[med-svn] r17575 - in trunk/packages/paml/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-07-30 13:19:08 +0000 (Wed, 30 Jul 2014)
New Revision: 17575

Added:
   trunk/packages/paml/trunk/debian/patches/fix_format_security.patch
Modified:
   trunk/packages/paml/trunk/debian/changelog
   trunk/packages/paml/trunk/debian/patches/hardening.patch
   trunk/packages/paml/trunk/debian/patches/makefile.patch
   trunk/packages/paml/trunk/debian/patches/series
Log:
Upload to unstable with updated patches + new format_security patch


Modified: trunk/packages/paml/trunk/debian/changelog
===================================================================
--- trunk/packages/paml/trunk/debian/changelog	2014-07-30 12:36:27 UTC (rev 17574)
+++ trunk/packages/paml/trunk/debian/changelog	2014-07-30 13:19:08 UTC (rev 17575)
@@ -1,4 +1,4 @@
-paml (4.8-1) UNRELEASED; urgency=medium
+paml (4.8+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * d/rules: Adapt get-orig-source to new uscan syntax
@@ -8,6 +8,7 @@
      - Priority: optional
      - cme fix dpkg-control
      - XS-Autobuild: yes
+  * d/patches/fix_format_security.patch: Fix some format security issues
 
  -- Andreas Tille <tille at debian.org>  Wed, 30 Jul 2014 14:30:38 +0200
 

Added: trunk/packages/paml/trunk/debian/patches/fix_format_security.patch
===================================================================
--- trunk/packages/paml/trunk/debian/patches/fix_format_security.patch	                        (rev 0)
+++ trunk/packages/paml/trunk/debian/patches/fix_format_security.patch	2014-07-30 13:19:08 UTC (rev 17575)
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 30 Jul 2014 14:30:38 +0200
+Description: Fix some format security issues
+
+--- a/src/mcmctree.c
++++ b/src/mcmctree.c
+@@ -324,7 +324,7 @@ int GetMem (void)
+          error2("oom conP");
+ 
+       com.conPin[1] = com.conPin[0] + com.sconP/sizeof(double);
+-      printf("\n%u bytes for conP\n", 2*com.sconP);
++      printf("\n%u bytes for conP\n", 2*(unsigned)com.sconP);
+ 
+       /* set gnodes[locus][].conP for tips and internal nodes */
+       com.curconP = 0;
+--- a/src/treesub.c
++++ b/src/treesub.c
+@@ -158,7 +158,7 @@ int ReadMorphology (FILE *fout, FILE *fi
+    }
+ 
+    for(i=0; i<com.ns; i++) {
+-      fprintf(fout, com.spname[i]);
++      fprintf(fout, "%s", com.spname[i]);
+       for(j=0; j<com.ls; j++)
+          fprintf(fout, " %8.5f", data.zmorph[locus][i][j]);
+       FPN(fout);

Modified: trunk/packages/paml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/paml/trunk/debian/patches/hardening.patch	2014-07-30 12:36:27 UTC (rev 17574)
+++ trunk/packages/paml/trunk/debian/patches/hardening.patch	2014-07-30 13:19:08 UTC (rev 17575)
@@ -13,33 +13,3 @@
  
  #MAC OSX G5:
  #CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions
-@@ -20,21 +20,21 @@ LIBS = -lm # -lM
- all : $(PRGS)
- 
- baseml : baseml.c tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.c tools.c $(LIBS)
- basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.c tools.c $(LIBS)
- codeml : codeml.c  tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.c tools.c $(LIBS)
- evolver : evolver.c  tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.c tools.c $(LIBS)
- pamp : pamp.c  tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.c tools.c $(LIBS)
- mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
--	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
- yn00: yn00.c tools.c paml.h
--	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.c tools.c $(LIBS)
- chi2 : chi2.c
--	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
- 
- PREFIX=/usr
- DESTDIR=/

Modified: trunk/packages/paml/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/paml/trunk/debian/patches/makefile.patch	2014-07-30 12:36:27 UTC (rev 17574)
+++ trunk/packages/paml/trunk/debian/patches/makefile.patch	2014-07-30 13:19:08 UTC (rev 17575)
@@ -16,7 +16,7 @@
 +
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -35,3 +35,11 @@ yn00: yn00.c tools.c paml.h
+@@ -36,3 +36,11 @@ yn00: yn00.c tools.c paml.h
  	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
  chi2 : chi2.c
  	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)

Modified: trunk/packages/paml/trunk/debian/patches/series
===================================================================
--- trunk/packages/paml/trunk/debian/patches/series	2014-07-30 12:36:27 UTC (rev 17574)
+++ trunk/packages/paml/trunk/debian/patches/series	2014-07-30 13:19:08 UTC (rev 17575)
@@ -1,2 +1,3 @@
+fix_format_security.patch
 makefile.patch
 hardening.patch