[med-svn] r16720 - in trunk/packages/wgs-assembler/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-04-17 13:33:58 +0000 (Thu, 17 Apr 2014)
New Revision: 16720

Added:
   trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch
Modified:
   trunk/packages/wgs-assembler/trunk/debian/changelog
   trunk/packages/wgs-assembler/trunk/debian/control
   trunk/packages/wgs-assembler/trunk/debian/patches/series
   trunk/packages/wgs-assembler/trunk/debian/rules
Log:
New upstream with adapted patches; stripped changelog of not yet released package


Modified: trunk/packages/wgs-assembler/trunk/debian/changelog
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/changelog	2014-04-17 12:53:01 UTC (rev 16719)
+++ trunk/packages/wgs-assembler/trunk/debian/changelog	2014-04-17 13:33:58 UTC (rev 16720)
@@ -1,17 +1,9 @@
-wgs-assembler (7.0-1) UNRELEASED; urgency=low
+wgs-assembler (8.1-1) UNRELEASED; urgency=low
 
   * TODO: does not build:
           cd kmer/build ; ln -s ../Make.compilers . ; make makepath
           /bin/sh: 1: cd: can't cd to kmer/build
 
-
-  [ Thorsten Alteholz ]
-  * debian/watch: new tarballs are compressed with bz2
-  * debian/rules: target get-orig-source added
-  * debian/control: debhelper changed to 8.0
-  * debian/control: standards version changed to 3.9.3 (no other changes)
-  * debian/control: VCS fields updated
-
   * Initial release (Closes: #395843)
 
- -- Thorsten Alteholz <debian at alteholz.de>  Mon, 05 Mar 2012 18:40:00 +0100
+ -- Andreas Tille <tille at debian.org>  Thu, 17 Apr 2014 15:04:22 +0200

Modified: trunk/packages/wgs-assembler/trunk/debian/control
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/control	2014-04-17 12:53:01 UTC (rev 16719)
+++ trunk/packages/wgs-assembler/trunk/debian/control	2014-04-17 13:33:58 UTC (rev 16720)
@@ -6,7 +6,8 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               libbz2-dev
+               libbz2-dev,
+               zlib1g-dev
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/wgs-assembler/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/wgs-assembler/trunk/

Added: trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch	                        (rev 0)
+++ trunk/packages/wgs-assembler/trunk/debian/patches/format-security.patch	2014-04-17 13:33:58 UTC (rev 16720)
@@ -0,0 +1,31 @@
+--- a/src/AS_REZ/StatisticsREZ.C
++++ b/src/AS_REZ/StatisticsREZ.C
+@@ -639,7 +639,7 @@ void print_all_scaffold_walk_stat_struct
+   for(y=0; y<GetNumScaffoldWalkStatisticsTs(ws->ScaffoldStats); y++)
+     {
+       ScaffoldWalkStatisticsT *scaffStatp = GetScaffoldWalkStatisticsT(ws->ScaffoldStats,y);
+-      fprintf(file,mesg);
++      fprintf(file,"%s",mesg);
+       print_scaffold_walk_stat_struct(scaffStatp,file,printGaps);
+     }
+   return;
+--- a/src/AS_CGW/Instrument_CGW.C
++++ b/src/AS_CGW/Instrument_CGW.C
+@@ -2263,7 +2263,7 @@ void PrintMateComparison(int32 numBefore
+   double ratioAfter = (totalAfter > 0) ?
+     ((double) numAfter) / totalAfter : 0.0f;
+ 
+-  fprintf(printTo, string);
++  fprintf(printTo, "%s", string);
+   if(totalBefore < 1.f || totalAfter < 1.f)
+     fprintf(printTo, "%s", "-      ");
+   else if(ratioAfter > ratioBefore + 0.000001)
+@@ -2271,7 +2271,7 @@ void PrintMateComparison(int32 numBefore
+   else if( ratioAfter < ratioBefore - 0.00001)
+     fprintf(printTo, "%s", (moreIsBetter) ? "worse  " : "better ");
+   else
+-    fprintf(printTo, "same   ");
++    fprintf(printTo, "%s", "same   ");
+ 
+   if(printRawNumbers)
+     fprintf(printTo, "(%8d = %7.3f%% before, %8d = %7.3f%% after)\n",

Modified: trunk/packages/wgs-assembler/trunk/debian/patches/series
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/patches/series	2014-04-17 12:53:01 UTC (rev 16719)
+++ trunk/packages/wgs-assembler/trunk/debian/patches/series	2014-04-17 13:33:58 UTC (rev 16720)
@@ -1 +1,2 @@
-make-implicit.patch
+# make-implicit.patch
+format-security.patch

Modified: trunk/packages/wgs-assembler/trunk/debian/rules
===================================================================
--- trunk/packages/wgs-assembler/trunk/debian/rules	2014-04-17 12:53:01 UTC (rev 16719)
+++ trunk/packages/wgs-assembler/trunk/debian/rules	2014-04-17 13:33:58 UTC (rev 16720)
@@ -19,9 +19,7 @@
 #	cd kmer; ln -sf Linux-* installdir
 
 	# do stuff for kmer
-	cd kmer; sh configure.sh
-	cd kmer; make install
-	cd kmer; ln -sf Linux-* installdir
+	cd kmer && sh configure.sh && make install && ln -sf Linux-* installdir
 	# do stuff for wgs-assembler
 	$(MAKE) -C src
 	ln -sf Linux-* installdir