diff options
Diffstat (limited to 'sci-biology/eugene')
| -rw-r--r-- | sci-biology/eugene/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/eugene/eugene-3.6-r1.ebuild (renamed from sci-biology/eugene/eugene-3.6.ebuild) | 7 | ||||
| -rw-r--r-- | sci-biology/eugene/files/eugene-3.6-overflow.patch | 13 | ||||
| -rw-r--r-- | sci-biology/eugene/files/eugene-3.6-plugins.patch | 43 |
4 files changed, 70 insertions, 3 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/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 |