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To: gentoo-commits@g.o
From: "Justin Lecher (jlec)" <jlec@g.o>
Subject: gentoo-x86 commit in sci-chemistry/molden: molden-4.8-r2.ebuild ChangeLog molden-5.0.ebuild metadata.xml molden-4.8-r1.ebuild molden-4.8.ebuild molden-4.7-r1.ebuild
Date: Sat, 23 Jun 2012 11:21:23 +0000 (UTC)
jlec        12/06/23 11:21:23

  Modified:             ChangeLog metadata.xml
  Added:                molden-4.8-r2.ebuild molden-5.0.ebuild
  Removed:              molden-4.8-r1.ebuild molden-4.8.ebuild
                        molden-4.7-r1.ebuild
  Log:
  sci-chemistry/molden: Fix buffer overflow, #342907; Version Bump, #355741; Fix build failures, #358917, #423015; drop old
  
  (Portage version: 2.2.0_alpha111/cvs/Linux x86_64)

Revision  Changes    Path
1.39                 sci-chemistry/molden/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/ChangeLog?rev=1.39&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/ChangeLog?rev=1.39&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/ChangeLog?r1=1.38&r2=1.39

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/molden/ChangeLog,v
retrieving revision 1.38
retrieving revision 1.39
diff -u -r1.38 -r1.39
--- ChangeLog	21 Jun 2011 16:03:06 -0000	1.38
+++ ChangeLog	23 Jun 2012 11:21:23 -0000	1.39
@@ -1,6 +1,16 @@
 # ChangeLog for sci-chemistry/molden
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/ChangeLog,v 1.38 2011/06/21 16:03:06 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/ChangeLog,v 1.39 2012/06/23 11:21:23 jlec Exp $
+
+*molden-5.0 (23 Jun 2012)
+*molden-4.8-r2 (23 Jun 2012)
+
+  23 Jun 2012; Justin Lecher <jlec@g.o> -molden-4.7-r1.ebuild,
+  -molden-4.8.ebuild, -molden-4.8-r1.ebuild, +molden-4.8-r2.ebuild,
+  files/molden-4.8-overflow.patch, +molden-5.0.ebuild,
+  +files/molden-5.0-ambfor.patch, metadata.xml:
+  Fix buffer overflow, #342907; Version Bump, #355741; Fix build failures,
+  #358917, #423015; drop old
 
   21 Jun 2011; Justin Lecher <jlec@g.o> molden-4.7.ebuild,
   molden-4.7-r1.ebuild, molden-4.8.ebuild, molden-4.8-r1.ebuild:



1.5                  sci-chemistry/molden/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/metadata.xml?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/metadata.xml?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/metadata.xml?r1=1.4&r2=1.5

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/molden/metadata.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- metadata.xml	20 Sep 2006 05:08:59 -0000	1.4
+++ metadata.xml	23 Jun 2012 11:21:23 -0000	1.5
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+	<herd>sci-chemistry</herd>
 </pkgmetadata>



1.1                  sci-chemistry/molden/molden-4.8-r2.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/molden-4.8-r2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/molden-4.8-r2.ebuild?rev=1.1&content-type=text/plain

Index: molden-4.8-r2.ebuild
===================================================================
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-4.8-r2.ebuild,v 1.1 2012/06/23 11:21:23 jlec Exp $

EAPI=4

inherit eutils fortran-2 flag-o-matic toolchain-funcs

MY_P="${PN}${PV}"

DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"

LICENSE="as-is"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ia64 ~x86"
IUSE="opengl"

RDEPEND="
	virtual/fortran
	x11-libs/libXmu
	opengl? (
		media-libs/freeglut
		virtual/opengl )"
DEPEND="${RDEPEND}
	x11-misc/gccmakedep
	app-editors/vim"
	# vim provides ex, which the build system uses (surf/Makefile, at least)

S="${WORKDIR}/${MY_P}"

src_prepare() {
	epatch "${FILESDIR}"/${P}-ambfor.patch \
		"${FILESDIR}"/${P}-overflow.patch \
		"${FILESDIR}"/${P}-ldflags.patch \
		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
	sed \
		-e 's:makedepend:gccmakedep:g' \
		-e "s:/usr/include/sgidefs.h::g" \
		-i surf/Makefile || die
	sed 's:shell g77:shell $(FC):g' -i makefile || die
}

src_compile() {
	# Use -mieee on alpha, according to the Makefile
	use alpha && append-flags -mieee

	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
	# unfortunately a bash bug prevents us from doing typeset and
	# assignment on the same line.
	typeset -a args
	args=(
			CC="$(tc-getCC) ${CFLAGS}" \
			FC="$(tc-getFC)" \
			LDR="$(tc-getFC)" \
			FFLAGS="${FFLAGS}" )

	einfo "Building Molden..."
	emake -j1 "${args[@]}"
	if use opengl ; then
		einfo "Building Molden OpenGL helper..."
		emake -j1 "${args[@]}" moldenogl
	fi
}

src_install() {
	dobin ${PN} g${PN}
	if use opengl ; then
		dobin ${PN}ogl
	fi

	dodoc HISTORY README REGISTER
	cd doc
	uncompress * && dodoc *
}



1.1                  sci-chemistry/molden/molden-5.0.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/molden-5.0.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/molden-5.0.ebuild?rev=1.1&content-type=text/plain

Index: molden-5.0.ebuild
===================================================================
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-5.0.ebuild,v 1.1 2012/06/23 11:21:23 jlec Exp $

EAPI=4

inherit eutils fortran-2 flag-o-matic toolchain-funcs

MY_P="${PN}${PV}"

DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"

LICENSE="as-is"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ia64 ~x86"
IUSE="opengl"

RDEPEND="
	virtual/fortran
	x11-libs/libXmu
	opengl? (
		media-libs/freeglut
		virtual/opengl )"
DEPEND="${RDEPEND}
	x11-misc/gccmakedep
	app-editors/vim"
	# vim provides ex, which the build system uses (surf/Makefile, at least)

S="${WORKDIR}/${MY_P}"

src_prepare() {
	epatch \
		"${FILESDIR}"/${P}-ambfor.patch \
		"${FILESDIR}"/${PN}-4.8-overflow.patch \
		"${FILESDIR}"/${PN}-4.8-ldflags.patch \
		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
	sed \
		-e 's:makedepend:gccmakedep:g' \
		-e "s:/usr/include/sgidefs.h::g" \
		-i surf/Makefile || die
	sed 's:shell g77:shell $(FC):g' -i makefile || die
}

src_compile() {
	# Use -mieee on alpha, according to the Makefile
	use alpha && append-flags -mieee

	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
	# unfortunately a bash bug prevents us from doing typeset and
	# assignment on the same line.
	typeset -a args
	args=(
			CC="$(tc-getCC) ${CFLAGS}" \
			FC="$(tc-getFC)" \
			LDR="$(tc-getFC)" \
			FFLAGS="${FFLAGS}" )

	einfo "Building Molden..."
	emake -j1 "${args[@]}"
	if use opengl ; then
		einfo "Building Molden OpenGL helper..."
		emake -j1 "${args[@]}" moldenogl
	fi
}

src_install() {
	dobin ${PN} g${PN}
	if use opengl ; then
		dobin ${PN}ogl
	fi

	dodoc HISTORY README REGISTER
	cd doc
	uncompress * && dodoc *
}





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Updated Jun 26, 2012

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