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To: gentoo-commits@g.o
From: "Justin Lecher (jlec)" <jlec@g.o>
Subject: gentoo-x86 commit in sci-chemistry/molden/files: molden-4.8-overflow.patch molden-5.0-ambfor.patch
Date: Sat, 23 Jun 2012 11:21:23 +0000 (UTC)
jlec        12/06/23 11:21:23

  Modified:             molden-4.8-overflow.patch
  Added:                molden-5.0-ambfor.patch
  Log:
  sci-chemistry/molden: Fix buffer overflow, #342907; Version Bump, #355741; Fix build failures, #358917, #423015; drop old
  
  (Portage version: 2.2.0_alpha111/cvs/Linux x86_64)

Revision  Changes    Path
1.2                  sci-chemistry/molden/files/molden-4.8-overflow.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/files/molden-4.8-overflow.patch?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/files/molden-4.8-overflow.patch?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/files/molden-4.8-overflow.patch?r1=1.1&r2=1.2

Index: molden-4.8-overflow.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/molden/files/molden-4.8-overflow.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- molden-4.8-overflow.patch	26 Feb 2010 05:33:33 -0000	1.1
+++ molden-4.8-overflow.patch	23 Jun 2012 11:21:23 -0000	1.2
@@ -1,7 +1,33 @@
-diff -Naur molden4.8/xwin.c molden4.8.new//xwin.c
---- molden4.8/xwin.c	2010-02-01 08:04:08.000000000 -0500
-+++ molden4.8.new//xwin.c	2010-02-26 00:03:36.000000000 -0500
-@@ -27353,7 +27353,7 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -13552,7 +13552,7 @@ void NewActiveStruct()
+ #ifdef CRAY
+     _fcd ztr;
+ #else
+-    char ztr;
++    char ztr[4];
+ #endif
+ #endif
+ 
+@@ -13650,8 +13650,10 @@ void NewActiveStruct()
+ */
+ 	clfpstr->ihashz = 0;
+ #else
+-	strncpy(&ztr,HetAtm[j],3);
+-	parhet_(&j1,&ztr);
++	if (HetAtm[j] != NULL) {
++	   strncpy(ztr,HetAtm[j],3);
++	   parhet_(&j1,ztr);
++	}
+ #endif
+ #endif
+     }
+@@ -27353,7 +27355,7 @@ char *errstr;
  	UpdateZME();
  	RedrawScroll(&zscroll);
      }



1.1                  sci-chemistry/molden/files/molden-5.0-ambfor.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/files/molden-5.0-ambfor.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/molden/files/molden-5.0-ambfor.patch?rev=1.1&content-type=text/plain

Index: molden-5.0-ambfor.patch
===================================================================
 ambfor/makefile |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/ambfor/makefile b/ambfor/makefile
index 8627a11..dbc23a1 100644
--- a/ambfor/makefile
+++ b/ambfor/makefile
@@ -47,7 +47,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(OBJS)
 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
 
 ambfor.o:	ambfor.f
-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
+	${FC} $(FFLAGS) -c -o ambfor.o ambfor.f
 
 allocmd.o:	alloc.c
 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o





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Updated Jun 26, 2012

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