sci-chemistry/mosflm: Fix Buffer overflow, #421843

Package-Manager: portage-2.2.0_alpha110/cvs/Linux x86_64

5 files changed, 134 insertions, 5 deletions

diff --git a/sci-chemistry/mosflm/ChangeLog b/sci-chemistry/mosflm/ChangeLog
index 26d7e29e257b..aba96cfc2954 100644
--- a/sci-chemistry/mosflm/ChangeLog
+++ b/sci-chemistry/mosflm/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/mosflm
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mosflm/ChangeLog,v 1.15 2012/04/28 07:58:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mosflm/ChangeLog,v 1.16 2012/06/19 06:21:16 jlec Exp $
+
+*mosflm-7.0.7-r2 (19 Jun 2012)
+
+  19 Jun 2012; Justin Lecher <jlec@gentoo.org> +mosflm-7.0.7-r2.ebuild,
+  +files/mosflm-7.0.7-buffer-overflow.patch,
+  +files/mosflm-7.0.7-impl-dec.patch:
+  Fix Buffer overflow, #421843
 
 *mosflm-7.0.7-r1 (28 Apr 2012)
 
diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest
index 8f4243915ccb..80d7ed3bf086 100644
--- a/sci-chemistry/mosflm/Manifest
+++ b/sci-chemistry/mosflm/Manifest
@@ -5,17 +5,21 @@ AUX 7.0.6-Makefile.patch 352 RMD160 69fd182574615b90bbeb1b633885006051e81683 SHA
 AUX 7.0.6-impl-dec.patch 949 RMD160 e2dc1b8236a1ac72836af911d19a1ce5e1d048bf SHA1 5f51546471f5ab3530f56d0e7bbdeb6a977f91be SHA256 7c39b9d37ea4ea01668dd16ccf1b31e288bca37eaef497c5b0c725d42ebeb8b2
 AUX 7.0.6-parallel.patch 654 RMD160 f28cdb670c3ecfcc4ec194dd44136182fbf9cf7f SHA1 bf6742b58d6e9ce67e76f38e81aeb64f88fae729 SHA256 c821e031a039502364c4ae151fd64886a6a33153e5c746d55838a99050d18c60
 AUX 7.0.7-parallel.patch 2482 RMD160 2aa7e34342fa46b7d7a55726f06e30b156d846a1 SHA1 3db79b77ba765eebcc2f1aa8b69d4ae3b39413c7 SHA256 7bb2636833a5332472c5c60a0736e5c75cd04691909784a5e363da64c3e254bb
+AUX mosflm-7.0.7-buffer-overflow.patch 492 RMD160 d4ae6366e01cee8730c7a097be30b52fdbcebd82 SHA1 0b6a799df54465c5f9d1b091ecda83564a67074b SHA256 8938c13a53bb59d0703f35ce8586257fb1427c2951bd2e800c6792fc4bdc5379
+AUX mosflm-7.0.7-impl-dec.patch 903 RMD160 3e1bd85edd96112ed26ee48f91793ad4e9c06647 SHA1 b9daeab6c472007dc0a84d49f61ff311eec4c56c SHA256 446d5eec4cae43ad08c819c6fc35f035436b0fc0a8dd70d20382eef937c6c343
 DIST mosflm706.tgz 3468405 RMD160 fb0b7e51ed9845d4d17aa804cb1424e5aa0f24b8 SHA1 f9a771c3991c7ad3125a7e39d5c59b3049784f4f SHA256 5e26a49fd37749a14e7a1d1e867c1c0333db3bbcc01376fb7a516d4a67b1ebb0
 DIST mosflm707.tgz 3401235 RMD160 0301c22df9f0229f8ee5ac5b87c1353a5608fa94 SHA1 6ac29381bbea57ea370d72b31f36660332316d07 SHA256 fb14a02834929423569a23a04800de62ed1da2a02966958b79c157a71b9b6118
 EBUILD mosflm-7.0.6-r2.ebuild 1778 RMD160 60cded72308c2158ac369cbcbed817a7baf99aaf SHA1 29729ca74b23d2de8b20dac9aeea56271ad476b7 SHA256 269b94ae627bc4d053a60ab6915273f76338d3187cfbd7f71ae6521df0646e84
 EBUILD mosflm-7.0.7-r1.ebuild 1703 RMD160 ed97fe6cf13ca41c6db3b4062156322f2bfcf69c SHA1 9a73cbb5c1c5b3fb596db020f02b078426987ddf SHA256 441ea84a02997badf6eb42ca1765950a9c0fa2b45f8fb8f65669bfe8563c8865
+EBUILD mosflm-7.0.7-r2.ebuild 1780 RMD160 2920352b88158c441245ae83417a91b14ec4e92b SHA1 8e8ecfc4922795ccc0e65cf123613d99976210b1 SHA256 1c07191058fa3c8dfbb50f541a208463968b5fda3bddf19daba5998112fa0811
 EBUILD mosflm-7.0.7.ebuild 1764 RMD160 7b8fff5a5841aa8b894233d8e9d15b212c69d148 SHA1 e6abc3d4a04deb86ea07dbcbbad2014962e01a6c SHA256 92449bc206253b5ae3ce06f261f225fb479a188c3f21f36bf120fb776c8fd7c1
-MISC ChangeLog 2205 RMD160 ff800e3394bad1442096b2c1a13b4c34a44b5af0 SHA1 3ea82c4b65be5a827ae93c75f3a52857d52ba2f8 SHA256 a7483cc9fec6a13dcf5c44ae79fffdb3638951b3a54102f0b57b47643586ddcb
+MISC ChangeLog 2424 RMD160 15fa404f4678341938bb84cd13809d1463db8c5a SHA1 f894e6f8b65c7062ded46a598559ee926d1cc89f SHA256 3ca4fe27c7131439a51a3ca9099fa781069af1fe9a1bf7a5de7aed6235c9e543
