Drop old; fix for format-security; drop broken doc generation, bug #461000

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 39 insertions, 69 deletions

diff --git a/sci-biology/eugene/ChangeLog b/sci-biology/eugene/ChangeLog
index 2d7b7d457766..9cf22a2cce9a 100644
--- a/sci-biology/eugene/ChangeLog
+++ b/sci-biology/eugene/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/eugene
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.10 2013/03/09 19:24:44 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.11 2015/03/20 16:38:39 jlec Exp $
+
+  20 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/eugene-4.1-format-security.patch, -eugene-3.5g.ebuild,
+  eugene-3.6-r1.ebuild, eugene-4.1.ebuild:
+  Drop old; fix for format-security; drop broken doc generation, bug #461000
 
 *eugene-4.1 (09 Mar 2013)
 
@@ -44,4 +49,3 @@
 
   04 Jan 2009; weaver <weaver@gentoo.org> +eugene-3.5d.ebuild:
   Initial commit, ebuild written by me
-
diff --git a/sci-biology/eugene/eugene-3.5g.ebuild b/sci-biology/eugene/eugene-3.5g.ebuild
deleted file mode 100644
index 82e3a98f4d07..000000000000
--- a/sci-biology/eugene/eugene-3.5g.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.5g.ebuild,v 1.2 2009/10/31 17:58:24 maekke Exp $
-
-EAPI=2
-
-inherit autotools
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-# self-signed https SRC_URI
-#SRC_URI="http://mulcyber.toulouse.inra.fr/gf/download/frsrelease/220/3675/${P}-1.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-RESTRICT="test"
-
-DEPEND="media-libs/gd[png]
-	media-libs/libpng
-	doc? ( dev-lang/tcl
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexrecommended
-		dev-texlive/texlive-latexextra
-		)"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	if ( ! use doc ); then
-		sed -i -e '/SUBDIRS/ s/doc//' \
-			-e '/INSTALL.*doc/ s/\(.*\)//' \
-			Makefile.am || die
-		eautoreconf
-	fi
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-}
diff --git a/sci-biology/eugene/eugene-3.6-r1.ebuild b/sci-biology/eugene/eugene-3.6-r1.ebuild
index 088f0bb3b39e..702b1c551d6d 100644
--- a/sci-biology/eugene/eugene-3.6-r1.ebuild
+++ b/sci-biology/eugene/eugene-3.6-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.4 2011/02/11 19:51:04 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.5 2015/03/20 16:38:39 jlec Exp $
 
 EAPI=2
 
@@ -20,8 +20,8 @@ KEYWORDS="amd64 x86"
 RESTRICT="test"
 
 DEPEND="media-libs/gd[png]
-	media-libs/libpng
-	doc? ( dev-lang/tcl
+	media-libs/libpng:0
+	doc? ( dev-lang/tcl:0
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexrecommended
 		dev-texlive/texlive-latexextra
diff --git a/sci-biology/eugene/eugene-4.1.ebuild b/sci-biology/eugene/eugene-4.1.ebuild
index 15a663c1e63f..acbcbf4a1cd8 100644
--- a/sci-biology/eugene/eugene-4.1.ebuild
+++ b/sci-biology/eugene/eugene-4.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-4.1.ebuild,v 1.1 2013/03/09 19:24:45 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-4.1.ebuild,v 1.2 2015/03/20 16:38:39 jlec Exp $
 
 EAPI=5
 
@@ -12,17 +12,13 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1157/${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE="doc"
 KEYWORDS="~amd64 ~x86"
+IUSE=""
 
 DEPEND="
 	media-libs/gd[png]
-	media-libs/libpng
-	doc? ( dev-lang/tcl
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexrecommended
-		dev-texlive/texlive-latexextra
-		)"
+	media-libs/libpng:0=
+	"
 RDEPEND="${DEPEND}"
 
 RESTRICT="test"
@@ -31,15 +27,11 @@ src_prepare() {
 	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
 	epatch \
 		"${FILESDIR}"/${PN}-3.6-overflow.patch \
-		"${FILESDIR}"/${PN}-3.6-plugins.patch
-	if ( ! use doc ); then
-		sed -i -e '/SUBDIRS/ s/doc//' \
-			-e '/INSTALL.*doc/ s/\(.*\)//' \
-			Makefile.am || die
-		eautoreconf
-	fi
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
+		"${FILESDIR}"/${PN}-3.6-plugins.patch \
+		"${FILESDIR}"/${P}-format-security.patch
+	sed \
+		-e '/SUBDIRS/ s/doc//' \
+		-e '/INSTALL.*doc/ s/\(.*\)//' \
+		-i Makefile.am || die
+	eautoreconf
 }
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
new file mode 100644
index 000000000000..e6e4a6cc8bd7
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch
@@ -0,0 +1,16 @@
+ src/Hits.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Hits.cc b/src/Hits.cc
+index edfe178..b228be6 100755
+--- a/src/Hits.cc
++++ b/src/Hits.cc
+@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
+     while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
+                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
+     {
+-        if (HSP) fprintf(stderr,HSP);
++        if (HSP) fprintf(stderr, "%s", HSP);
+         if (phase < 0  &&  deb > fin)
+         {
+             int tmp = deb;