Fixes for overflows, 337779

Package-Manager: portage-2.2_rc88/cvs/Linux x86_64

5 files changed, 102 insertions, 9 deletions

diff --git a/sci-chemistry/prekin/ChangeLog b/sci-chemistry/prekin/ChangeLog
index 47e68d5f385a..2595587cf474 100644
--- a/sci-chemistry/prekin/ChangeLog
+++ b/sci-chemistry/prekin/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/prekin
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/prekin/ChangeLog,v 1.1 2010/07/18 08:57:09 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/prekin/ChangeLog,v 1.2 2010/10/03 08:28:36 jlec Exp $
+
+*prekin-6.51.081122-r1 (03 Oct 2010)
+
+  03 Oct 2010; Justin Lecher <jlec@gentoo.org>
+  +files/6.51.081122-overflow.patch, prekin-6.51.081122.ebuild,
+  +prekin-6.51.081122-r1.ebuild:
+  Fixes for overflows, 337779
 
 *prekin-6.51.081122 (18 Jul 2010)
 
diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest
index 358f6dc68791..c10287464206 100644
--- a/sci-chemistry/prekin/Manifest
+++ b/sci-chemistry/prekin/Manifest
@@ -2,14 +2,16 @@
 Hash: SHA1
 
 AUX 6.51.081122-Makefile.patch 1456 RMD160 2274cc1f803bb38ea5d1cba0f28b583859e7520d SHA1 7fb4e5b1f8e33e211dced62b779e5c09034e5857 SHA256 7f1b2d39007683b4ecb391ec5bd711ca32115f361dcfc0aa05b25fe52817bb4c
+AUX 6.51.081122-overflow.patch 1156 RMD160 155e1c64d2518b506d60a7a6140e954f59096047 SHA1 4000cddc53555d63c723254d72f0297e6fc18f2d SHA256 987a530c35f34b25783ce1b4ce0094614f06e97ae8ed652324b8b8ea7f897259
 DIST prekin.6.51.081122.src.tgz 350756 RMD160 a48df8558ee98396492851b0f1b73723cb4b9559 SHA1 7b3c1da210c26fd9740ecba4de02e985efdbbe61 SHA256 74a771cd8be000df13ac908f23a2e945e8bd3590884c6bc6ccff75804cc0fb7a
-EBUILD prekin-6.51.081122.ebuild 1157 RMD160 531d8d0ccd1820d9439fe185f2e9b49bbfd1d1cd SHA1 c93f8a3603c62c4ab6b0c1cbe7a4eb16af5db9de SHA256 5a72b0c1b851e264883ec9689bb45f6e1a05b5981e5a4ff5a9886df3615e0c15
-MISC ChangeLog 391 RMD160 5e0f7e6b054e2732d9f4a8627abaffbbeb18364f SHA1 2e5f4f482dba0558f5b4cf677d9a8cc5ff0cfc3e SHA256 9a9be35acd3bf3238b8c97ab3ac99cbaf4021f60e719ed65aa8a50c1837e533e
+EBUILD prekin-6.51.081122-r1.ebuild 1203 RMD160 3d9a56b1e0b75687c497d764b694068247559e0d SHA1 4e948e730ac7c81cb80afe6110840cec36dd182d SHA256 3fc2c6f88e3b3369073a191047b6912ae65de70afd0bef1f70990a827544d8a2
+EBUILD prekin-6.51.081122.ebuild 1200 RMD160 c638c91ffabe446189c9410df14f3b41d64f3858 SHA1 9850b82fb3e767c9ec520cd453d980bf641d5834 SHA256 cdf3d8bc6371d457b5903045abaa1bf6693c0a1f2b3393c721db5a731de92283
+MISC ChangeLog 604 RMD160 aeb73bb59e098abb6754071e075d4f0ef229d749 SHA1 890138a16cfa5be6187ee5ad7f2403eb30e62e29 SHA256 d4d6882fd8dd8d49a4e06fa6317b636bdbea065d76848e049c4200caf21f379c
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkxEfaYACgkQgAnW8HDreRa6awCgsS0DmMbBz1Sn/7fgrU8Oq+Ic
-Wv8AoM/WgWjXirYWAvFknTsGyEFawsXX
-=RpU7
+iEYEARECAAYFAkyoPrsACgkQgAnW8HDreRYUBgCeKVybfIlrOoHcJ7uvElmOD8HI
+o4UAn2qbYaGqbb6ybmqWNyeEYN7nNTp9
+=vk6N
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/prekin/files/6.51.081122-overflow.patch b/sci-chemistry/prekin/files/6.51.081122-overflow.patch
new file mode 100644
index 000000000000..27bc01d61a52
--- /dev/null
