Fix overflows wrt bug 336604 and install path wrt bug 297536. Thanks to Diego for the reports.

Package-Manager: portage-2.1.9/cvs/Linux x86_64

5 files changed, 86 insertions, 5 deletions

diff --git a/sci-biology/eugene/ChangeLog b/sci-biology/eugene/ChangeLog
index 87f2b44aaaf4..b847330dd4ac 100644
--- a/sci-biology/eugene/ChangeLog
+++ b/sci-biology/eugene/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/eugene
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.5 2010/05/07 19:31:27 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.6 2010/09/10 16:37:04 xarthisius Exp $
+
+*eugene-3.6-r1 (10 Sep 2010)
+
+  10 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -eugene-3.6.ebuild,
+  +eugene-3.6-r1.ebuild, +files/eugene-3.6-overflow.patch,
+  +files/eugene-3.6-plugins.patch:
+  Fix overflows wrt bug 336604 and install path wrt bug 297536. Thanks to
+  Diego for the reports.
 
 *eugene-3.6 (07 May 2010)
 
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index 1f7533675068..feb4847ef9e1 100644
--- a/sci-biology/eugene/Manifest
+++ b/sci-biology/eugene/Manifest
@@ -1,6 +1,20 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX eugene-3.6-overflow.patch 252 RMD160 7fc29f8e454ade0a9df101a57d8958599ba456f3 SHA1 9e6cf67741f09c2bff73c3201b0baec0a749ee05 SHA256 cc8795d5f4525a299bc3e17da1e26c1e5fe3ef0c2371c5bf9de36b5037972fc7
+AUX eugene-3.6-plugins.patch 1784 RMD160 750e439ac0b42659bb333882123e6e43a3f6f4f8 SHA1 b906b029f4892cd8686894877905be6c804b3709 SHA256 0ec9c0d2bf6009e89612c3d95711b211aefc267d3eb6b75bc6279318256bc46d
 DIST eugene-3.5g.tar.gz 5439002 RMD160 30ea0a7862e2d8c4a52a2526d00e1e5002fec244 SHA1 d8575c499f70db83782ace40e6f7412410c35a4d SHA256 7837619bcd03b89123e4a03c43fa74060251d98f7bc503de0d92ba78e9efefac
 DIST eugene-3.6.tar.gz 5589654 RMD160 337c492ab0b407cf0c80238d5a04f3816f982536 SHA1 7cb66bcf64b0f532f38b666bd6a03ed17c512986 SHA256 731757d65f182e2eb2a18ee1fb2e710519a705aa91ef268136053698e07cb227
 EBUILD eugene-3.5g.ebuild 967 RMD160 c4e15d607702d93cdd4c6b9738bc33145a2c16a2 SHA1 6824a87444222b550d6f345e9d10c61abd802ad3 SHA256 2dfb0351ce49e4078d985228461082ed2504baf72cf0260bbf8ed45a5f3a3a78
-EBUILD eugene-3.6.ebuild 968 RMD160 db4246b642257536993261135ff272ba38dfe41d SHA1 498180836047a54278f4410cc0b3279e735d0cd8 SHA256 a5395cdef21a29ba9951c07c8d11786af5ed9f55352392fbc9c13781fee4c22b
-MISC ChangeLog 831 RMD160 e8470ad461f0ef922e029e46ebc2aa58b34bf4d7 SHA1 2f0f8d383dc6f0468009adb698d58285122ec83f SHA256 1f6159083bfae632f34799d876673993e744241127a536c6858f1200d7e98344
+EBUILD eugene-3.6-r1.ebuild 1138 RMD160 61b06d807fc4efac12faaae0f2f50be11d05fdc8 SHA1 9736f06c816f02eca3f63c1df0b393dd89bdb101 SHA256 7bedb6e666ce80a4be65e79f59a6cf802d960b1f8f27e1a88a8284d02416a87f
+MISC ChangeLog 1133 RMD160 a9eac238d39ac7e93c839d9d87c6783ce7419ba1 SHA1 83625b621eb8c0ac9a36f883f5df1211426a819b SHA256 b3e9d03f65f16d89e8820bb94a2b2171568ed57f65fe6ba5cd8d40453d7ad1a5
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iJwEAQECAAYFAkyKXroACgkQIiMqcbOVdxR/VwP/RJ97vG7AsyYrUARVnPPD+4sW
+l1KBhpguTclAm6S4m2cakWqUe0qflYbyDm/mSGKI/SU+3wUtaZd4wQjlgSmxJt8A
+11FZ+Y3lfa3KCJyVWOK4yOTtTlCp10yo18AqPr5lssAgzrnWoTgLoKzrv8YE/9Bb
+DnHe3CFAIhyVIqeYYCs=
+=Hxi/
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/eugene/eugene-3.6.ebuild b/sci-biology/eugene/eugene-3.6-r1.ebuild
index 95144de428a1..96f148007bc5 100644
--- a/sci-biology/eugene/eugene-3.6.ebuild
+++ b/sci-biology/eugene/eugene-3.6-r1.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6.ebuild,v 1.1 2010/05/07 19:31:27 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.1 2010/09/10 16:37:04 xarthisius Exp $
 
 EAPI=2
 
-inherit autotools
+inherit autotools eutils
 
 DESCRIPTION="Eukaryotic gene predictor"
 HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
@@ -29,6 +29,9 @@ DEPEND="media-libs/gd[png]
 RDEPEND="${DEPEND}"
 
 src_prepare() {
+	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 
+	epatch "${FILESDIR}"/${P}-overflow.patch \
+		"${FILESDIR}"/${P}-plugins.patch
 	if ( ! use doc ); then
 		sed -i -e '/SUBDIRS/ s/doc//' \
 			-e '/INSTALL.*doc/ s/\(.*\)//' \
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
new file mode 100644
index 000000000000..7222530ad771
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-overflow.patch
@@ -0,0 +1,13 @@
+http://bugs.gentoo.org/show_bug.cgi?id=336607
+
+--- eugene-3.6/src/Sensor.cc
++++ eugene-3.6/src/Sensor.cc
+@@ -224,7 +224,7 @@
+ //--------------------------
+ void Signals :: PrintS ()
+ {
+-  char t[7];
++  char t[10];
+   char s = '+';
+ 
+   switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
new file mode 100644
index 000000000000..1e910a13d5b1
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch
@@ -0,0 +1,43 @@
+http://bugs.gentoo.org/show_bug.cgi?id=297536
+
+--- eugene-3.6/src/Makefile.am
++++ eugene-3.6/src/Makefile.am
+@@ -20,7 +20,7 @@
+ 
+ SUBDIRS = Parametrization GDIF . SensorPlugins
+ 
+-AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
++AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
+ AM_CFLAGS = 
+ 
+ bin_PROGRAMS = eugene
+--- eugene-3.6/src/MSensor.cc
++++ eugene-3.6/src/MSensor.cc
+@@ -97,7 +97,7 @@
+   std::string use_name;
+ 
+   if (!IsInitialized) {
+-    PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
++    PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
+ 
+     // On récupère les couples nom de sensor/priorité du .par
+     PAR.ResetIter();
+--- eugene-3.6/Makefile.am
++++ eugene-3.6/Makefile.am
+@@ -125,7 +125,7 @@
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
+-	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
++	$(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
+@@ -144,6 +144,6 @@
+ 	$(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
+ 	$(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
+ 	$(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
+-	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(pkgdatadir)/plugins
++	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(libdir)/eugene/plugins
+ 	$(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
+ 	$(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get