sci-biology/mcl/Manifest                           |  1 +
 .../mcl-14.137-qa-implicit-declarations.patch      | 27 ++++++++++++++++
 sci-biology/mcl/mcl-14.137.ebuild                  | 36 ++++++++++++++++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
 create mode 100644 sci-biology/mcl/mcl-14.137.ebuild

diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest
index 88b4aef28107..dcdaee7f54f5 100644
--- a/sci-biology/mcl/Manifest
+++ b/sci-biology/mcl/Manifest
@@ -1,2 +1,3 @@
 DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e
 DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279
+DIST mcl-14-137.tar.gz 3035491 SHA256 b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 WHIRLPOOL 6a4afda86cc91c3ddacb64740f020cec2235e22411430281cde9106fb8399663c7854eb1ba5f477624d825280a7762cf5a3f7c6ec824a784a7e200e92d42a168
diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
new file mode 100644
index 000000000000..df4309874d48
--- /dev/null
+++ b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
@@ -0,0 +1,27 @@
+Fix QA issues related to implicit declarations.
+
+* QA Notice: Package triggers severe warnings which indicate that it
+*            may exhibit random runtime failures.
+* clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration]
+* mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration]
+
+--- mcl-14-137/src/shcl/clmadjust.c
++++ mcl-14-137/src/shcl/clmadjust.c
+@@ -14,6 +14,7 @@
+ #include "report.h"
+ #include "clmadjust.h"
+ 
++#include "util/alloc.h"
+ #include "util/io.h"
+ #include "util/types.h"
+ #include "util/err.h"
+--- mcl-14-137/src/shmcx/mcxi.c
++++ mcl-14-137/src/shmcx/mcxi.c
+@@ -8,6 +8,7 @@
+ */
+ 
+ #include <stdio.h>
++#include <unistd.h>
+ 
+ #include "stack.h"
+ #include "glob.h"
diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild
new file mode 100644
index 000000000000..6912351fd2ed
--- /dev/null
+++ b/sci-biology/mcl/mcl-14.137.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+MY_P="${PN}-${PV/./-}"
+
+DESCRIPTION="A Markov Cluster Algorithm implementation"
+HOMEPAGE="http://micans.org/mcl/"
+SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+blast"
+
+PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch")
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	find \
+		-name Makefile.am \
+		-exec sed \
+			-e '/docdir/d' \
+			-e '/exampledir/s:doc::g' \
+			-i '{}' + || die
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable blast)
+}
-- 
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