[med-svn] r15742 - in trunk/packages/ampliconnoise/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Sun Jan 12 20:57:40 UTC 2014 

Author: tille
Date: 2014-01-12 20:57:40 +0000 (Sun, 12 Jan 2014)
New Revision: 15742

Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/control
   trunk/packages/ampliconnoise/trunk/debian/patches/fix-segfault-on-non-fasta-input.patch
   trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch
Log:
New upstream version


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/changelog	2014-01-12 09:05:07 UTC (rev 15741)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog	2014-01-12 20:57:40 UTC (rev 15742)
@@ -1,3 +1,12 @@
+ampliconnoise (1.29-1) unstable; urgency=medium
+
+  * New upstream version
+  * debian/control:
+     - cme fix dpkg-control
+     - shorter short decription
+
+ -- Andreas Tille <tille at debian.org>  Sun, 12 Jan 2014 21:14:08 +0100
+
 ampliconnoise (1.28-1) unstable; urgency=low
 
   * New upstream version uploaded to Debian

Modified: trunk/packages/ampliconnoise/trunk/debian/control
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/control	2014-01-12 09:05:07 UTC (rev 15741)
+++ trunk/packages/ampliconnoise/trunk/debian/control	2014-01-12 20:57:40 UTC (rev 15742)
@@ -7,7 +7,7 @@
 Build-Depends: debhelper (>= 9),
                libgsl0-dev,
                libopenmpi-dev
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ampliconnoise/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ampliconnoise/trunk/
 Homepage: http://code.google.com/p/ampliconnoise/
@@ -19,7 +19,7 @@
          libgsl0ldbl,
          mafft
 Recommends: openmpi-bin
-Description: Programs for the removal of noise from 454 sequenced PCR amplicons
+Description: removal of noise from 454 sequenced PCR amplicons
  AmpliconNoise is a package of applications to clean up high-throughput
  sequence data.  It consists of three main parts:
  .

Modified: trunk/packages/ampliconnoise/trunk/debian/patches/fix-segfault-on-non-fasta-input.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/fix-segfault-on-non-fasta-input.patch	2014-01-12 09:05:07 UTC (rev 15741)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/fix-segfault-on-non-fasta-input.patch	2014-01-12 20:57:40 UTC (rev 15742)
@@ -58,7 +58,7 @@
    }
 --- a/Perseus/Perseus.c
 +++ b/Perseus/Perseus.c
-@@ -725,6 +725,13 @@ void readData(char* szInputFile, t_Data
+@@ -793,6 +793,13 @@ void readData(char* szInputFile, t_Data
  	nPos = 0;
        }
        else{
@@ -72,7 +72,7 @@
  	i = 0;
  	while(strrchr(szSequence,szLine[i]) != NULL){
  	  i++;
-@@ -732,6 +739,10 @@ void readData(char* szInputFile, t_Data
+@@ -800,6 +807,10 @@ void readData(char* szInputFile, t_Data
  	}
        }
      }
@@ -85,7 +85,7 @@
    }
 --- a/PerseusD/PerseusD.c
 +++ b/PerseusD/PerseusD.c
-@@ -782,6 +782,13 @@ void readData(char* szInputFile, t_Data
+@@ -844,6 +844,13 @@ void readData(char* szInputFile, t_Data
  	nPos = 0;
        }
        else{
@@ -99,7 +99,7 @@
  	i = 0;
  	while(strrchr(szSequence,szLine[i]) != NULL){
  	  i++;
-@@ -789,6 +796,10 @@ void readData(char* szInputFile, t_Data
+@@ -851,6 +858,10 @@ void readData(char* szInputFile, t_Data
  	}
        }
      }

Modified: trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch	2014-01-12 09:05:07 UTC (rev 15741)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch	2014-01-12 20:57:40 UTC (rev 15742)
@@ -2,37 +2,6 @@
 LastChanged: Tue, 30 Jul 2013 09:49:02 +0200
 Description: Propagate hardening options
 
---- a/makefile
-+++ b/makefile
-@@ -1,16 +1,16 @@
- all:
--	(cd FCluster && make)
--	(cd FastaUnique && make)
--	(cd NDist && make)
--	(cd PyroDist && make)
--	(cd PyroNoise && make)
--	(cd SeqDist && make)
--	(cd PyroNoiseM && make)
--	(cd SeqNoise && make)
--	(cd SplitClusterEven && make)
--	(cd SplitClusterClust && make)  		
--	(cd Perseus && make) 		
--	(cd PerseusD && make) 		
-+	(cd FCluster && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd FastaUnique && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd NDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd PyroDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd PyroNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd SeqDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd PyroNoiseM && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd SeqNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd SplitClusterEven && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
-+	(cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
- clean:
- 	(cd FCluster && make clean)
- 	(cd FastaUnique && make clean)
 --- a/FCluster/makefile
 +++ b/FCluster/makefile
 @@ -1,6 +1,6 @@
@@ -165,3 +134,36 @@
  EFILE  = SplitClusterEven
  LIBS   = -lm 
  OBJS   = SplitClusterEven.o
+--- a/makefile
++++ b/makefile
+@@ -1,17 +1,17 @@
+ all:
+-	(cd FCluster && make)
+-	(cd FastaUnique && make)
+-	(cd NDist && make)
+-	(cd PyroDist && make)
+-	(cd PyroNoise && make)
+-	(cd SeqDist && make)
+-	(cd PyroNoiseM && make)
+-	(cd PyroNoiseA && make)
+-	(cd SeqNoise && make)
+-	(cd SplitClusterEven && make)
+-	(cd SplitClusterClust && make)  		
+-	(cd Perseus && make) 		
+-	(cd PerseusD && make) 		
++	(cd FCluster && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd FastaUnique && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd NDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SeqDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroNoiseM && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroNoiseA && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SeqNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SplitClusterEven && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)  		
++	(cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make) 		
++	(cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make) 		
+ clean:
+ 	(cd FCluster && make clean)
+ 	(cd FastaUnique && make clean)

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