[gentoo-commits] proj/sci:ccp4 commit in: sci-chemistry/shiftx/files/, sci-chemistry/shiftx/

[gentoo-commits] proj/sci:ccp4 commit in: sci-chemistry/shiftx/files/, sci-chemistry/shiftx/

[Justin Lecher]

commit:     bd1128296381c552e7061eb8623ac5ca1ab168a6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 20 11:54:00 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 20 11:54:00 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd112829

sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix

Package-Manager: portage-2.2.0_alpha182

---
 sci-chemistry/shiftx/ChangeLog                    |  4 ++++
 sci-chemistry/shiftx/files/1.1-Makefile.patch     | 15 ++++++++++-----
 sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 ++++++++++++++++
 sci-chemistry/shiftx/metadata.xml                 |  2 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild            |  4 +++-
 5 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/shiftx/ChangeLog b/sci-chemistry/shiftx/ChangeLog
index e588d4f..85e5049 100644
--- a/sci-chemistry/shiftx/ChangeLog
+++ b/sci-chemistry/shiftx/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild,
+  files/1.1-Makefile.patch, +files/1.1-bfr-overflow.patch, metadata.xml:
+  Fix patch and add patch for buffer overflow fix
+
   16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml:
   Bump to EAPI=5 and fix license
 

diff --git a/sci-chemistry/shiftx/files/1.1-Makefile.patch b/sci-chemistry/shiftx/files/1.1-Makefile.patch
index 1678752..f208d08 100644
--- a/sci-chemistry/shiftx/files/1.1-Makefile.patch
+++ b/sci-chemistry/shiftx/files/1.1-Makefile.patch
@@ -1,17 +1,22 @@
---- Makefile	2004-08-03 20:33:20.000000000 +0200
-+++ Makefile.new	2009-06-14 10:49:40.000000000 +0200
+ Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 5401c07..ffd8157 100644
+--- a/Makefile
++++ b/Makefile
 @@ -6,8 +6,8 @@
  # E-Mail:   anip@redpoll.pharmacy.ualberta.ca
  #
  #CC=gcc -Xcpluscomm -cckr
 -CC=/usr/bin/gcc
--CFLAGS=-O3
+-CFLAGS=-O
 +#CC=/usr/bin/gcc
-+#CFLAGS=-O3
++#CFLAGS=-O
  SYSLIB=
  INCLUDES=-I/usr/include
  LIBS=$(SYSLIB) -lm 
-@@ -25,7 +25,7 @@
+@@ -25,7 +25,7 @@ OBJS=Main.o Nn.o Ssbond.o Residue.o Hetatm.o Vector.o Torison.o Cs.o Phipsi.o \
  all: shiftx
  
  shiftx:	$(OBJS)

diff --git a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
new file mode 100644
index 0000000..68507a3
--- /dev/null
+++ b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ Display.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Display.c b/Display.c
+index 671d3ee..9a03c48 100644
+--- a/Display.c
++++ b/Display.c
+@@ -85,7 +85,7 @@ DISPLAY_DATA   *CreateDisplayData( int len, int prop, int nuc )
+ void  display_selected_nucleus( DISPLAY_DATA *d )
+ {
+   int   i, j;
+-  char  nucleus[5];
++  char  nucleus[8];
+ 
+   /* Print Header Information */
+ 

diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml
index 9ac9ffd..51fdeda 100644
--- a/sci-chemistry/shiftx/metadata.xml
+++ b/sci-chemistry/shiftx/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/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild
index 5f26ed3..5d3cc0f 100644
--- a/sci-chemistry/shiftx/shiftx-1.1.ebuild
+++ b/sci-chemistry/shiftx/shiftx-1.1.ebuild
@@ -17,7 +17,9 @@ IUSE=""
 
 S="${WORKDIR}"/${PN}
 
-PATCHES=( "${FILESDIR}"/${PV}-Makefile.patch )
+PATCHES=(
+	"${FILESDIR}"/${PV}-Makefile.patch
+	"${FILESDIR}"/${PV}-bfr-overflow.patch )
 
 DOCS="README FEATURES *.pdb *.out"