 MISC metadata.xml 219 RMD160 e9da2d4271f89b9dbac478d145a519318f0f3314 SHA1 6d4a101013d6a40cd61cb2d8c6b517c443013bc7 SHA256 0be94b46df4c9a73494034f33b1371769951f52890e5c857ebe1dc9bc729d0a8
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 Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
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diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
new file mode 100644
index 000000000000..90158eb458d5
--- /dev/null
+++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch
@@ -0,0 +1,16 @@
+ mosflm/pilatus_c.c |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c
+index 1eaae26..cce5a02 100644
+--- a/mosflm/pilatus_c.c
++++ b/mosflm/pilatus_c.c
+@@ -34,7 +34,7 @@ delete them later */
+   int cbf_int[16];
+   long cbf_int4[16];
+   double cbf_double[16];
+-  char cbf_char[16][24];
++  char cbf_char[16][32];
+   /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll 
+ delete them later */
+   int id, index, iindex;
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
new file mode 100644
index 000000000000..32f251f8e00c
--- /dev/null
+++ b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch
@@ -0,0 +1,29 @@
+ mosflm/mosflm_jpeg.c           |    1 +
+ src/dps/index/ind_gen_direct.c |    2 ++
+ 2 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c
+index 2b32b2e..54684d0 100644
+--- a/mosflm/mosflm_jpeg.c
++++ b/mosflm/mosflm_jpeg.c
+@@ -76,6 +76,7 @@ G. Winter
+ #include <fcntl.h>
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #if (defined _MSC_VER) 
+ /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/
+ #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC
+diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c
+index 6e143df..2eea61b 100644
+--- a/src/dps/index/ind_gen_direct.c
++++ b/src/dps/index/ind_gen_direct.c
+@@ -41,6 +41,8 @@
+ /* #include <malloc.h> */
+ #include "util.h"
+ #include "ind_gen_direct.h"
++#include "ind_help.h"
++#include "ind_sort_merge.h"
+ /* char *strcat( char *, const char *); */
+ 
+ 
diff --git a/sci-chemistry/mosflm/mosflm-7.0.7-r2.ebuild b/sci-chemistry/mosflm/mosflm-7.0.7-r2.ebuild
new file mode 100644
index 000000000000..378c232b0bad
--- /dev/null
+++ b/sci-chemistry/mosflm/mosflm-7.0.7-r2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mosflm/mosflm-7.0.7-r2.ebuild,v 1.1 2012/06/19 06:21:16 jlec Exp $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs versionator
+
+MY_PV="$(delete_all_version_separators)"
+MY_P="${PN}${MY_PV}"
+
+DESCRIPTION="A program for integrating single crystal diffraction data from area detectors"
+HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/"
+SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	virtual/fortran
+	app-shells/tcsh
+	virtual/jpeg
+	sci-libs/cbflib
+	sci-libs/ccp4-libs
+	sys-libs/ncurses
+	x11-libs/libxdl_view"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed \
+		-e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \
+		-e "s:../jpg/libjpeg.a:-ljpeg:g" \
+		-i ${PN}/Makefile || die
+
+	sed \
+		-e '/jinclude.h/d' \
+		-i mosflm/mosflm_jpeg.c || die
+
+	epatch \
+		"${FILESDIR}"/${PV}-parallel.patch \
+		"${FILESDIR}"/7.0.6-impl-dec.patch \
+		"${FILESDIR}"/${P}-buffer-overflow.patch \
+		"${FILESDIR}"/${P}-impl-dec.patch
+
+	rm -rf test.f {cbf,jpg}/*.{h,c} || die
+}
+
+src_compile() {
+	emake \
+		MOSHOME="${S}" \
+		DPS="${S}" \
+		FC=$(tc-getFC) \
+		FLINK=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		AR_FLAGS=vru \
+		MOSLIBS='-lccp4f -lccp4c -lxdl_view -lcurses -lXt -lmmdb -lccif -lstdc++' \
+		MCFLAGS="-O0 -fno-second-underscore" \
+		MOSFLAGS="${FFLAGS} -fno-second-underscore" \
+		FFLAGS="${FFLAGS} -fno-second-underscore" \
+		CFLAGS="${CFLAGS}" \
+		MOSCFLAGS="${CFLAGS}" \
+		LFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin/
+	doexe bin/ipmosflm
+	dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN}
+}