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)

7 files changed, 104 insertions, 104 deletions

diff --git a/sci-chemistry/molden/ChangeLog b/sci-chemistry/molden/ChangeLog
index 07ab84ae6da4..dda69226ab63 100644
--- a/sci-chemistry/molden/ChangeLog
+++ b/sci-chemistry/molden/ChangeLog
@@ -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@gentoo.org> -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@gentoo.org> molden-4.7.ebuild,
   molden-4.7-r1.ebuild, molden-4.8.ebuild, molden-4.8-r1.ebuild:
diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch
index 811664d4923b..7cbd7f436f57 100644
--- a/sci-chemistry/molden/files/molden-4.8-overflow.patch
+++ b/sci-chemistry/molden/files/molden-4.8-overflow.patch
@@ -1,7 +1,33 @@
-diff -Naur molden4.8/xwin.c molden4.8.new//xwin.c
---- molden4.8/xwin.c	2010-02-01 08:04:08.000000000 -0500
-+++ molden4.8.new//xwin.c	2010-02-26 00:03:36.000000000 -0500
-@@ -27353,7 +27353,7 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -13552,7 +13552,7 @@ void NewActiveStruct()
+ #ifdef CRAY
+     _fcd ztr;
+ #else
+-    char ztr;
++    char ztr[4];
+ #endif
+ #endif
+ 
+@@ -13650,8 +13650,10 @@ void NewActiveStruct()
+ */
+ 	clfpstr->ihashz = 0;
+ #else
+-	strncpy(&ztr,HetAtm[j],3);
+-	parhet_(&j1,&ztr);
++	if (HetAtm[j] != NULL) {
++	   strncpy(ztr,HetAtm[j],3);
++	   parhet_(&j1,ztr);
++	}
+ #endif
+ #endif
+     }
+@@ -27353,7 +27355,7 @@ char *errstr;
  	UpdateZME();
  	RedrawScroll(&zscroll);
      }
diff --git a/sci-chemistry/molden/files/molden-5.0-ambfor.patch b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
new file mode 100644
index 000000000000..9656ff7a79be
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
@@ -0,0 +1,16 @@
+ ambfor/makefile |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ambfor/makefile b/ambfor/makefile
+index 8627a11..dbc23a1 100644
+--- a/ambfor/makefile
++++ b/ambfor/makefile
+@@ -47,7 +47,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(OBJS)
+ 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
+ 
+ ambfor.o:	ambfor.f
+-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
++	${FC} $(FFLAGS) -c -o ambfor.o ambfor.f
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml
index 9ac9ffdb3a41..e42d0af60f42 100644
--- a/sci-chemistry/molden/metadata.xml
+++ b/sci-chemistry/molden/metadata.xml
@@ -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>
diff --git a/sci-chemistry/molden/molden-4.8-r1.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild
index 3981bb455aee..4935980f2615 100644
--- a/sci-chemistry/molden/molden-4.8-r1.ebuild
+++ b/sci-chemistry/molden/molden-4.8-r2.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-r1.ebuild,v 1.6 2011/06/21 16:03:06 jlec Exp $
+# $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="3"
+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."
+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"
 
@@ -19,7 +19,6 @@ IUSE="opengl"
 
 RDEPEND="
 	virtual/fortran
-
 	x11-libs/libXmu
 	opengl? (
 		media-libs/freeglut
@@ -36,7 +35,11 @@ src_prepare() {
 		"${FILESDIR}"/${P}-overflow.patch \
 		"${FILESDIR}"/${P}-ldflags.patch \
 		"${FILESDIR}"/${PN}-4.7-implicit-dec.patch
-	sed 's:makedepend:gccmakedep:g' -i surf/Makefile
+	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() {
@@ -47,24 +50,27 @@ src_compile() {
 	# 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}" )
+	args=(
+			CC="$(tc-getCC) ${CFLAGS}" \
+			FC="$(tc-getFC)" \
+			LDR="$(tc-getFC)" \
+			FFLAGS="${FFLAGS}" )
 
 	einfo "Building Molden..."
-	emake -j1 "${args[@]}" || die "molden emake failed"
+	emake -j1 "${args[@]}"
 	if use opengl ; then
 		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" moldenogl || die "moldenogl emake failed"
+		emake -j1 "${args[@]}" moldenogl
 	fi
 }
 
 src_install() {
-	dobin ${PN} g${PN} || die "failed to install molden executable."
+	dobin ${PN} g${PN}
 	if use opengl ; then
-		dobin ${PN}ogl || die "failed to install moldenogl."
+		dobin ${PN}ogl
 	fi
 
