sci-biology/recon: Respect CFLAGS and CC, #432660

Package-Manager: portage-2.2.0_alpha122/cvs/Linux x86_64

4 files changed, 84 insertions, 12 deletions

diff --git a/sci-biology/recon/ChangeLog b/sci-biology/recon/ChangeLog
index 618f3a099331..2117774912a5 100644
--- a/sci-biology/recon/ChangeLog
+++ b/sci-biology/recon/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/recon
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/ChangeLog,v 1.2 2011/03/10 11:12:46 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/ChangeLog,v 1.3 2012/08/26 13:01:44 jlec Exp $
+
+*recon-1.06-r2 (26 Aug 2012)
+
+  26 Aug 2012; Justin Lecher <jlec@gentoo.org> +recon-1.06-r2.ebuild,
+  +files/recon-1.06-respect.patch:
+  Respect CFLAGS and CC, #432660
 
 *recon-1.06-r1 (10 Mar 2011)
 
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index 6a3f92d2c7b0..c94dc2da005f 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1,15 +1,18 @@
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-DIST RECON1.06.tar.gz 109484 RMD160 c232cd052d360625d5d841ff29db75710988bf82 SHA1 a46d564a4a52fbd1b9a686897ffec97020334313 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461
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+AUX recon-1.06-respect.patch 557 SHA256 3ccf34ad288b0fcd3fce60166a4a8e598bd27365e1ba662c0e234e8c38d28ab6 SHA512 672be71a54c553c950a123cfbcc10897a74abfdcacd4d897b115caf838318b7bbffb0f31f5fc5e433c38f5452719390df48265007e0d343a7b9f4323bf62143b WHIRLPOOL 07a4b700a1a7e44fb497325f3d3a7dd68643c1aef3d80543a848ccae6ae1e1db5c30c65fc452018582b0181e77a32c85ed87079ea35e401f5617a0f3bd8b3fc3
+DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec
+EBUILD recon-1.06-r1.ebuild 955 SHA256 3c0d17a1f74da52b58592189eda9e0c9779d746175e473c03356ba0597d2a13d SHA512 8fa49c0444195ceaea622fa226c0ae81725c6f5ca3cf877c62300aa2fc21985cbf4074623d5221f94dc6c9adc8d8d64df6ca426567655f31f8d4a91f354a7519 WHIRLPOOL a4ce1228df22594d1c046f6852480fc423f38f01ac85ed2648c1abd4eb96c83d32d3cd79f689007f99fc8c869f47530f7503c28aa773e4e96fbfe09d8f5108aa
+EBUILD recon-1.06-r2.ebuild 1026 SHA256 370f862b96ed1fe81b9fe93937ec059f856a5c33e3a211ea13875b15d2f9cbd0 SHA512 e4c59988241cbe46573d70618fe127e3ac2be6c755cc4db616175218b5b68820f75bef39698731e7d3368264d26a572979e0765b2c9dc557ceed448a99be73ba WHIRLPOOL 8b48ae7f9a6fdd882dfb4176cce84d54b85935407792e20b30deebb1a5195f475de815dac70962c7f2f50b779a32297ae274f5b6f06b1d8fbea4de661cc8b39a
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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/recon-1.06-r2.ebuild b/sci-biology/recon/recon-1.06-r2.ebuild
new file mode 100644
index 000000000000..797d294eac73
--- /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
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/recon-1.06-r2.ebuild,v 1.1 2012/08/26 13:01:44 jlec Exp $
+
+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
+}