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

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

4 files changed, 126 insertions, 1 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/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}
+}