+++ b/sci-chemistry/prekin/files/6.51.081122-overflow.patch
@@ -0,0 +1,28 @@
+diff --git a/PKIN.h b/PKIN.h
+index 6cb6670..c9c6b89 100755
+--- a/PKIN.h
++++ b/PKIN.h
+@@ -533,8 +533,8 @@ EXTERN float xnext,ynext,znext,onext,Bnext,Uvalnext;
+ EXTERN char  aspectstrnext[MAXaspects+3]; /*in parens: (XXXX)*/
+ 
+ /* possible overlap with earlier PREKIN variables */
+-EXTERN char word[256],texts[256],temps[256];
+-EXTERN char alertstr[256],alertstr2[256],alertstr3[256];
++EXTERN char word[256],texts[256],temps[512];
++EXTERN char alertstr[1024],alertstr2[256],alertstr3[256];
+ EXTERN char oldstr[256],olderstr[256],newstr[256],InfoStr[256],MolNameStr[16];
+ EXTERN char NameStr[256],OutfileStr[256],ScriptinStr[256],ShortNameStr[256];
+ EXTERN char DirStr[256],PDBfileStr[256],helpoutStr[256]; /*040425 helpout*/
+diff --git a/PKINCOUT.c b/PKINCOUT.c
+index af8eb24..a9f3a5f 100755
+--- a/PKINCOUT.c
++++ b/PKINCOUT.c
+@@ -17,7 +17,7 @@ static float VRMLx=0,VRMLy=0,VRMLz=0;
+ void   writeoutput()
+ {
+   char  cntl[5];  /* 4 actual characters */
+-  char  kol[20],extra[256],aname[13];
++  char  kol[20],extra[256],aname[32];
+   char  chain[32],atoms[32],cpks[32],hygen[32],hbond[32];
+   char  subname[32],allstr[32];
+   char  mastername[32]; /*051128*/
diff --git a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
new file mode 100644
index 000000000000..c7ee55b7b884
--- /dev/null
+++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild,v 1.1 2010/10/03 08:28:36 jlec Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs eutils multilib
+
+MY_P="${PN}.${PV}"
+
+DESCRIPTION="Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/prekin.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/prekin/${MY_P}.src.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X"
+
+RDEPEND="
+	x11-libs/libX11
+	x11-libs/libXt
+	X? ( 	x11-libs/openmotif )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-Makefile.patch \
+		"${FILESDIR}"/${PV}-overflow.patch
+	sed  \
+		-e 's:cc:$(CC):g' \
+		-e "s:GENTOOLIBDIR:$(get_libdir):g" \
+		"${S}"/Makefile.linux > Makefile
+}
+
+src_compile() {
+	local mytarget
+
+	if use X; then
+		mytarget="${PN}"
+	else
+		mytarget="nogui"
+	fi
+
+	emake \
+		CC="$(tc-getCC)" \
+		${mytarget} || die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/prekin || die "dobin failed"
+}
diff --git a/sci-chemistry/prekin/prekin-6.51.081122.ebuild b/sci-chemistry/prekin/prekin-6.51.081122.ebuild
index efe0dabb7ea2..47d3d446b1b2 100644
--- a/sci-chemistry/prekin/prekin-6.51.081122.ebuild
+++ b/sci-chemistry/prekin/prekin-6.51.081122.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/prekin/prekin-6.51.081122.ebuild,v 1.1 2010/07/18 08:57:09 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/prekin/prekin-6.51.081122.ebuild,v 1.2 2010/10/03 08:28:36 jlec Exp $
 
 EAPI="2"
 
@@ -26,7 +26,9 @@ DEPEND="${RDEPEND}"
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-Makefile.patch
+	epatch \
+		"${FILESDIR}"/${PV}-Makefile.patch \
+		"${FILESDIR}"/${PV}-overflow.patch
 	sed  \
 		-e 's:cc:$(CC):g' \
 		-e "s:GENTOOLIBDIR:$(get_libdir):g" \