-	dodoc HISTORY README REGISTER || die "failed to install docs."
+	dodoc HISTORY README REGISTER
 	cd doc
-	uncompress * && dodoc * || die "failed to install docs."
+	uncompress * && dodoc *
 }
diff --git a/sci-chemistry/molden/molden-4.8.ebuild b/sci-chemistry/molden/molden-4.8.ebuild
deleted file mode 100644
index 00968699b1e7..000000000000
--- a/sci-chemistry/molden/molden-4.8.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-4.8.ebuild,v 1.5 2011/06/21 16:03:06 jlec Exp $
-
-EAPI="2"
-
-inherit eutils fortran-2 toolchain-funcs flag-o-matic
-
-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
-	opengl? ( media-libs/freeglut
-	virtual/opengl )
-	x11-libs/libXmu"
-DEPEND="${RDEPEND}
-	app-editors/vim"
-	# vim provides ex, which the build system uses (surf/Makefile, at least)
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-ambfor.patch \
-		"${FILESDIR}"/${P}-overflow.patch \
-		"${FILESDIR}"/${P}-ldflags.patch
-}
-
-src_compile() {
-	# Use -mieee on alpha, according to the Makefile
-	use alpha && append-flags -mieee
-
-	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
-	# unfortunately a bash bug prevents us from doing typeset and
-	# assignment on the same line.
-	typeset -a args
-	args=( CC="$(tc-getCC) ${CFLAGS}" \
-		FC="$(tc-getFC)" LDR="$(tc-getFC)" FFLAGS="${FFLAGS}" )
-
-	einfo "Building Molden..."
-	emake -j1 "${args[@]}" || die "molden emake failed"
-	if use opengl ; then
-		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" moldenogl || die "moldenogl emake failed"
-	fi
-}
-
-src_install() {
-	dobin molden || die "failed to install molden executable."
-	if use opengl ; then
-		dobin moldenogl || die "failed to install moldenogl."
-	fi
-
-	dodoc HISTORY README REGISTER || die "failed to install docs."
-	cd doc
-	uncompress * && dodoc * || die "failed to install docs."
-}
diff --git a/sci-chemistry/molden/molden-4.7-r1.ebuild b/sci-chemistry/molden/molden-5.0.ebuild
index 801ebe8d5ad5..d8064afec832 100644
--- a/sci-chemistry/molden/molden-4.7-r1.ebuild
+++ b/sci-chemistry/molden/molden-5.0.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2011 Gentoo Foundation
+# 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-4.7-r1.ebuild,v 1.6 2011/06/21 16:03:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-5.0.ebuild,v 1.1 2012/06/23 11:21:23 jlec Exp $
 
-EAPI="3"
+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."
+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"
 
@@ -19,7 +19,6 @@ IUSE="opengl"
 
 RDEPEND="
 	virtual/fortran
-
 	x11-libs/libXmu
 	opengl? (
 		media-libs/freeglut
@@ -32,10 +31,16 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-glibc-2.11.patch \
-		"${FILESDIR}"/${P}-ldflags.patch \
-		"${FILESDIR}"/${P}-implicit-dec.patch
-	sed 's:makedepend:gccmakedep:g' -i surf/Makefile
+	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() {
@@ -46,24 +51,27 @@ src_compile() {
 	# 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) ${LDFLAGS}" FFLAGS="${FFLAGS}" )
+	args=(
+			CC="$(tc-getCC) ${CFLAGS}" \
+			FC="$(tc-getFC)" \
+			LDR="$(tc-getFC)" \
+			FFLAGS="${FFLAGS}" )
 
 	einfo "Building Molden..."
-	emake -j1 "${args[@]}" || die "molden emake failed"
+	emake -j1 "${args[@]}"
 	if use opengl ; then
 		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" moldenogl || die "moldenogl emake failed"
+		emake -j1 "${args[@]}" moldenogl
 	fi
 }
 
 src_install() {
-	dobin ${PN} g${PN} || die "failed to install molden executable."
+	dobin ${PN} g${PN}
 	if use opengl ; then
-		dobin ${PN}ogl || die "failed to install moldenogl."
+		dobin ${PN}ogl
 	fi
 
-	dodoc HISTORY README REGISTER || die "failed to install docs."
+	dodoc HISTORY README REGISTER
 	cd doc
-	uncompress * && dodoc * || die "failed to install docs."
+	uncompress * && dodoc *
 }