sci-chemistry/molden: Fix buffer overflow, #342907; Version Bump, #355741; Fix build failures, #358917, #423015; drop old

Package-Manager: portage-2.2.0_alpha111/cvs/Linux x86_64

8 files changed, 117 insertions, 115 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/Manifest b/sci-chemistry/molden/Manifest
index 6f934c7a67a9..90d189149139 100644
--- a/sci-chemistry/molden/Manifest
+++ b/sci-chemistry/molden/Manifest
@@ -1,24 +1,26 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX molden-4.7-glibc-2.11.patch 3292 RMD160 ef810cd22e390e695ade68f245a92d4c8872b64e SHA1 0a69273d54a3b36278f5b85aa340b0ff5ad8d0a0 SHA256 26fec65a1fa92a84ef73a0c7e1ff26e99aab0727c0fd176b4b4131340c82d7a1
 AUX molden-4.7-implicit-dec.patch 225 RMD160 43c43699eb91a5904145576e14ceee9e8fab26b4 SHA1 ecf75134f57919dd81852a9e525560cc87756655 SHA256 368b5a83f8fae257a48c43f5d3cb10f5d8aedd345d5fdd7dbf73c99295bebeab
 AUX molden-4.7-ldflags.patch 361 RMD160 fa78eeaecdf012d4b2bf2a31f99cc0cd8fb26285 SHA1 9fccaead5c0a6d459af1d708e39ec1c8102c8a95 SHA256 0c9496c3e1b606db287a6af186b1552e0849d124ab26b93c48363c62af3c781a
 AUX molden-4.8-ambfor.patch 480 RMD160 ac9108f3963d1381250605b934c36e18783f4c3f SHA1 cbd312b49510c6f6c43f2cacaf962ba7dec15963 SHA256 d3b0f3a1ec8fe2b31dc94e1138b4eafd6b5f105ca637ec773a6d37b2c12872b1
 AUX molden-4.8-ldflags.patch 866 RMD160 226851a1dd0a47c2c882c89283f3e46c9e0da132 SHA1 a35609b1b195c466e9516658d1b851823d09c502 SHA256 14346b0f255ac2e7c85321a13112af857c4f55dd5574f007a3a32e61006c947b
-AUX molden-4.8-overflow.patch 334 RMD160 261b98ea733a1f4751781ec473dd9289a9a3369a SHA1 5992cdbe259dc6c867d4d2ebe546d28519344f84 SHA256 b84b5130a7a9f3bf95ec3b5725969c4773e7c0ad35866c2e222d0baaba6e649e
+AUX molden-4.8-overflow.patch 714 RMD160 ae6b24902911b308a0fa29150af39b543837bdd1 SHA1 7e377daa5b6070b93e0a01ee6cb006ee8f3e8508 SHA256 bf25341d0b7dc8f4dd61bb160c345d29fad5e303309c0690d64ad9f69f5b2b79
+AUX molden-5.0-ambfor.patch 523 RMD160 ce8e2e486ea02816ba565a520b0630245631b50e SHA1 53be8099791e129490e733cd7828ee68f74455a0 SHA256 65611167c51b773f1b64468712a0e075be673d7d460b73629ce85b202b19ebf6
 DIST molden4.7.tar.gz 2821826 RMD160 29a05f7637656ea2641fa81efa9068f9815e84ca SHA1 2cc1d5d2be947da6da89b53b4522342615601b8d SHA256 f4dc82ebaf597cee937f5714124cb905474c33e365508961598bf7625643d761
 DIST molden4.8.tar.gz 2969701 RMD160 6b3203c5e72680b6c23611f7cc97c3275fddca15 SHA1 67c1ae7b3b053352540fcc084d2819a15a8e82fa SHA256 314d9b9bdede2fd63d1e2f26e0212711576952244634fc28ea6c97ce2f7029b1
-EBUILD molden-4.7-r1.ebuild 1940 RMD160 eef2072783103454c367b02c058d7374f430bbe9 SHA1 d68df869dbbe53fd2fcf4c15f9de856aed714d53 SHA256 c18c40d7a3dcc32bdd036d6099d15ccc578340a43164389319f728275aaf672f
+DIST molden5.0.tar.gz 3063244 RMD160 5877a640bbeb1b3468936a0166bd9148e90becbc SHA1 9112673a26858497c51b486b3e5fc794b4ce6c22 SHA256 c9cf8f656adf2f2c7a8b8b64fa07b5feaa9c3ca36c4803e1f58ac33de1cffdc4
 EBUILD molden-4.7.ebuild 1689 RMD160 25971d279f1b88a2fd4aad21918bc9e56b5bcb2d SHA1 5468042e14dd3edc61eb8ab61fe5d5c34886a19e SHA256 f0f9d37d47e505d822de3825b8e3a5f98f045edc2f19419cd3bd3c57b0e0ccdb
-EBUILD molden-4.8-r1.ebuild 1968 RMD160 c91dbd6bcb462223972c319c71f0b28ec526732a SHA1 c743e0e5a7ab2f6ff6fe5e8697580dd5ca235133 SHA256 8e5bcb2c58a07acf2e55ec18289863bdbe0519d1746285a1219002c0af21b95d
-EBUILD molden-4.8.ebuild 1842 RMD160 53afaaa4a192f97d8ab722f021acd93c15393135 SHA1 b48292ea0a313ea3390abbdc238bfd3d64bde1c6 SHA256 51245ff23c421695260b4db7caadefe7b911bb3e4fa0f1a7da1d22614d2a761b
-MISC ChangeLog 7566 RMD160 20f4926bf40b18b8f8b6920215a52c7364de7251 SHA1 7ca53396fb8fc331cd57d3be8b84fab9d75c2585 SHA256 33daaf635f73534c467e98449ed9c3c12e46da896c7360ae2c942d8561dfe47a
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+EBUILD molden-4.8-r2.ebuild 1874 RMD160 f796f0c6cfbb5d3bfeb7645a09d7c135d2a8acc1 SHA1 656f502283ffdfaf8dcb4d3358bda3eaedd44376 SHA256 3b11c7037f36b66d370929d64a22d202e87d5f2419321d2e139990b5f6eedfec
+EBUILD molden-5.0.ebuild 1885 RMD160 0f846395eecc48d3da7a9d1cf615be6dae291c61 SHA1 1a0257a79fa151a1af81f816628c7fa5559b23e2 SHA256 70e871cb76534b8a501eee4b9ce2f82a48bb74cb7a17649eb5abd7b888244a10
+MISC ChangeLog 7968 RMD160 d298d0c172c883311a043fa82b6f6e2822a39621 SHA1 f2d26c11b8b4bd02415087f900f12ff8f491c1fa SHA256 46853d80d3749f35af4e1213d39123f46227f90597883c7938f16f0dcae09677
+MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
-iEYEARECAAYFAk4AwMAACgkQgAnW8HDreRbudwCeK7svAlpYSIaUQZHKQvmOlS9v
-2jYAoJws3Z3v1qgDOFq/xjOxiygkdRtH
-=nlF7
+iEYEAREKAAYFAk/lprsACgkQgAnW8HDreRZf7wCfTpZgfiXip2m7eULavtug2Pfd
+cDIAn2AwPLgNuGrVN4nDa9l+Ji4GutNA
+=hd9a
 -----END PGP SIGNATURE-----
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 *
 }