From 9ee84fa74a5bc48850d98dd49edbe223e8085e5a Mon Sep 17 00:00:00 2001
From: cel <cel.gentoo@gmail.com>
Date: Thu, 26 Sep 2013 21:35:23 +0200
Subject: sci-biology/bowtie: fixed check for sse2 support.

---
 sci-biology/bowtie/Manifest            |  2 +-
 sci-biology/bowtie/bowtie-2.1.0.ebuild | 21 ++++++++-------------
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index a441c96d8..9321813d2 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,4 +1,4 @@
 AUX bowtie-2.1.0-buildsystem.patch 734 SHA256 8cc4d242c2b61a34503bc5f82a8baaa16c50b743751162060cefb9a3a3234587 SHA512 1d1f61e331874acb9503c4002c45b49f58145b3d7fb0e03245029e88f2783eb0ba01a6b47c1238d7c6fb82e9a3d7e103808f957151d79208b889f4a212d424f8 WHIRLPOOL e53d25c40781cb8eaffbd6990e2da6aaf44f56cf96caea7d89db17db55a48546f5308d682593a24b3a421a97d830dd21c047da9eb82138da29e1a7318319f2ab
 DIST bowtie-2.1.0-source.zip 5697131 SHA256 90a9d3a6bd19ddc3a8f90b935c6a2288478572de2ad4039b29f91016b95ef4b0 SHA512 47535c0539674d81dfac16bf0f0730c766afce93fa91bef7eb4f73df2b73fb7988bc344495a909f81374a60ec79117b141442ff13a61af96fe4043dc0e47cc7c WHIRLPOOL fca873eb10c514c22e2aa46cce685050234c9d2838b7a66c6d5648425b980d93a627c187f26af16e74c6b70e8addb8c267dab5af68023b65591f8ad2616344fa
-EBUILD bowtie-2.1.0.ebuild 1213 SHA256 f9755689df887af0c63c3821dbdf22a737f1d3b0519f28700f2643b52b7b7297 SHA512 5f05a0417e9be44afbf7936d60c8312abe9494a55fc7cac82c5a09c8a6cd2de99d2a615db7aac4d4e81c4f4f7180fe34dabd950d623ddbfe4aa107aeecbf48c3 WHIRLPOOL 4377327390df0633335738ad15b643660d4244bbd4638b46f8f90450ae0c59d4f227b60adf44c0c33954752e56cb61763fdce073b726d7b66f80446f9fe1da7f
+EBUILD bowtie-2.1.0.ebuild 1133 SHA256 6a54b6e1b2ac2437fc29bc5e7813312601e176d1786ce607e03e906d54d9ffb5 SHA512 e93d3d51fafb4f39e50a8abf883fa0c6c2df9947a41acf19a69d9cf7432bb411da232545f54925781a7457dec5ca4529bc45a441f188799ec02bc04e66a88f56 WHIRLPOOL cd45fe7e3106861db6e7f0afff34392f13d4c88b2ba7a435f4100e0ad46e13f885514d5c4cf94cbd3d94329bfb4a600314d44b1b2c68bf1955b64ba17a3268f4
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild
index c2c502442..26bf770ca 100644
--- a/sci-biology/bowtie/bowtie-2.1.0.ebuild
+++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit eutils flag-o-matic toolchain-funcs
+inherit eutils toolchain-funcs
 
 DESCRIPTION="An ultrafast memory-efficient short read aligner"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/"
@@ -12,23 +12,19 @@ SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
 
 LICENSE="GPL-3"
 SLOT="2"
-IUSE="sse2 examples"
+IUSE="examples"
 KEYWORDS="~amd64 ~x86"
 
-CDEPEND="dev-lang/perl"
-DEPEND="${CDEPEND} \
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}
 		app-arch/unzip"
-RDEPEND="${CDEPEND}"
 
 S="${WORKDIR}/${PN}2-${PV}"
 
 pkg_pretend() {
-	if ! use sse2 ; then
-		ebegin
-		eerror "bowtie2 requires sse2 support. Please make sure your system supports"
-		eerror "sse2 and enable the sse2 use flag."
-		eend
-		die
+	grep "sse2" /proc/cpuinfo > /dev/null
+	if [[ $? -ne 0 ]] ; then
+		ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine."
 	fi
 }
 
@@ -37,12 +33,11 @@ src_prepare() {
 }
 
 src_compile() {
-	use sse2 && append-cxxflags -msse2
 	emake \
 		CC="$(tc-getCC)" \
 		CPP="$(tc-getCXX)" \
 		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS}"
+		RELEASE_FLAGS="${CXXFLAGS} -msse2"
 }
 
 src_install() {
-- 
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