_FORTIFY_SOURCE indicates presence of overflow Fix, #341715

Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64

4 files changed, 145 insertions, 7 deletions

diff --git a/sci-chemistry/psi/ChangeLog b/sci-chemistry/psi/ChangeLog
index 23732f018d8b..7f4f5b491625 100644
--- a/sci-chemistry/psi/ChangeLog
+++ b/sci-chemistry/psi/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/psi
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/ChangeLog,v 1.13 2010/07/06 11:36:22 jlec Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/ChangeLog,v 1.14 2011/04/25 15:49:30 jlec Exp $
+
+*psi-3.4.0-r2 (25 Apr 2011)
+
+  25 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/3.4.0-fortify.patch,
+  +psi-3.4.0-r2.ebuild:
+  _FORTIFY_SOURCE indicates presence of overflow Fix, #341715
 
 *psi-3.4.0-r1 (06 Jul 2010)
 
diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest
index b1296e46ce91..d8b741fd8326 100644
--- a/sci-chemistry/psi/Manifest
+++ b/sci-chemistry/psi/Manifest
@@ -4,6 +4,7 @@ Hash: SHA1
 AUX 3.3.0-gcc-4.3.patch 506 RMD160 40661bfb73577988ab160bd00e64a9590d47ccab SHA1 6f163fd1fbab1cf8b058e045a50896760ccea22f SHA256 6107fc41da44143f12904ca0fb317c0498b36b51af933badad48e2e878471e89
 AUX 3.4.0-destdir.patch 1320 RMD160 4f33ac3c171797bc0cab9ac492ab6ee1f32d12aa SHA1 54b524e161d5dcffc6817eb559aa4aff3ee44802 SHA256 17909af7b5dff643ef8ea134bf4468cd361457ba9192a1f9155a5870470af7a6
 AUX 3.4.0-dont-build-libint.patch 432 RMD160 d9e68e68c54e0cd237c9f1793f8b4ff905c0163a SHA1 8781f9e507817a00b1179cb21140e6cc7733ef01 SHA256 2bceacc5e924b033b2ef774df789cb5cd11278452da7ea2aad5d51d3b7a8d43c
+AUX 3.4.0-fortify.patch 1889 RMD160 72bcd5fca73a42643f394aac4b6ff3ad85a21b05 SHA1 228e898e2fdb8485c82539e39a5df0cd574f5891 SHA256 f901b42e64e6fdf1aed2d87bfc8efa503ab193d0464e9739be67c60daf249cd6
 AUX 3.4.0-gcc-4.3.patch 8000 RMD160 794a4b67832238f7d58344816b44977952e11798 SHA1 37a0127809d786af4b24025351f77df8dc4095bc SHA256 f0b354c3ce8c65956f4ace3ed19afd9ff9b6ab43b3cf21aa33a94c8af44989da
 AUX 3.4.0-ldflags.patch 403 RMD160 cf860a1bccfc3c556859f5613903b552f2974b6a SHA1 f886611b58304ba599d36cf2a24892d42ecd4e63 SHA256 edd2030d2d1f4f62d5297d7eab453fbe4d81d1b9ab8fe5f88b7ca8ca8ac70077
 AUX 3.4.0-man_paths.patch 603 RMD160 4e120383a47f66dc32387660fcf47e2d4888b43b SHA1 4ee49e7610860d5103ebd4b6ddadb9717ef110c3 SHA256 a8307a45d0af403e88299ea474f8af9cf26eafc3207cd991e53af1796ff8357b
@@ -21,12 +22,13 @@ DIST psi-3.4.0.tar.gz 7413072 RMD160 34f34d2fb1fcabc973992eff19bb7fa1e80ce6a6 SH
 EBUILD psi-3.2.3.ebuild 1289 RMD160 ee73ce6652cfd35329d323dd8a891373640aab8e SHA1 70d3f63c27caea1dc84a2f288acf1c28000a5539 SHA256 9af788bd07c05c74b4bfa031e7b0f33b27519ef12aaef1ecb8da7b745861295a
 EBUILD psi-3.3.0.ebuild 1356 RMD160 7b1c2a45a5ef171dab649941091e662cc0f5ce34 SHA1 131841321424178b807322551ecea126cf1063eb SHA256 d4ad7a5deba5750a97b729734f54448df2d172ed7fedad3ce208d4ca85ec2330
 EBUILD psi-3.4.0-r1.ebuild 1711 RMD160 62cee6eec5280c5cf7e9bcf276a94a86ffdddbdf SHA1 050350c0f43a39bb15b2626e4ae03e76d798abcb SHA256 17fc7f4b4d0cdccde8c7e0f331e74001c16e69dd99bbf68a0f99fee75592288a
-MISC ChangeLog 2585 RMD160 c01e08bd480545632ced234d29db7cb3c216c02c SHA1 0dccdb1676d0327f91a3c32707137a893bb85b41 SHA256 9a42e06716ea745a4b806abdbfea4c4501820635213792579ac3ff028541922a
+EBUILD psi-3.4.0-r2.ebuild 1749 RMD160 48abaa23cc8994accb22c578a9000f8dff2722e7 SHA1 ecdb451b6149ec52e2650f7c36d12eae8717ec36 SHA256 07951cf3b88012014a3f39fa0fd9ea2b1d5cad1416cf64988f79692335ff12fc
+MISC ChangeLog 2776 RMD160 ec7c1f920fe8904fddb4a9b68e0ab227dc831552 SHA1 836863e25dae15e989b1383c71a8e903cb2488d1 SHA256 2f5ada108478f2583eea31d54c945a0cf707270caa03fc91dac0ca86e99182fe
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAkwzFTwACgkQgAnW8HDreRaA3QCaAqEhAn2YwreoyDbP0Ad70TNv
-gkUAniR1D0OrA3pKuynROgQqxdBV0sp7
-=mxyQ
+iEYEARECAAYFAk21mBAACgkQgAnW8HDreRa5zgCghi1uUBqxSkEWdcm9LI5d0krC
+uL0AoJYTtyd1JKyK+LAPWVQ3mv1oimN1
+=9NZA
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diff --git a/sci-chemistry/psi/files/3.4.0-fortify.patch b/sci-chemistry/psi/files/3.4.0-fortify.patch
