sci-biology/eugene: version bump

Package-Manager: portage-2.2.26

6 files changed, 115 insertions, 0 deletions

diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
new file mode 100644
index 000000000..598c64283
--- /dev/null
+++ b/sci-biology/eugene/Manifest
@@ -0,0 +1 @@
+DIST eugene-4.1d.tar.gz 7473965 SHA256 c160e6b4206e6700c866f38fee2c8fd0d69972d51ebc5b4cb7680774a419f4c0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5 WHIRLPOOL 7ab116acd48648673d2cc633bae26908bf8250c5a17b9d5e8719dfd56edcdf716406b80af26a99700d9ec81e625737c57fe16493f670245f21999fef1c6911eb
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild
new file mode 100644
index 000000000..a2fb2818c
--- /dev/null
+++ b/sci-biology/eugene/eugene-4.1d.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils
+
+DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
+HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
+SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+	media-libs/gd[png]
+	media-libs/libpng:0=
+	"
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+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 \
+		"${FILESDIR}"/${PN}-4.1-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-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
new file mode 100644
index 000000000..7222530ad
--- /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 000000000..1e910a13d
--- /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
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 000000000..e6e4a6cc8
--- /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;
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
new file mode 100644
index 000000000..f17a827e3
--- /dev/null
+++ b/sci-biology/eugene/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>