new file mode 100644
index 000000000000..5f098399ad3f
--- /dev/null
+++ b/sci-chemistry/psi/files/3.4.0-fortify.patch
@@ -0,0 +1,58 @@
+ src/bin/ccenergy/get_params.cc   |    2 +-
+ src/bin/cclambda/get_params.cc   |    2 +-
+ src/bin/ccresponse/get_params.cc |    2 +-
+ src/bin/ccsort/get_params.cc     |    2 +-
+ 4 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/bin/ccenergy/get_params.cc b/src/bin/ccenergy/get_params.cc
+index 53f4c83..a2fa932 100644
+--- a/src/bin/ccenergy/get_params.cc
++++ b/src/bin/ccenergy/get_params.cc
+@@ -193,7 +193,7 @@ void get_params()
+     }
+   }
+   else if(params.local) {
+-    local.weakp = (char *) malloc(4 * sizeof(char));
++    local.weakp = (char *) malloc(5 * sizeof(char));
+     sprintf(local.weakp, "%s", "NONE");
+   }
+ 
+diff --git a/src/bin/cclambda/get_params.cc b/src/bin/cclambda/get_params.cc
+index 4a9d2c8..8a2ae17 100644
+--- a/src/bin/cclambda/get_params.cc
++++ b/src/bin/cclambda/get_params.cc
+@@ -150,7 +150,7 @@ void get_params(void)
+     }
+   }
+   else if(params.local) {
+-    local.weakp = (char *) malloc(4 * sizeof(char));
++    local.weakp = (char *) malloc(5 * sizeof(char));
+     sprintf(local.weakp, "%s", "NONE");
+   }
+   
+diff --git a/src/bin/ccresponse/get_params.cc b/src/bin/ccresponse/get_params.cc
+index a96db13..5c40aa0 100644
+--- a/src/bin/ccresponse/get_params.cc
++++ b/src/bin/ccresponse/get_params.cc
+@@ -207,7 +207,7 @@ void get_params()
+     }
+   }
+   else if(params.local) {
+-    local.weakp = (char *) malloc(4 * sizeof(char));
++    local.weakp = (char *) malloc(5 * sizeof(char));
+     sprintf(local.weakp, "%s", "NONE");
+   }
+ 
+diff --git a/src/bin/ccsort/get_params.cc b/src/bin/ccsort/get_params.cc
+index ad7f0c3..6ee1993 100644
+--- a/src/bin/ccsort/get_params.cc
++++ b/src/bin/ccsort/get_params.cc
+@@ -120,7 +120,7 @@ void get_params()
+     }
+   }
+   else if(params.local) {
+-    local.weakp = (char *) malloc(4 * sizeof(char));
++    local.weakp = (char *) malloc(5 * sizeof(char));
+     sprintf(local.weakp, "%s", "NONE");
+   }
+ 
diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r2.ebuild
new file mode 100644
index 000000000000..fde0d32b314b
--- /dev/null
+++ b/sci-chemistry/psi/psi-3.4.0-r2.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/psi/psi-3.4.0-r2.ebuild,v 1.1 2011/04/25 15:49:30 jlec Exp $
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="Suite of ab initio quantum chemistry programs to compute various molecular properties"
+HOMEPAGE="http://www.psicode.org/"
+SRC_URI="mirror://sourceforge/psicode/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+# File collision, see bug #249423
+RDEPEND="
+	!sci-visualization/extrema
+	virtual/blas
+	virtual/lapack
+	>=sci-libs/libint-1.1.4"
+DEPEND="${RDEPEND}
+	test? ( dev-lang/perl )"
+
+S="${WORKDIR}/${PN}${PV:0:1}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-dont-build-libint.patch \
+		"${FILESDIR}"/use-external-libint.patch \
+		"${FILESDIR}"/${PV}-gcc-4.3.patch \
+		"${FILESDIR}"/${PV}-destdir.patch \
+		"${FILESDIR}"/${P}-parallel-make.patch \
+		"${FILESDIR}"/${PV}-man_paths.patch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${PV}-parallel_fix.patch \
+		"${FILESDIR}"/${PV}-fortify.patch
+
+	# Broken test
+	sed \
+		-e 's:scf-mvd-opt ::g' \
+		-e 's:scf-mvd-opt-puream ::g' \
+		-i tests/Makefile.in || die
+
+	sed \
+		-e "/LIBPATTERNS/d" \
+		-i src/{bin,util,samples}/MakeVars.in || die
+	eautoreconf
+}
+
+src_configure() {
+	# This variable gets set sometimes to /usr/lib/src and breaks stuff
+	unset CLIBS
+
+	econf \
+		--with-opt="${CXXFLAGS}" \
+		--datadir="${EPREFIX}"/usr/share/${PN} \
+		--with-blas="$(pkg-config blas --libs)"
+}
+
+src_compile() {
+	emake SCRATCH="${WORKDIR}/libint" DODEPEND="no" || die
+}
+
+src_test() {
+	emake EXECDIR="${S}"/bin TESTFLAGS="" -j1 tests || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" DODEPEND="no" install || die
+}